From 0bf822f17b54731cb6bffa66e7660842381b2ae7 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Thu, 11 Feb 2016 16:48:54 -0800
Subject: [PATCH 01/19] update and add another entity script

---
 .../CellScience/Scripts/moveRandomly.js       | 138 ++-------------
 .../Scripts/zoomAndMoveRandomly.js            | 159 ++++++++++++++++++
 .../CellScience/backgroundMusicAC.js          |   8 +-
 .../CellScience/importCellScience.js          |   4 +-
 4 files changed, 181 insertions(+), 128 deletions(-)
 create mode 100644 unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js

diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
index a975f74733..8c3a6c0852 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
@@ -8,124 +8,32 @@
 
     var self = this;
 
-    this.preload = function(entityId) {
-        //print('preload move randomly')
+    this.preload=function(entityId){
         this.isConnected = false;
         this.entityId = entityId;
-        this.updateInterval = 100;
-        this.posFrame = 0;
-        this.rotFrame = 0;
-        this.posInterval = 100;
-        this.rotInterval = 100;
         this.minVelocity = 1;
         this.maxVelocity = 5;
         this.minAngularVelocity = 0.01;
         this.maxAngularVelocity = 0.03;
-
-        this.initialize(entityId);
-        this.initTimeout = null;
-
-
-        var userData = {
-            ownershipKey: {
-                owner: MyAvatar.sessionUUID
-            },
-            grabbableKey: {
-                grabbable: false
-            }
-        };
-
-        Entities.editEntity(entityId, {
-            userData: JSON.stringify(userData)
-        })
+        Script.setTimeout(self.move,self.getTotalWait())
     }
 
-    this.initialize = function(entityId) {
-        //print('move randomly  should initialize' + entityId)
-        var properties = Entities.getEntityProperties(entityId);
-        if (properties.userData.length === 0 || properties.hasOwnProperty('userData') === false) {
-            self.initTimeout = Script.setTimeout(function() {
-                //print('no user data yet, try again in one second')
-                self.initialize(entityId);
-            }, 1000)
 
-        } else {
-            //print('userdata before parse attempt' + properties.userData)
-            self.userData = null;
-            try {
-                self.userData = JSON.parse(properties.userData);
-            } catch (err) {
-                //print('error parsing json');
-                //print('properties are:' + properties.userData);
-                return;
-            }
-            Script.update.connect(self.update);
-            this.isConnected = true;
-        }
-    }
-
-    this.update = function(deltaTime) {
-        // print('jbp in update')
-        var data = Entities.getEntityProperties(self.entityId, 'userData').userData;
-        var userData;
-        try {
-            userData = JSON.parse(data)
-        } catch (e) {
-            //print('error parsing json' + data)
-            return;
-        };
-
-        // print('userdata is' + data)
-        //if the entity doesnt have an owner set yet
-        if (userData.hasOwnProperty('ownershipKey') !== true) {
-            //print('no movement owner yet')
-            return;
-        }
-
-        //print('owner is:::' + userData.ownershipKey.owner)
-            //get all the avatars to see if the owner is around
+    this.getTotalWait = function() {
         var avatars = AvatarList.getAvatarIdentifiers();
-        var ownerIsAround = false;
+        var avatarCount = avatars.length;
+        var random = Math.random() * 2000;
+        var totalWait = random * (avatarCount * 2);
 
-        //if the current owner is not me...
-        if (userData.ownershipKey.owner !== MyAvatar.sessionUUID) {
+        return totalWait
+    }
 
-            //look to see if the current owner is around anymore
-            for (var i = 0; i < avatars.length; i++) {
-                if (avatars[i] === userData.ownershipKey.owner) {
-                    ownerIsAround = true
-                        //the owner is around
-                    return;
-                };
-            }
 
-            //if the owner is not around, then take ownership
-            if (ownerIsAround === false) {
-                //print('taking ownership')
+    this.move = function() {
+            print('jbp im the owner so move it')
+          
+ 
 
-                var userData = {
-                    ownershipKey: {
-                        owner: MyAvatar.sessionUUID
-                    },
-                    grabbableKey: {
-                        grabbable: false
-                    }
-                };
-                Entities.editEntity(self.entityId, {
-                    userData: JSON.stringify(data)
-                })
-            }
-        }
-        //but if the current owner IS me, then move it
-        else {
-            //print('jbp im the owner so move it')
-            self.posFrame++;
-            self.rotFrame++;
-
-            if (self.posFrame > self.posInterval) {
-
-                self.posInterval = 100 * Math.random() + 300;
-                self.posFrame = 0;
 
                 var magnitudeV = self.maxVelocity;
                 var directionV = {
@@ -137,16 +45,9 @@
                 //print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
                 Entities.editEntity(self.entityId, {
                     velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV))
-
                 });
 
-            }
-
-            if (self.rotFrame > self.rotInterval) {
-
-                self.rotInterval = 100 * Math.random() + 250;
-                self.rotFrame = 0;
-
+  
                 var magnitudeAV = self.maxAngularVelocity;
 
                 var directionAV = {
@@ -160,20 +61,13 @@
 
                 });
 
-            }
-
-        }
+ 
 
+        Script.setTimeout(self.move,self.getTotalWait())
     }
 
-    this.unload = function() {
-        if (this.initTimeout !== null) {
-            Script.clearTimeout(this.initTimeout);
-        }
 
-        if (this.isConnected === true) {
-            Script.update.disconnect(this.update);
-        }
+    this.unload = function() {
 
     }
 
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
new file mode 100644
index 0000000000..f0f77b12e0
--- /dev/null
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
@@ -0,0 +1,159 @@
+//  Copyright 2016 High Fidelity, Inc.
+//
+//
+//  Distributed under the Apache License, Version 2.0.
+//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
+//
+
+(function() {
+    var teleport;
+    var portalDestination;
+    var animationURL;
+    var self = this;
+
+    this.entered = true;
+
+    this.preload = function(entityID) {
+        this.entityId = entityID;
+        this.initialize(entityID);
+        this.initTimeout = null;
+        this.minVelocity = 1;
+        this.maxVelocity = 5;
+        this.minAngularVelocity = 0.01;
+        this.maxAngularVelocity = 0.03;
+        Script.setTimeout(self.move, self.getTotalWait())
+    }
+
+    this.initialize = function(entityID) {
+        // print(' should initialize')
+        var properties = Entities.getEntityProperties(entityID);
+        if (properties.userData.length === 0 || properties.hasOwnProperty('userData') === false) {
+            self.initTimeout = Script.setTimeout(function() {
+                // print(' no user data yet, try again in one second')
+                self.initialize(entityID);
+            }, 1000)
+        } else {
+            // print(' has userData')
+            self.portalDestination = properties.userData;
+            animationURL = properties.modelURL;
+            self.soundOptions = {
+                stereo: true,
+                loop: false,
+                localOnly: false,
+                position: properties.position,
+                volume: 0.5
+            };
+
+            self.teleportSound = SoundCache.getSound("https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/Audio/whoosh.wav");
+            // print(" portal destination is " + self.portalDestination);
+        }
+    }
+
+    this.enterEntity = function(entityID) {
+        //print('ENTERED A BOUNDARY ENTITY, SHOULD ZOOM', entityID)
+        var data = JSON.parse(Entities.getEntityProperties(this.entityId).userData);
+        //print('DATA IS::' + data)
+        if (data != null) {
+            print("Teleporting to (" + data.location.x + ", " + data.location.y + ", " + data.location.z + ")");
+
+            MyAvatar.position = data.location;
+
+            // if (data.hasOwnProperty('entryPoint') && data.hasOwnProperty('target')) {
+            //     this.lookAtTarget(data.entryPoint, data.target);
+            // }
+            // else{
+
+            // }
+        }
+
+    }
+
+    this.lookAtTarget = function(entryPoint, target) {
+        //print('SHOULD LOOK AT TARGET')
+        var direction = Vec3.normalize(Vec3.subtract(entryPoint, target));
+        var pitch = Quat.angleAxis(Math.asin(-direction.y) * 180.0 / Math.PI, {
+            x: 1,
+            y: 0,
+            z: 0
+        });
+        var yaw = Quat.angleAxis(Math.atan2(direction.x, direction.z) * 180.0 / Math.PI, {
+            x: 0,
+            y: 1,
+            z: 0
+        });
+
+        MyAvatar.goToLocation(entryPoint, true, yaw);
+
+        MyAvatar.headYaw = 0;
+
+    }
+
+    this.leaveEntity = function(entityID) {
+        Entities.editEntity(entityID, {
+            animationURL: animationURL,
+            animationSettings: '{ "frameIndex": 1, "running": false }'
+        });
+        this.entered = false;
+        if (this.initTimeout !== null) {
+            Script.clearTimeout(this.initTimeout);
+        }
+        //playSound();
+    }
+
+    this.unload = function() {
+        if (this.initTimeout !== null) {
+            Script.clearTimeout(this.initTimeout);
+        }
+    }
+
+    this.hoverEnterEntity = function(entityID) {
+        Entities.editEntity(entityID, {
+            animationURL: animationURL,
+            animationSettings: '{ "fps": 24, "firstFrame": 1, "lastFrame": 25, "frameIndex": 1, "running": true, "hold": true }'
+        });
+    }
+
+    this.getTotalWait = function() {
+        var avatars = AvatarList.getAvatarIdentifiers();
+        var avatarCount = avatars.length;
+        var random = Math.random() * 2000;
+        var totalWait = random * (avatarCount * 2);
+
+        return totalWait
+    }
+
+
+    this.move = function() {
+        print('jbp im the owner so move it')
+
+        var magnitudeV = self.maxVelocity;
+        var directionV = {
+            x: Math.random() - 0.5,
+            y: Math.random() - 0.5,
+            z: Math.random() - 0.5
+        };
+
+        //print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
+        Entities.editEntity(self.entityId, {
+            velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV))
+        });
+
+
+
+        var magnitudeAV = self.maxAngularVelocity;
+
+        var directionAV = {
+            x: Math.random() - 0.5,
+            y: Math.random() - 0.5,
+            z: Math.random() - 0.5
+        };
+        //print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
+        Entities.editEntity(self.entityId, {
+            angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
+
+        });
+
+        Script.setTimeout(self.move, self.getTotalWait())
+    }
+
+})
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/backgroundMusicAC.js b/unpublishedScripts/DomainContent/CellScience/backgroundMusicAC.js
index 0ee5b3bf32..1b4c06caaa 100644
--- a/unpublishedScripts/DomainContent/CellScience/backgroundMusicAC.js
+++ b/unpublishedScripts/DomainContent/CellScience/backgroundMusicAC.js
@@ -7,7 +7,7 @@ var soundMap = [{
                 y: 15850,
                 z: 15850
             },
-            volume: 0.1,
+            volume: 0.03,
             loop: true
         }
     }, {
@@ -19,7 +19,7 @@ var soundMap = [{
                 y: 15950,
                 z: 15950
             },
-            volume: 0.1,
+            volume: 0.03,
             loop: true
         }
     }, {
@@ -31,7 +31,7 @@ var soundMap = [{
                 y: 15650,
                 z: 15650
             },
-            volume: 0.1,
+            volume: 0.03,
             loop: true
         }
     }, {
@@ -43,7 +43,7 @@ var soundMap = [{
                 y: 15750,
                 z: 15750
             },
-            volume: 0.1,
+            volume: 0.03,
             loop: true
         }
     }
diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index ca0eb21f21..7d9a49294f 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -5,7 +5,7 @@
 //  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
 //
 
-var version = 1035;
+var version = 1039;
 var cellLayout;
 var baseLocation = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 
@@ -120,7 +120,7 @@ var scenes = [{
             location: locations.cellLayout[1],
             baseURL: baseLocation
         }),
-        script: "zoom.js?" + version,
+        script: "zoomAndMoveRandomly.js?" + version,
         visible: true
     }],
     boundary: {

From f346ac7023c4ea9f4819bc13677867ac9b9add91 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Fri, 12 Feb 2016 13:58:02 -0800
Subject: [PATCH 02/19] logging

---
 examples/gridTest.js                          |  5 +++--
 .../CellScience/Scripts/moveRandomly.js       |  8 ++------
 .../CellScience/Scripts/navigationButton.js   |  6 +++---
 .../CellScience/Scripts/showIdentification.js |  3 ++-
 .../DomainContent/CellScience/Scripts/zoom.js |  1 +
 .../Scripts/zoomAndMoveRandomly.js            |  1 -
 .../CellScience/importCellScience.js          | 20 +++++++++++--------
 7 files changed, 23 insertions(+), 21 deletions(-)

diff --git a/examples/gridTest.js b/examples/gridTest.js
index 0d6040470f..5bbd3246ae 100644
--- a/examples/gridTest.js
+++ b/examples/gridTest.js
@@ -17,8 +17,8 @@ var SIZE = 10.0;
 var SEPARATION = 20.0;
 var ROWS_X = 30; 
 var ROWS_Z = 30;
-var TYPE = "Sphere";            //   Right now this can be "Box" or "Model" or "Sphere"
-var MODEL_URL = "https://hifi-public.s3.amazonaws.com/models/props/LowPolyIsland/CypressTreeGroup.fbx";
+var TYPE = "Model";            //   Right now this can be "Box" or "Model" or "Sphere"
+var MODEL_URL = "http://hifi-content.s3.amazonaws.com/DomainContent/CellScience/Instances/vesicle.fbx";
 var MODEL_DIMENSION = { x: 33, y: 16, z: 49 };
 var RATE_PER_SECOND = 1000;    //    The entity server will drop data if we create things too fast.
 var SCRIPT_INTERVAL = 100;
@@ -38,6 +38,7 @@ Script.setInterval(function () {
     var numToCreate = RATE_PER_SECOND * (SCRIPT_INTERVAL / 1000.0);
     for (var i = 0; i < numToCreate; i++) {
         var position = { x: SIZE + (x * SEPARATION), y: SIZE, z: SIZE + (z * SEPARATION) };
+        print('position:'+JSON.stringify(position))
         if (TYPE == "Model") {
             Entities.addEntity({ 
             type: TYPE,
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
index 8c3a6c0852..2cced94672 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
@@ -9,6 +9,7 @@
     var self = this;
 
     this.preload=function(entityId){
+        print('JBP MOVE RANDOMLY PRELOAD')
         this.isConnected = false;
         this.entityId = entityId;
         this.minVelocity = 1;
@@ -22,7 +23,7 @@
     this.getTotalWait = function() {
         var avatars = AvatarList.getAvatarIdentifiers();
         var avatarCount = avatars.length;
-        var random = Math.random() * 2000;
+        var random = Math.random() * 5000;
         var totalWait = random * (avatarCount * 2);
 
         return totalWait
@@ -30,11 +31,6 @@
 
 
     this.move = function() {
-            print('jbp im the owner so move it')
-          
- 
-
-
                 var magnitudeV = self.maxVelocity;
                 var directionV = {
                     x: Math.random() - 0.5,
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/navigationButton.js b/unpublishedScripts/DomainContent/CellScience/Scripts/navigationButton.js
index 4136f1f81b..16fb31189a 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/navigationButton.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/navigationButton.js
@@ -17,6 +17,7 @@
     var baseURL = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 
     this.preload = function(entityId) {
+        print('JBP NAV PRELOAD')
         this.entityId = entityId;
         this.initialize(entityId);
         this.initTimeout = null;
@@ -58,14 +59,13 @@
             self.buttonImageURL = baseURL + "GUI/GUI_" + self.userData.name + ".png?" + version;
             print('JBP BUTTON IMAGE URL:' + self.buttonImageURL)
             if (self.button === undefined) {
-                // print('NAV NO BUTTON ADDING ONE!!')
+                print('JBP NO BUTTON ADDING ONE!!')
                 self.button = true;
                 self.addButton();
 
             } else {
-                // print('NAV SELF ALREADY HAS A BUTTON!!')
+                print('JBP SELF ALREADY HAS A BUTTON!!')
             }
-
         }
     }
 
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/showIdentification.js b/unpublishedScripts/DomainContent/CellScience/Scripts/showIdentification.js
index d8b32ab176..b7aad5e652 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/showIdentification.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/showIdentification.js
@@ -10,8 +10,9 @@
     var self = this;
     var baseURL = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 
-    var version = 2;
+    var version = 3;
     this.preload = function(entityId) {
+        print('JBP SHOW IDENTIFICATION PRELOAD')
         this.soundPlaying = null;
         this.entityId = entityId;
         self.initTimeout = null;
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js
index da41ec64ba..d075966524 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js
@@ -14,6 +14,7 @@
     this.entered = true;
 
     this.preload = function(entityID) {
+        print('JBP Zoom PRELOAD')
         this.entityId = entityID;
         this.initialize(entityID);
         this.initTimeout = null;
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
index f0f77b12e0..e4ee59cb6b 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
@@ -124,7 +124,6 @@
 
 
     this.move = function() {
-        print('jbp im the owner so move it')
 
         var magnitudeV = self.maxVelocity;
         var directionV = {
diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index 7d9a49294f..bf112f5bad 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -5,7 +5,7 @@
 //  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
 //
 
-var version = 1039;
+var version = 1041;
 var cellLayout;
 var baseLocation = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 
@@ -645,8 +645,7 @@ function createLayoutLights() {
 }
 
 function CreateNavigationButton(scene, number) {
-    // print('NAV NAVIGATION CREATING NAV!!' +scene.name + " " + number)
-
+    print('JBP NAVIGATION CREATING NAV!!' +scene.name + " " + number)
 
     Entities.addEntity({
         type: "Box",
@@ -657,11 +656,11 @@ function CreateNavigationButton(scene, number) {
             blue: 0
         },
         dimensions: {
-            x: 16000,
-            y: 16000,
-            z: 16000
+            x: 14000,
+            y: 14000,
+            z: 14000
         },
-        visible: false,
+        visible: true,
         userData: JSON.stringify({
             name: scene.name,
             entryPoint: scene.entryPoint,
@@ -9045,4 +9044,9 @@ createLayoutLights();
 
 Script.scriptEnding.connect(function() {
     Entities.addingEntity.disconnect(makeUngrabbable);
-});
\ No newline at end of file
+});
+
+Script.setTimeout(function(){
+    print('JBP stopping cell science import');
+    Script.stop();
+},30000)
\ No newline at end of file

From e828a7e6e2b2fd0dfae93bfa202108b01698ce87 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Fri, 12 Feb 2016 19:38:40 -0800
Subject: [PATCH 03/19] quiet prints

---
 .../CellScience/Scripts/moveRandomly.js       |  1 -
 .../CellScience/Scripts/navigationButton.js   | 22 +++++++++----------
 .../CellScience/Scripts/showIdentification.js |  1 -
 .../DomainContent/CellScience/Scripts/zoom.js |  1 -
 .../CellScience/importCellScience.js          | 14 +++++-------
 5 files changed, 15 insertions(+), 24 deletions(-)

diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
index 2cced94672..cc822ddf8a 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
@@ -9,7 +9,6 @@
     var self = this;
 
     this.preload=function(entityId){
-        print('JBP MOVE RANDOMLY PRELOAD')
         this.isConnected = false;
         this.entityId = entityId;
         this.minVelocity = 1;
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/navigationButton.js b/unpublishedScripts/DomainContent/CellScience/Scripts/navigationButton.js
index 16fb31189a..c1187bc6d5 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/navigationButton.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/navigationButton.js
@@ -7,7 +7,7 @@
 
 (function() {
 
-    var version = 11;
+    var version = 12;
     var added = false;
     this.frame = 0;
     var utilsScript = Script.resolvePath('utils.js');
@@ -17,29 +17,27 @@
     var baseURL = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 
     this.preload = function(entityId) {
-        print('JBP NAV PRELOAD')
         this.entityId = entityId;
         this.initialize(entityId);
         this.initTimeout = null;
     }
 
     this.initialize = function(entityId) {
-        print('JBP nav button should initialize' + entityId)
         var properties = Entities.getEntityProperties(entityId);
         if (properties.userData.length === 0 || properties.hasOwnProperty('userData') === false) {
             self.initTimeout = Script.setTimeout(function() {
-                print('JBP no user data yet, try again in one second')
+                //    print(' no user data yet, try again in one second')
                 self.initialize(entityId);
             }, 1000)
 
         } else {
-            print('JBP userdata before parse attempt' + properties.userData)
+            // print('userdata before parse attempt' + properties.userData)
             self.userData = null;
             try {
                 self.userData = JSON.parse(properties.userData);
             } catch (err) {
-                print('JBP error parsing json');
-                print('JBP properties are:' + properties.userData);
+                //  print(' error parsing json');
+                //  print(' properties are:' + properties.userData);
                 return;
             }
 
@@ -47,9 +45,9 @@
             var mySavedSettings = Settings.getValue(entityId);
 
             if (mySavedSettings.buttons !== undefined) {
-                print('JBP preload buttons' + mySavedSettings.buttons)
+                // print(' preload buttons' + mySavedSettings.buttons)
                 mySavedSettings.buttons.forEach(function(b) {
-                    print('JBP deleting button' + b)
+                    // print(' deleting button' + b)
                     Overlays.deleteOverlay(b);
                 })
                 Settings.setValue(entityId, '')
@@ -57,14 +55,14 @@
 
 
             self.buttonImageURL = baseURL + "GUI/GUI_" + self.userData.name + ".png?" + version;
-            print('JBP BUTTON IMAGE URL:' + self.buttonImageURL)
+            // print(' BUTTON IMAGE URL:' + self.buttonImageURL)
             if (self.button === undefined) {
-                print('JBP NO BUTTON ADDING ONE!!')
+                //    print(' NO BUTTON ADDING ONE!!')
                 self.button = true;
                 self.addButton();
 
             } else {
-                print('JBP SELF ALREADY HAS A BUTTON!!')
+                //print(' SELF ALREADY HAS A BUTTON!!')
             }
         }
     }
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/showIdentification.js b/unpublishedScripts/DomainContent/CellScience/Scripts/showIdentification.js
index b7aad5e652..3f6067693c 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/showIdentification.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/showIdentification.js
@@ -12,7 +12,6 @@
 
     var version = 3;
     this.preload = function(entityId) {
-        print('JBP SHOW IDENTIFICATION PRELOAD')
         this.soundPlaying = null;
         this.entityId = entityId;
         self.initTimeout = null;
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js
index d075966524..da41ec64ba 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js
@@ -14,7 +14,6 @@
     this.entered = true;
 
     this.preload = function(entityID) {
-        print('JBP Zoom PRELOAD')
         this.entityId = entityID;
         this.initialize(entityID);
         this.initTimeout = null;
diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index bf112f5bad..db50635f93 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -5,7 +5,7 @@
 //  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
 //
 
-var version = 1041;
+var version = 1043;
 var cellLayout;
 var baseLocation = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 
@@ -609,12 +609,10 @@ function ImportScene(scene) {
 clearAllNav();
 
 function clearAllNav() {
-    // print('NAV CLEARING ALL NAV');
     var result = Entities.findEntities(MyAvatar.position, 25000);
     result.forEach(function(r) {
         var properties = Entities.getEntityProperties(r, "name");
         if (properties.name.indexOf('navigation button') > -1) {
-            // print('NAV DELETING NAV BUTTON AT START:: '+r)
             Entities.deleteEntity(r);
         }
     })
@@ -645,8 +643,6 @@ function createLayoutLights() {
 }
 
 function CreateNavigationButton(scene, number) {
-    print('JBP NAVIGATION CREATING NAV!!' +scene.name + " " + number)
-
     Entities.addEntity({
         type: "Box",
         name: scene.name + " navigation button",
@@ -656,11 +652,11 @@ function CreateNavigationButton(scene, number) {
             blue: 0
         },
         dimensions: {
-            x: 14000,
-            y: 14000,
-            z: 14000
+            x: 16000,
+            y: 16000,
+            z: 16000
         },
-        visible: true,
+        visible: false,
         userData: JSON.stringify({
             name: scene.name,
             entryPoint: scene.entryPoint,

From 214723f1bfdf86cf1821265742e53d016be628a0 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Thu, 18 Feb 2016 14:27:47 -0800
Subject: [PATCH 04/19] baton for moving vesicles" "

---
 .../CellScience/Scripts/colorRandomly.js      | 104 +++++
 .../CellScience/Scripts/moveRandomly.js       |  71 ----
 .../CellScience/Scripts/moveRandomly2.js      |  95 +++++
 .../CellScience/Scripts/virtualBaton.js       | 381 ++++++++++++++++++
 .../Scripts/zoomAndMoveRandomly.js            |  48 ++-
 .../CellScience/importCellScience.js          |  10 +-
 6 files changed, 618 insertions(+), 91 deletions(-)
 create mode 100644 unpublishedScripts/DomainContent/CellScience/Scripts/colorRandomly.js
 delete mode 100644 unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
 create mode 100644 unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js
 create mode 100644 unpublishedScripts/DomainContent/CellScience/Scripts/virtualBaton.js

diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/colorRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/colorRandomly.js
new file mode 100644
index 0000000000..cf4ee810e7
--- /dev/null
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/colorRandomly.js
@@ -0,0 +1,104 @@
+//  Copyright 2016 High Fidelity, Inc.
+//
+//
+//  Distributed under the Apache License, Version 2.0.
+//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
+//
+(function() {
+
+    Script.include(Script.resolvePath('virtualBaton.js'));
+
+    var self = this;
+
+    var baton;
+    var iOwn = false;
+    var currentInterval;
+    var _entityId;
+
+    function startUpdate() {
+        iOwn = true;
+        print('i am the owner ' + _entityId)
+    }
+
+    function stopUpdateAndReclaim() {
+        print('i released the object ' + _entityId)
+        iOwn = false;
+        baton.claim(startUpdate, stopUpdateAndReclaim);
+    }
+
+    this.preload = function(entityId) {
+        this.isConnected = false;
+        this.entityId = entityId;
+        _entityId = entityId;
+        this.minVelocity = 1;
+        this.maxVelocity = 5;
+        this.minAngularVelocity = 0.01;
+        this.maxAngularVelocity = 0.03;
+        baton = virtualBaton({
+            batonName: 'io.highfidelity.vesicles:' + entityId, // One winner for each entity
+        });
+        stopUpdateAndReclaim();
+       currentInterval =  Script.setInterval(self.move, self.getTotalWait())
+    }
+
+
+    this.getTotalWait = function() {
+        return (Math.random() * 5000) * 2;
+        // var avatars = AvatarList.getAvatarIdentifiers();
+        // var avatarCount = avatars.length;
+        // var random = Math.random() * 5000;
+        // var totalWait = random * (avatarCount * 2);
+        // print('cellscience color avatarcount, totalwait: ', avatarCount, totalWait)
+        // return totalWait
+    }
+
+
+    this.move = function() {
+        if (!iOwn) {
+            return;
+        }
+
+        var properties = Entities.getEntityProperties(self.entityId);
+        var color = properties.color;
+
+        var newColor;
+        var red = {
+            red: 255,
+            green: 0,
+            blue: 0
+        }
+        var green = {
+            red: 0,
+            green: 255,
+            blue: 0
+        }
+        var blue = {
+            red: 0,
+            green: 0,
+            blue: 255
+        }
+        if (color.red > 0) {
+            newColor = green;
+        }
+        if (color.green > 0) {
+            newColor = blue;
+        }
+        if (color.blue > 0) {
+            newColor = red
+        }
+        Entities.editEntity(self.entityId, {
+            color: newColor
+        });
+
+
+    }
+
+
+    this.unload = function() {
+        baton.release(function() {});
+        Script.clearTimeout(currentInterval);
+    }
+
+
+
+})
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
deleted file mode 100644
index cc822ddf8a..0000000000
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly.js
+++ /dev/null
@@ -1,71 +0,0 @@
-//  Copyright 2016 High Fidelity, Inc.
-//
-//
-//  Distributed under the Apache License, Version 2.0.
-//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
-//
-(function() {
-
-    var self = this;
-
-    this.preload=function(entityId){
-        this.isConnected = false;
-        this.entityId = entityId;
-        this.minVelocity = 1;
-        this.maxVelocity = 5;
-        this.minAngularVelocity = 0.01;
-        this.maxAngularVelocity = 0.03;
-        Script.setTimeout(self.move,self.getTotalWait())
-    }
-
-
-    this.getTotalWait = function() {
-        var avatars = AvatarList.getAvatarIdentifiers();
-        var avatarCount = avatars.length;
-        var random = Math.random() * 5000;
-        var totalWait = random * (avatarCount * 2);
-
-        return totalWait
-    }
-
-
-    this.move = function() {
-                var magnitudeV = self.maxVelocity;
-                var directionV = {
-                    x: Math.random() - 0.5,
-                    y: Math.random() - 0.5,
-                    z: Math.random() - 0.5
-                };
-
-                //print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
-                Entities.editEntity(self.entityId, {
-                    velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV))
-                });
-
-  
-                var magnitudeAV = self.maxAngularVelocity;
-
-                var directionAV = {
-                    x: Math.random() - 0.5,
-                    y: Math.random() - 0.5,
-                    z: Math.random() - 0.5
-                };
-                //print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
-                Entities.editEntity(self.entityId, {
-                    angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
-
-                });
-
- 
-
-        Script.setTimeout(self.move,self.getTotalWait())
-    }
-
-
-    this.unload = function() {
-
-    }
-
-
-
-})
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js
new file mode 100644
index 0000000000..f720ca91cc
--- /dev/null
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js
@@ -0,0 +1,95 @@
+//  Copyright 2016 High Fidelity, Inc.
+//
+//
+//  Distributed under the Apache License, Version 2.0.
+//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
+//
+(function() {
+
+    Script.include('virtualBaton.js');
+
+    var self = this;
+
+    var baton;
+    var iOwn = false;
+    var currentInterval;
+    var _entityId;
+
+    function startUpdate() {
+        iOwn = true;
+        print('i am the owner ' + _entityId)
+    }
+
+    function stopUpdateAndReclaim() {
+        print('i released the object ' + _entityId)
+        iOwn = false;
+        baton.claim(startUpdate, stopUpdateAndReclaim);
+    }
+
+    this.preload = function(entityId) {
+        this.isConnected = false;
+        this.entityId = entityId;
+        _entityId = entityId;
+        this.minVelocity = 1;
+        this.maxVelocity = 5;
+        this.minAngularVelocity = 0.01;
+        this.maxAngularVelocity = 0.03;
+        baton = virtualBaton({
+            batonName: 'io.highfidelity.vesicles:' + entityId, // One winner for each entity
+        });
+        stopUpdateAndReclaim();
+        currentInterval = Script.setInterval(self.move, self.getTotalWait())
+    }
+
+
+    this.getTotalWait = function() {
+        return (Math.random() * 5000) * 2;
+        // var avatars = AvatarList.getAvatarIdentifiers();
+        // var avatarCount = avatars.length;
+        // var random = Math.random() * 5000;
+        // var totalWait = random * (avatarCount * 2);
+        // print('cellscience color avatarcount, totalwait: ', avatarCount, totalWait)
+        // return totalWait
+    }
+
+
+    this.move = function() {
+        if (!iOwn) {
+            return;
+        }
+
+        var magnitudeV = self.maxVelocity;
+        var directionV = {
+            x: Math.random() - 0.5,
+            y: Math.random() - 0.5,
+            z: Math.random() - 0.5
+        };
+
+        //print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
+
+        var magnitudeAV = self.maxAngularVelocity;
+
+        var directionAV = {
+            x: Math.random() - 0.5,
+            y: Math.random() - 0.5,
+            z: Math.random() - 0.5
+        };
+        //print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
+        Entities.editEntity(self.entityId, {
+            velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV)),
+            angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
+
+        });
+
+
+    }
+
+
+    this.unload = function() {
+        baton.release(function() {});
+        Script.clearInterval(currentInterval);
+    }
+
+
+
+})
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/virtualBaton.js b/unpublishedScripts/DomainContent/CellScience/Scripts/virtualBaton.js
new file mode 100644
index 0000000000..63f96a5c1e
--- /dev/null
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/virtualBaton.js
@@ -0,0 +1,381 @@
+"use strict";
+/*jslint nomen: true, plusplus: true, vars: true */
+/*global Messages, Script, MyAvatar, AvatarList, Entities, print */
+
+//  Created by Howard Stearns
+//  Copyright 2016 High Fidelity, Inc.
+//  
+//  Distributed under the Apache License, Version 2.0.
+//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
+//
+//  Allows cooperating scripts to pass a "virtual baton" between them,
+//  which is useful when part of a script should only be executed by
+//  the one participant that is holding this particular baton.
+// 
+//  A virtual baton is simply any string agreed upon by the scripts
+//  that use it. Only one script at a time can hold the baton, and it
+//  holds it until that script releases it, or the other scripts
+//  determine that the holding script is not responding. The script
+//  automatically determines who among claimants has the baton, if anyone,
+//  and holds an "election" if necessary.
+//
+//  See entityScript/tribble.js as an example, and the functions
+//  virtualBaton(), claim(), release().
+//
+
+// Answers a new virtualBaton for the given parameters, of which 'key'
+// is required.
+function virtualBatonf(options) {
+    // Answer averages (number +/- variability). Avoids having everyone act in lockstep.
+    function randomize(number, variability) {
+        var allowedDeviation = number * variability; // one side of the deviation range
+        var allowedDeviationRange = allowedDeviation * 2; // total range for +/- deviation
+        var randomDeviation = Math.random() * allowedDeviationRange;
+        var result = number - allowedDeviation + randomDeviation;
+        return result;
+    }
+    // Allow testing outside in a harness outside of High Fidelity.
+    // See sourceCodeSandbox/tests/mocha/test/testVirtualBaton.js
+    var globals = options.globals || {},
+        messages = globals.Messages || Messages,
+        myAvatar = globals.MyAvatar || MyAvatar,
+        avatarList = globals.AvatarList || AvatarList,
+        entities = globals.Entities || Entities,
+        timers = globals.Script || Script,
+        log = globals.print || print;
+
+    var batonName = options.batonName,  // The identify of the baton.
+        // instanceId is the identify of this particular copy of the script among all copies using the same batonName
+        // in the domain. For example, if you wanted only one entity among multiple entity scripts to hold the baton,
+        // you could specify virtualBaton({batonName: 'someBatonName', instanceId: MyAvatar.sessionUUID + entityID}).
+        instanceId = options.instanceId || myAvatar.sessionUUID,
+        // virtualBaton() returns the exports object with properties. You can pass in an object to be side-effected.
+        exports = options.exports || {},
+        // Handy to set false if we believe the optimizations are wrong, or to use both values in a test harness.
+        useOptimizations = (options.useOptimizations === undefined) ? true : options.useOptimizations,
+        electionTimeout = options.electionTimeout || randomize(500, 0.2), // ms. If no winner in this time, hold a new election.
+        recheckInterval = options.recheckInterval || randomize(500, 0.2), // ms. Check that winners remain connected.
+        // If you supply your own instanceId, you might also supply a connectionTest that answers
+        // truthy iff the given id is still valid and connected, and is run at recheckInterval. You
+        // can use exports.validId (see below), and the default answers truthy if id is valid or a
+        // concatenation of two valid ids. (This handles the most common cases of instanceId being
+        // either (the default) MyAvatar.sessionUUID, an entityID, or the concatenation (in either
+        // order) of both.)
+        connectionTest = options.connectionTest || function connectionTest(id) {
+            var idLength = 38;
+            if (id.length === idLength) {
+                return exports.validId(id);
+            }
+            return (id.length === 2 * idLength) && exports.validId(id.slice(0, idLength)) && exports.validId(id.slice(idLength));
+        };
+
+    if (!batonName) {
+        throw new Error("A virtualBaton must specify a batonName.");
+    }
+    // Truthy if id exists as either a connected avatar or valid entity.
+    exports.validId = function validId(id) {
+        var avatar = avatarList.getAvatar(id);
+        if (avatar && (avatar.sessionUUID === id)) {
+            return true;
+        }
+        var properties = entities.getEntityProperties(id, ['type']);
+        return properties && properties.type;
+    };
+
+    // Various logging, controllable through options.
+    function debug() { // Display the arguments not just [Object object].
+        log.apply(null, [].map.call(arguments, JSON.stringify));
+    }
+    function debugFlow() {
+        if (options.debugFlow) {
+            debug.apply(null, arguments);
+        }
+    }
+    function debugSend(destination, operation, data) {
+        if (options.debugSend) {
+            debug('baton:', batonName, instanceId, 's=>', destination, operation, data);
+        }
+    }
+    function debugReceive(senderID, operation, data) { // senderID is client sessionUUID -- not necessarily instanceID!
+        if (options.debugReceive) {
+            debug('baton:', batonName, senderID, '=>r', instanceId, operation, data);
+        }
+    }
+
+    // Messages: Just synactic sugar for hooking things up to Messages system.
+    // We create separate subchannel strings for each operation within our general channelKey, instead of using
+    // a switch in the receiver.
+    var channelKey = "io.highfidelity.virtualBaton:" + batonName,
+        subchannelHandlers = {}, // Message channel string => {receiver, op}
+        subchannelKeys = {};     // operation => Message channel string
+    function subchannelKey(operation) {
+        return channelKey + ':' + operation;
+    }
+    function receive(operation, handler) { // Record a handler for an operation on our channelKey
+        var subKey = subchannelKey(operation);
+        subchannelHandlers[subKey] = {receiver: handler, op: operation};
+        subchannelKeys[operation] = subKey;
+        messages.subscribe(subKey);
+    }
+    function sendHelper(subchannel, data) {
+        var message = JSON.stringify(data);
+        messages.sendMessage(subchannel, message);
+    }
+    function send1(operation, destination, data) { // Send data for an operation to just one destination on our channelKey.
+        debugSend(destination, operation, data);
+        sendHelper(subchannelKey(operation) + destination, data);
+    }
+    function send(operation, data) {  // Send data for an operation on our channelKey.
+        debugSend('-', operation, data);
+        sendHelper(subchannelKeys[operation], data);
+    }
+    function messageHandler(channel, messageString, senderID) {
+        var handler = subchannelHandlers[channel];
+        if (!handler) {
+            return;
+        }
+        var data = JSON.parse(messageString);
+        debugReceive(senderID, handler.op, data);
+        handler.receiver(data);
+    }
+    messages.messageReceived.connect(messageHandler);
+
+    var nPromises = 0, nAccepted = 0, electionWatchdog;
+
+    // It would be great if we had a way to know how many subscribers our channel has. Failing that...
+    var nNack = 0, previousNSubscribers = 0, lastGathering = 0, thisTimeout = electionTimeout;
+    function nSubscribers() { // Answer the number of subscribers.
+        // To find nQuorum, we need to know how many scripts are being run using this batonName, which isn't
+        // the same as the number of clients!
+        //
+        // If we overestimate by too much, we may fail to reach consensus, which triggers a new
+        // election proposal, so we take the number of acceptors to be the max(nPromises, nAccepted)
+        // + nNack reported in the previous round.
+        //
+        // If we understimate by too much, there can be different pockets on the Internet that each
+        // believe they have agreement on different holders of the baton, which is precisely what
+        // the virtualBaton is supposed to avoid. Therefore we need to allow 'nack' to gather stragglers.
+
+        var now = Date.now(), elapsed = now - lastGathering;
+        if (elapsed >= thisTimeout) {
+            previousNSubscribers = Math.max(nPromises, nAccepted) + nNack;
+            lastGathering = now;
+        } // ...otherwise we use the previous value unchanged.
+
+        // On startup, we do one proposal that we cannot possibly close, so that we'll
+        // lock things up for the full electionTimeout to gather responses.
+        if (!previousNSubscribers) {
+            var LARGE_INTEGER = Number.MAX_SAFE_INTEGER || (-1 >>> 1); // QT doesn't define the ECMA constant. Max int will do for our purposes.
+            previousNSubscribers = LARGE_INTEGER;
+        }
+        return previousNSubscribers;
+    }
+
+    // MAIN ALGORITHM
+    //
+    // Internally, this uses the Paxos algorith to hold elections.
+    // Alternatively, we could have the message server pick and maintain a winner, but it would
+    // still have to deal with the same issues of verification in the presence of lost/delayed/reordered messages.
+    // Paxos is known to be optimal under these circumstances, except that its best to have a dedicated proposer
+    // (such as the server).
+    function betterNumber(number, best) {
+        return (number.number || 0) > best.number;
+    }
+    // Paxos Proposer behavior
+    var proposalNumber = 0,
+        nQuorum = 0,
+        bestPromise = {number: 0},
+        claimCallback,
+        releaseCallback;
+    function propose() {  // Make a new proposal, so that we learn/update the proposalNumber and winner.
+        // Even though we send back a 'nack' if the proposal is obsolete, with network errors
+        // there's no way to know for certain that we've failed. The electionWatchdog will try a new
+        // proposal if we have not been accepted by a quorum after election Timeout.
+        if (electionWatchdog) {
+            // If we had a means of determining nSubscribers other than by counting, we could just
+            // timers.clearTimeout(electionWatchdog) and not return.
+            return;
+        }
+        thisTimeout = randomize(electionTimeout, 0.5); // Note use in nSubcribers.
+        electionWatchdog = timers.setTimeout(function () {
+            electionWatchdog = null;
+            propose();
+        }, thisTimeout);
+        var nAcceptors = nSubscribers();
+        nQuorum = Math.floor(nAcceptors / 2) + 1;
+
+        proposalNumber = Math.max(proposalNumber, bestPromise.number) + 1;
+        debugFlow('baton:', batonName, instanceId, 'propose', proposalNumber,
+                  'claim:', !!claimCallback, 'nAcceptors:', nAcceptors, nPromises, nAccepted, nNack);
+        nPromises = nAccepted = nNack = 0;
+        send('prepare!', {number: proposalNumber, proposerId: instanceId});
+    }
+    // We create a distinguished promise subchannel for our id, because promises need only be sent to the proposer.
+    receive('promise' + instanceId, function (data) {
+        if (betterNumber(data, bestPromise)) {
+            bestPromise = data;
+        }
+        if ((data.proposalNumber === proposalNumber) && (++nPromises >= nQuorum)) { // Note check for not being a previous round
+            var answer = {number: data.proposalNumber, proposerId: data.proposerId, winner: bestPromise.winner}; // Not data.number.
+            if (!answer.winner || (answer.winner === instanceId)) { // We get to pick.
+                answer.winner = claimCallback ? instanceId : null;
+            }
+            send('accept!', answer);
+        }
+    });
+    receive('nack' + instanceId, function (data) { // An acceptor reports more recent data...
+        if (data.proposalNumber === proposalNumber) {
+            nNack++;  // For updating nQuorum.
+            // IWBNI if we started our next proposal right now/here, but we need a decent nNack count.
+            // Lets save that optimization for another day...
+        }
+    });
+    // Paxos Acceptor behavior
+    var bestProposal = {number: 0}, accepted = {};
+    function acceptedId() {
+        return accepted && accepted.winner;
+    }
+    receive('prepare!', function (data) {
+        var response = {proposalNumber: data.number, proposerId: data.proposerId};
+        if (betterNumber(data, bestProposal)) {
+            bestProposal = data;
+            if (accepted.winner && connectionTest(accepted.winner)) {
+                response.number = accepted.number;
+                response.winner = accepted.winner;
+            }
+            send1('promise', data.proposerId, response);
+        } else {
+            send1('nack', data.proposerId, response);
+        }
+    });
+    receive('accept!', function (data) {
+        if (!betterNumber(bestProposal, data)) {
+            bestProposal = accepted = data; // Update both with current data. Might have missed the proposal earlier.
+            if (useOptimizations) {
+                // The Paxos literature describes every acceptor sending 'accepted' to
+                // every proposer and learner. In our case, these are the same nodes that received
+                // the 'accept!' message, so we can send to just the originating proposer and invoke
+                // our own accepted handler directly.
+                // Note that this optimization cannot be used with Byzantine Paxos (which needs another
+                // multi-broadcast to detect lying and collusion).
+                debugSend('/', 'accepted', data);
+                debugReceive(instanceId, 'accepted', data); // direct on next line, which doesn't get logging.
+                subchannelHandlers[subchannelKey('accepted') + instanceId].receiver(data);
+                if (data.proposerId !== instanceId) { // i.e., we didn't already do it directly on the line above.
+                    send1('accepted', data.proposerId, data);
+                }
+            } else {
+                send('accepted', data);
+            }
+        } else {
+            send1('nack', data.proposerId, {proposalNumber: data.number});
+        }
+    });
+    // Paxos Learner behavior.
+    function localRelease() {
+        var callback = releaseCallback;
+        debugFlow('baton:', batonName, 'localRelease', 'callback:', !!releaseCallback);
+        if (!releaseCallback) {
+            return;
+        } // Already released, but we might still receive a stale message. That's ok.
+        releaseCallback = undefined;
+        callback(batonName);  // Pass batonName so that clients may use the same handler for different batons.
+    }
+    receive('accepted' + (useOptimizations ? instanceId : ''), function (data) { // See note in 'accept!' regarding use of instanceId here.
+        if (betterNumber(accepted, data)) { // Especially when !useOptimizations, we can receive other acceptances late.
+            return;
+        }
+        var oldAccepted = accepted;
+        debugFlow('baton:', batonName, instanceId, 'accepted', data.number, data.winner);
+        accepted = data;
+        // If we are proposer, make sure we get a quorum of acceptances.
+        if ((data.proposerId === instanceId) && (data.number === proposalNumber) && (++nAccepted >= nQuorum)) {
+            if (electionWatchdog) {
+                timers.clearTimeout(electionWatchdog);
+                electionWatchdog = null;
+            }
+        }
+        // If we are the winner -- regardless of whether we were the proposer.
+        if (acceptedId() === instanceId) {
+            if (claimCallback) {
+                var callback = claimCallback;
+                claimCallback = undefined;
+                callback(batonName);
+            } else if (!releaseCallback) { // We won, but have been released and are no longer interested.
+                // Propose that someone else take the job.
+                timers.setTimeout(propose, 0); // Asynchronous to queue message handling if some are synchronous and others not.
+            }
+        } else if (releaseCallback && (oldAccepted.winner === instanceId)) { // We've been released by someone else!
+            localRelease(); // This can happen if enough people thought we'd disconnected.
+        }
+    });
+
+    // Public Interface
+    //
+    // Registers an intent to hold the baton:
+    // Calls onElection(batonName) once, if you are elected by the scripts
+    //    to be the unique holder of the baton, which may be never.
+    // Calls onRelease(batonName) once, if the baton held by you is released,
+    //    whether this is by you calling release(), or by losing
+    //    an election when you become disconnected.
+    // You may claim again at any time after the start of onRelease
+    // being called.
+    exports.claim = function claim(onElection, onRelease) {
+        debugFlow('baton:', batonName, instanceId, 'claim');
+        if (claimCallback) {
+            log("Ignoring attempt to claim virtualBaton " + batonName + ", which is already waiting for claim.");
+            return;
+        }
+        if (releaseCallback) {
+            log("Ignoring attempt to claim virtualBaton " + batonName + ", which is somehow incorrect released, and that should not happen.");
+            return;
+        }
+        claimCallback = onElection;
+        releaseCallback = onRelease;
+        propose();
+        return exports; // Allows chaining. e.g., var baton = virtualBaton({batonName: 'foo'}.claim(onClaim, onRelease);
+    };
+    // Release the baton you hold, or just log that you are not holding it.
+    exports.release = function release(optionalReplacementOnRelease) {
+        debugFlow('baton:', batonName, instanceId, 'release');
+        if (optionalReplacementOnRelease) { // If you want to change.
+            releaseCallback = optionalReplacementOnRelease;
+        }
+        if (acceptedId() !== instanceId) {
+            log("Ignoring attempt to release virtualBaton " + batonName + ", which is not being held.");
+            return;
+        }
+        localRelease();
+        if (!claimCallback) { // No claim set in release callback.
+            propose();
+        }
+        return exports;
+    };
+    exports.recheckWatchdog = timers.setInterval(function recheck() {
+        var holder = acceptedId();  // If we're waiting and we notice the holder is gone, ...
+        if (holder && claimCallback && !electionWatchdog && !connectionTest(holder)) {
+            bestPromise.winner = null; // used if the quorum agrees that old winner is not there
+            propose();  // ... propose an election.
+        }
+    }, recheckInterval);
+    exports.unload = function unload() { // Disconnect from everything.
+        messages.messageReceived.disconnect(messageHandler);
+        timers.clearInterval(exports.recheckWatchdog);
+        if (electionWatchdog) {
+            timers.clearTimeout(electionWatchdog);
+        }
+        electionWatchdog = claimCallback = releaseCallback = null;
+        Object.keys(subchannelHandlers).forEach(messages.unsubscribe);
+        debugFlow('baton:', batonName, instanceId, 'unload');
+        return exports;
+    };
+
+    // Gather nAcceptors by making two proposals with some gathering time, even without a claim.
+    propose();
+    return exports;
+}
+if (typeof module !== 'undefined') { // Allow testing in nodejs.
+    module.exports = virtualBatonf;
+} else {
+    virtualBaton = virtualBatonf;
+}
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
index e4ee59cb6b..16c83b29dd 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
@@ -9,19 +9,42 @@
     var teleport;
     var portalDestination;
     var animationURL;
-    var self = this;
 
     this.entered = true;
+    Script.include('virtualBaton.js');
+
+    var self = this;
+    var baton;
+    var iOwn = false;
+    var currentInterval;
+    var _entityId;
+
+    function startUpdate() {
+        iOwn = true;
+        print('i am the owner ' + _entityId)
+    }
+
+    function stopUpdateAndReclaim() {
+        print('i released the object ' + _entityId)
+        iOwn = false;
+        baton.claim(startUpdate, stopUpdateAndReclaim);
+    }
 
     this.preload = function(entityID) {
         this.entityId = entityID;
+        _entityId = entityID;
         this.initialize(entityID);
         this.initTimeout = null;
         this.minVelocity = 1;
         this.maxVelocity = 5;
         this.minAngularVelocity = 0.01;
         this.maxAngularVelocity = 0.03;
-        Script.setTimeout(self.move, self.getTotalWait())
+        baton = virtualBaton({
+            batonName: 'io.highfidelity.vesicles:' + entityId, // One winner for each entity
+        });
+        stopUpdateAndReclaim();
+        currentInterval = Script.setInterval(self.move, self.getTotalWait())
+
     }
 
     this.initialize = function(entityID) {
@@ -104,6 +127,8 @@
         if (this.initTimeout !== null) {
             Script.clearTimeout(this.initTimeout);
         }
+        baton.release(function() {});
+        Script.clearInterval(currentInterval);
     }
 
     this.hoverEnterEntity = function(entityID) {
@@ -114,16 +139,13 @@
     }
 
     this.getTotalWait = function() {
-        var avatars = AvatarList.getAvatarIdentifiers();
-        var avatarCount = avatars.length;
-        var random = Math.random() * 2000;
-        var totalWait = random * (avatarCount * 2);
-
-        return totalWait
+        return (Math.random() * 5000) * 2;
     }
 
-
     this.move = function() {
+        if (!iOwn) {
+            return;
+        }
 
         var magnitudeV = self.maxVelocity;
         var directionV = {
@@ -133,11 +155,6 @@
         };
 
         //print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
-        Entities.editEntity(self.entityId, {
-            velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV))
-        });
-
-
 
         var magnitudeAV = self.maxAngularVelocity;
 
@@ -148,11 +165,12 @@
         };
         //print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
         Entities.editEntity(self.entityId, {
+            velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV)),
             angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
 
         });
 
-        Script.setTimeout(self.move, self.getTotalWait())
+
     }
 
 })
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index db50635f93..63f99c53a3 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -5,7 +5,7 @@
 //  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
 //
 
-var version = 1043;
+var version = 1049;
 var cellLayout;
 var baseLocation = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 
@@ -194,7 +194,7 @@ var scenes = [{
                     grabbable: false
                 }
             }),
-            script: "moveRandomly.js?" + version,
+            script: "moveRandomly2.js?" + version,
             visible: true
         }, { //golgi vesicles
             model: "vesicle",
@@ -238,7 +238,7 @@ var scenes = [{
                     grabbable: false
                 }
             }),
-            script: "moveRandomly.js?" + version,
+            script: "moveRandomly2.js?" + version,
             visible: true
         }, {
             model: "vesicle",
@@ -304,7 +304,7 @@ var scenes = [{
                     grabbable: false
                 }
             }),
-            script: "moveRandomly.js?" + version,
+            script: "moveRandomly2.js?" + version,
             visible: true
         }, { //outer vesicles
             model: "vesicle",
@@ -326,7 +326,7 @@ var scenes = [{
                     grabbable: false
                 }
             }),
-            script: "moveRandomly.js?" + version,
+            script: "moveRandomly2.js?" + version,
             visible: true
         },
         //          {//wigglies

From f0d8ffce6582fc63e6adf9486a10c1d511f94250 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Mon, 22 Feb 2016 10:25:56 -0800
Subject: [PATCH 05/19] cleanup errors

---
 .../DomainContent/CellScience/Scripts/moveRandomly2.js | 10 +++-------
 .../CellScience/Scripts/zoomAndMoveRandomly.js         |  7 +++++--
 .../DomainContent/CellScience/importCellScience.js     |  2 +-
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js
index f720ca91cc..ec7b249db0 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js
@@ -44,12 +44,6 @@
 
     this.getTotalWait = function() {
         return (Math.random() * 5000) * 2;
-        // var avatars = AvatarList.getAvatarIdentifiers();
-        // var avatarCount = avatars.length;
-        // var random = Math.random() * 5000;
-        // var totalWait = random * (avatarCount * 2);
-        // print('cellscience color avatarcount, totalwait: ', avatarCount, totalWait)
-        // return totalWait
     }
 
 
@@ -86,7 +80,9 @@
 
 
     this.unload = function() {
-        baton.release(function() {});
+        if (baton) {
+            baton.release(function() {});
+        }
         Script.clearInterval(currentInterval);
     }
 
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
index 16c83b29dd..21e585cd91 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
@@ -40,7 +40,7 @@
         this.minAngularVelocity = 0.01;
         this.maxAngularVelocity = 0.03;
         baton = virtualBaton({
-            batonName: 'io.highfidelity.vesicles:' + entityId, // One winner for each entity
+            batonName: 'io.highfidelity.vesicles:' + entityID, // One winner for each entity
         });
         stopUpdateAndReclaim();
         currentInterval = Script.setInterval(self.move, self.getTotalWait())
@@ -127,7 +127,10 @@
         if (this.initTimeout !== null) {
             Script.clearTimeout(this.initTimeout);
         }
-        baton.release(function() {});
+        if (baton) {
+            baton.release(function() {});
+        }
+
         Script.clearInterval(currentInterval);
     }
 
diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index 63f99c53a3..900a54d9e3 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -5,7 +5,7 @@
 //  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
 //
 
-var version = 1049;
+var version = 1051;
 var cellLayout;
 var baseLocation = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 

From f7b3da078b2ec28209118bbd60ccd5ba2e41cb4a Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Mon, 22 Feb 2016 11:36:53 -0800
Subject: [PATCH 06/19] dont move cells in space, just angular velocity

---
 .../CellScience/Scripts/zoomAndMoveRandomly.js     | 14 +++++++-------
 .../DomainContent/CellScience/importCellScience.js |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
index 21e585cd91..bf249a4644 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
@@ -150,12 +150,12 @@
             return;
         }
 
-        var magnitudeV = self.maxVelocity;
-        var directionV = {
-            x: Math.random() - 0.5,
-            y: Math.random() - 0.5,
-            z: Math.random() - 0.5
-        };
+        // var magnitudeV = self.maxVelocity;
+        // var directionV = {
+        //     x: Math.random() - 0.5,
+        //     y: Math.random() - 0.5,
+        //     z: Math.random() - 0.5
+        // };
 
         //print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
 
@@ -168,7 +168,7 @@
         };
         //print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
         Entities.editEntity(self.entityId, {
-            velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV)),
+            // velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV)),
             angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
 
         });
diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index 900a54d9e3..b061dc6931 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -5,7 +5,7 @@
 //  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
 //
 
-var version = 1051;
+var version = 1052;
 var cellLayout;
 var baseLocation = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 

From e4bc0ce69103ccdd950793255384f9a6b3719a66 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Mon, 22 Feb 2016 13:08:58 -0800
Subject: [PATCH 07/19] tests

---
 .../DomainContent/CellScience/Scripts/zoom.js | 12 ----------
 .../Scripts/zoomAndMoveRandomly.js            | 23 +++++++------------
 .../CellScience/importCellScience.js          |  2 +-
 3 files changed, 9 insertions(+), 28 deletions(-)

diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js
index da41ec64ba..3fc5acae2a 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/zoom.js
@@ -52,13 +52,7 @@
             print("Teleporting to (" + data.location.x + ", " + data.location.y + ", " + data.location.z + ")");
 
              MyAvatar.position = data.location;
-             
-            // if (data.hasOwnProperty('entryPoint') && data.hasOwnProperty('target')) {
-            //     this.lookAtTarget(data.entryPoint, data.target);
-            // }
-            // else{
 
-            // }
         }
 
     }
@@ -103,10 +97,4 @@
         }
     }
 
-    this.hoverEnterEntity = function(entityID) {
-        Entities.editEntity(entityID, {
-            animationURL: animationURL,
-            animationSettings: '{ "fps": 24, "firstFrame": 1, "lastFrame": 25, "frameIndex": 1, "running": true, "hold": true }'
-        });
-    }
 })
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
index bf249a4644..703c4ead33 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
@@ -15,18 +15,19 @@
 
     var self = this;
     var baton;
-    var iOwn = false;
+
+    this.iOwn = false;
     var currentInterval;
     var _entityId;
 
     function startUpdate() {
-        iOwn = true;
+        self.iOwn = true;
         print('i am the owner ' + _entityId)
     }
 
     function stopUpdateAndReclaim() {
         print('i released the object ' + _entityId)
-        iOwn = false;
+        self.iOwn = false;
         baton.claim(startUpdate, stopUpdateAndReclaim);
     }
 
@@ -40,7 +41,7 @@
         this.minAngularVelocity = 0.01;
         this.maxAngularVelocity = 0.03;
         baton = virtualBaton({
-            batonName: 'io.highfidelity.vesicles:' + entityID, // One winner for each entity
+            batonName: 'io.highfidelity.cells:' + entityID, // One winner for each entity
         });
         stopUpdateAndReclaim();
         currentInterval = Script.setInterval(self.move, self.getTotalWait())
@@ -146,19 +147,11 @@
     }
 
     this.move = function() {
-        if (!iOwn) {
+        if (self.iOwn===false) {
+            print('cell is not owned by me...')
             return;
         }
 
-        // var magnitudeV = self.maxVelocity;
-        // var directionV = {
-        //     x: Math.random() - 0.5,
-        //     y: Math.random() - 0.5,
-        //     z: Math.random() - 0.5
-        // };
-
-        //print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
-
         var magnitudeAV = self.maxAngularVelocity;
 
         var directionAV = {
@@ -166,7 +159,7 @@
             y: Math.random() - 0.5,
             z: Math.random() - 0.5
         };
-        //print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
+        print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
         Entities.editEntity(self.entityId, {
             // velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV)),
             angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index b061dc6931..4ae5e5de36 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -5,7 +5,7 @@
 //  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
 //
 
-var version = 1052;
+var version = 1055;
 var cellLayout;
 var baseLocation = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 

From 46aebabd9b2330567dc89feca3f57a1ed42a0e66 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Mon, 22 Feb 2016 17:54:45 -0800
Subject: [PATCH 08/19] switch branches

---
 .../Scripts/zoomAndMoveRandomly.js            | 20 ++++++-------------
 .../CellScience/importCellScience.js          | 10 +++++-----
 2 files changed, 11 insertions(+), 19 deletions(-)

diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
index 703c4ead33..dd6a48c617 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
@@ -38,8 +38,8 @@
         this.initTimeout = null;
         this.minVelocity = 1;
         this.maxVelocity = 5;
-        this.minAngularVelocity = 0.01;
-        this.maxAngularVelocity = 0.03;
+        this.minAngularVelocity = 0.03;
+        this.maxAngularVelocity = 0.10;
         baton = virtualBaton({
             batonName: 'io.highfidelity.cells:' + entityID, // One winner for each entity
         });
@@ -69,7 +69,7 @@
             };
 
             self.teleportSound = SoundCache.getSound("https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/Audio/whoosh.wav");
-            // print(" portal destination is " + self.portalDestination);
+
         }
     }
 
@@ -81,13 +81,6 @@
             print("Teleporting to (" + data.location.x + ", " + data.location.y + ", " + data.location.z + ")");
 
             MyAvatar.position = data.location;
-
-            // if (data.hasOwnProperty('entryPoint') && data.hasOwnProperty('target')) {
-            //     this.lookAtTarget(data.entryPoint, data.target);
-            // }
-            // else{
-
-            // }
         }
 
     }
@@ -143,11 +136,11 @@
     }
 
     this.getTotalWait = function() {
-        return (Math.random() * 5000) * 2;
+        return (Math.random() * 5000) * 3;
     }
 
     this.move = function() {
-        if (self.iOwn===false) {
+        if (self.iOwn === false) {
             print('cell is not owned by me...')
             return;
         }
@@ -159,9 +152,8 @@
             y: Math.random() - 0.5,
             z: Math.random() - 0.5
         };
-        print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
+        // print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
         Entities.editEntity(self.entityId, {
-            // velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV)),
             angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
 
         });
diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index 4ae5e5de36..25323495d1 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -5,7 +5,7 @@
 //  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
 //
 
-var version = 1055;
+var version = 1057;
 var cellLayout;
 var baseLocation = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 
@@ -103,16 +103,16 @@ var scenes = [{
     instances: [{
         model: "Cell",
         dimensions: {
-            x: 550,
-            y: 620,
-            z: 550
+            x: 500,
+            y: 570,
+            z: 500
         },
         offset: {
             x: 0,
             y: 0,
             z: 0
         },
-        radius: 500,
+        radius: 450,
         number: 10,
         userData: JSON.stringify({
             entryPoint: locations.cellLayout[1],

From 6fd149f22dbc63075243af6f42ba93c4a4ccf3d2 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Tue, 23 Feb 2016 12:27:05 -0800
Subject: [PATCH 09/19] no avatar

---
 .../DomainContent/CellScience/motorProteinControllerAC.js       | 2 --
 1 file changed, 2 deletions(-)

diff --git a/unpublishedScripts/DomainContent/CellScience/motorProteinControllerAC.js b/unpublishedScripts/DomainContent/CellScience/motorProteinControllerAC.js
index 672ec1fd92..59577d49ba 100644
--- a/unpublishedScripts/DomainContent/CellScience/motorProteinControllerAC.js
+++ b/unpublishedScripts/DomainContent/CellScience/motorProteinControllerAC.js
@@ -18,8 +18,6 @@ if (USE_LOCAL_HOST === true) {
 
 var USE_LOCAL_HOST = false;
 
-Agent.isAvatar = true;
-
 EntityViewer.setPosition({
     x: 3000,
     y: 13500,

From 46fbf38b5d38e7e7a1a9447d1e9e805fdc477ea7 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Wed, 24 Feb 2016 12:36:18 -0800
Subject: [PATCH 10/19] ac movers

---
 .../CellScience/Scripts/colorRandomly.js      | 104 -----
 .../CellScience/Scripts/moveRandomly2.js      |  91 -----
 .../Scripts/showButtonToPlaySound.js          |   4 -
 .../CellScience/Scripts/virtualBaton.js       | 381 ------------------
 .../Scripts/zoomAndMoveRandomly.js            | 164 --------
 .../CellScience/importCellScience.js          |  43 +-
 .../DomainContent/CellScience/moveCellsAC.js  |  96 +++++
 .../CellScience/moveVesiclesAC.js             | 106 +++++
 8 files changed, 212 insertions(+), 777 deletions(-)
 delete mode 100644 unpublishedScripts/DomainContent/CellScience/Scripts/colorRandomly.js
 delete mode 100644 unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js
 delete mode 100644 unpublishedScripts/DomainContent/CellScience/Scripts/virtualBaton.js
 delete mode 100644 unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
 create mode 100644 unpublishedScripts/DomainContent/CellScience/moveCellsAC.js
 create mode 100644 unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js

diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/colorRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/colorRandomly.js
deleted file mode 100644
index cf4ee810e7..0000000000
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/colorRandomly.js
+++ /dev/null
@@ -1,104 +0,0 @@
-//  Copyright 2016 High Fidelity, Inc.
-//
-//
-//  Distributed under the Apache License, Version 2.0.
-//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
-//
-(function() {
-
-    Script.include(Script.resolvePath('virtualBaton.js'));
-
-    var self = this;
-
-    var baton;
-    var iOwn = false;
-    var currentInterval;
-    var _entityId;
-
-    function startUpdate() {
-        iOwn = true;
-        print('i am the owner ' + _entityId)
-    }
-
-    function stopUpdateAndReclaim() {
-        print('i released the object ' + _entityId)
-        iOwn = false;
-        baton.claim(startUpdate, stopUpdateAndReclaim);
-    }
-
-    this.preload = function(entityId) {
-        this.isConnected = false;
-        this.entityId = entityId;
-        _entityId = entityId;
-        this.minVelocity = 1;
-        this.maxVelocity = 5;
-        this.minAngularVelocity = 0.01;
-        this.maxAngularVelocity = 0.03;
-        baton = virtualBaton({
-            batonName: 'io.highfidelity.vesicles:' + entityId, // One winner for each entity
-        });
-        stopUpdateAndReclaim();
-       currentInterval =  Script.setInterval(self.move, self.getTotalWait())
-    }
-
-
-    this.getTotalWait = function() {
-        return (Math.random() * 5000) * 2;
-        // var avatars = AvatarList.getAvatarIdentifiers();
-        // var avatarCount = avatars.length;
-        // var random = Math.random() * 5000;
-        // var totalWait = random * (avatarCount * 2);
-        // print('cellscience color avatarcount, totalwait: ', avatarCount, totalWait)
-        // return totalWait
-    }
-
-
-    this.move = function() {
-        if (!iOwn) {
-            return;
-        }
-
-        var properties = Entities.getEntityProperties(self.entityId);
-        var color = properties.color;
-
-        var newColor;
-        var red = {
-            red: 255,
-            green: 0,
-            blue: 0
-        }
-        var green = {
-            red: 0,
-            green: 255,
-            blue: 0
-        }
-        var blue = {
-            red: 0,
-            green: 0,
-            blue: 255
-        }
-        if (color.red > 0) {
-            newColor = green;
-        }
-        if (color.green > 0) {
-            newColor = blue;
-        }
-        if (color.blue > 0) {
-            newColor = red
-        }
-        Entities.editEntity(self.entityId, {
-            color: newColor
-        });
-
-
-    }
-
-
-    this.unload = function() {
-        baton.release(function() {});
-        Script.clearTimeout(currentInterval);
-    }
-
-
-
-})
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js b/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js
deleted file mode 100644
index ec7b249db0..0000000000
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/moveRandomly2.js
+++ /dev/null
@@ -1,91 +0,0 @@
-//  Copyright 2016 High Fidelity, Inc.
-//
-//
-//  Distributed under the Apache License, Version 2.0.
-//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
-//
-(function() {
-
-    Script.include('virtualBaton.js');
-
-    var self = this;
-
-    var baton;
-    var iOwn = false;
-    var currentInterval;
-    var _entityId;
-
-    function startUpdate() {
-        iOwn = true;
-        print('i am the owner ' + _entityId)
-    }
-
-    function stopUpdateAndReclaim() {
-        print('i released the object ' + _entityId)
-        iOwn = false;
-        baton.claim(startUpdate, stopUpdateAndReclaim);
-    }
-
-    this.preload = function(entityId) {
-        this.isConnected = false;
-        this.entityId = entityId;
-        _entityId = entityId;
-        this.minVelocity = 1;
-        this.maxVelocity = 5;
-        this.minAngularVelocity = 0.01;
-        this.maxAngularVelocity = 0.03;
-        baton = virtualBaton({
-            batonName: 'io.highfidelity.vesicles:' + entityId, // One winner for each entity
-        });
-        stopUpdateAndReclaim();
-        currentInterval = Script.setInterval(self.move, self.getTotalWait())
-    }
-
-
-    this.getTotalWait = function() {
-        return (Math.random() * 5000) * 2;
-    }
-
-
-    this.move = function() {
-        if (!iOwn) {
-            return;
-        }
-
-        var magnitudeV = self.maxVelocity;
-        var directionV = {
-            x: Math.random() - 0.5,
-            y: Math.random() - 0.5,
-            z: Math.random() - 0.5
-        };
-
-        //print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
-
-        var magnitudeAV = self.maxAngularVelocity;
-
-        var directionAV = {
-            x: Math.random() - 0.5,
-            y: Math.random() - 0.5,
-            z: Math.random() - 0.5
-        };
-        //print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
-        Entities.editEntity(self.entityId, {
-            velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV)),
-            angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
-
-        });
-
-
-    }
-
-
-    this.unload = function() {
-        if (baton) {
-            baton.release(function() {});
-        }
-        Script.clearInterval(currentInterval);
-    }
-
-
-
-})
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/showButtonToPlaySound.js b/unpublishedScripts/DomainContent/CellScience/Scripts/showButtonToPlaySound.js
index 6651e435b4..8ee5e0092e 100644
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/showButtonToPlaySound.js
+++ b/unpublishedScripts/DomainContent/CellScience/Scripts/showButtonToPlaySound.js
@@ -36,8 +36,6 @@
                     return;
                 }
 
-
-
                 self.addButton();
                 self.buttonShowing = false;
                 self.showDistance = self.userData.showDistance;
@@ -51,8 +49,6 @@
                 };
                 self.sound = SoundCache.getSound(this.soundURL);
 
-
-
             }
 
             this.addButton = function() {
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/virtualBaton.js b/unpublishedScripts/DomainContent/CellScience/Scripts/virtualBaton.js
deleted file mode 100644
index 63f96a5c1e..0000000000
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/virtualBaton.js
+++ /dev/null
@@ -1,381 +0,0 @@
-"use strict";
-/*jslint nomen: true, plusplus: true, vars: true */
-/*global Messages, Script, MyAvatar, AvatarList, Entities, print */
-
-//  Created by Howard Stearns
-//  Copyright 2016 High Fidelity, Inc.
-//  
-//  Distributed under the Apache License, Version 2.0.
-//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
-//
-//  Allows cooperating scripts to pass a "virtual baton" between them,
-//  which is useful when part of a script should only be executed by
-//  the one participant that is holding this particular baton.
-// 
-//  A virtual baton is simply any string agreed upon by the scripts
-//  that use it. Only one script at a time can hold the baton, and it
-//  holds it until that script releases it, or the other scripts
-//  determine that the holding script is not responding. The script
-//  automatically determines who among claimants has the baton, if anyone,
-//  and holds an "election" if necessary.
-//
-//  See entityScript/tribble.js as an example, and the functions
-//  virtualBaton(), claim(), release().
-//
-
-// Answers a new virtualBaton for the given parameters, of which 'key'
-// is required.
-function virtualBatonf(options) {
-    // Answer averages (number +/- variability). Avoids having everyone act in lockstep.
-    function randomize(number, variability) {
-        var allowedDeviation = number * variability; // one side of the deviation range
-        var allowedDeviationRange = allowedDeviation * 2; // total range for +/- deviation
-        var randomDeviation = Math.random() * allowedDeviationRange;
-        var result = number - allowedDeviation + randomDeviation;
-        return result;
-    }
-    // Allow testing outside in a harness outside of High Fidelity.
-    // See sourceCodeSandbox/tests/mocha/test/testVirtualBaton.js
-    var globals = options.globals || {},
-        messages = globals.Messages || Messages,
-        myAvatar = globals.MyAvatar || MyAvatar,
-        avatarList = globals.AvatarList || AvatarList,
-        entities = globals.Entities || Entities,
-        timers = globals.Script || Script,
-        log = globals.print || print;
-
-    var batonName = options.batonName,  // The identify of the baton.
-        // instanceId is the identify of this particular copy of the script among all copies using the same batonName
-        // in the domain. For example, if you wanted only one entity among multiple entity scripts to hold the baton,
-        // you could specify virtualBaton({batonName: 'someBatonName', instanceId: MyAvatar.sessionUUID + entityID}).
-        instanceId = options.instanceId || myAvatar.sessionUUID,
-        // virtualBaton() returns the exports object with properties. You can pass in an object to be side-effected.
-        exports = options.exports || {},
-        // Handy to set false if we believe the optimizations are wrong, or to use both values in a test harness.
-        useOptimizations = (options.useOptimizations === undefined) ? true : options.useOptimizations,
-        electionTimeout = options.electionTimeout || randomize(500, 0.2), // ms. If no winner in this time, hold a new election.
-        recheckInterval = options.recheckInterval || randomize(500, 0.2), // ms. Check that winners remain connected.
-        // If you supply your own instanceId, you might also supply a connectionTest that answers
-        // truthy iff the given id is still valid and connected, and is run at recheckInterval. You
-        // can use exports.validId (see below), and the default answers truthy if id is valid or a
-        // concatenation of two valid ids. (This handles the most common cases of instanceId being
-        // either (the default) MyAvatar.sessionUUID, an entityID, or the concatenation (in either
-        // order) of both.)
-        connectionTest = options.connectionTest || function connectionTest(id) {
-            var idLength = 38;
-            if (id.length === idLength) {
-                return exports.validId(id);
-            }
-            return (id.length === 2 * idLength) && exports.validId(id.slice(0, idLength)) && exports.validId(id.slice(idLength));
-        };
-
-    if (!batonName) {
-        throw new Error("A virtualBaton must specify a batonName.");
-    }
-    // Truthy if id exists as either a connected avatar or valid entity.
-    exports.validId = function validId(id) {
-        var avatar = avatarList.getAvatar(id);
-        if (avatar && (avatar.sessionUUID === id)) {
-            return true;
-        }
-        var properties = entities.getEntityProperties(id, ['type']);
-        return properties && properties.type;
-    };
-
-    // Various logging, controllable through options.
-    function debug() { // Display the arguments not just [Object object].
-        log.apply(null, [].map.call(arguments, JSON.stringify));
-    }
-    function debugFlow() {
-        if (options.debugFlow) {
-            debug.apply(null, arguments);
-        }
-    }
-    function debugSend(destination, operation, data) {
-        if (options.debugSend) {
-            debug('baton:', batonName, instanceId, 's=>', destination, operation, data);
-        }
-    }
-    function debugReceive(senderID, operation, data) { // senderID is client sessionUUID -- not necessarily instanceID!
-        if (options.debugReceive) {
-            debug('baton:', batonName, senderID, '=>r', instanceId, operation, data);
-        }
-    }
-
-    // Messages: Just synactic sugar for hooking things up to Messages system.
-    // We create separate subchannel strings for each operation within our general channelKey, instead of using
-    // a switch in the receiver.
-    var channelKey = "io.highfidelity.virtualBaton:" + batonName,
-        subchannelHandlers = {}, // Message channel string => {receiver, op}
-        subchannelKeys = {};     // operation => Message channel string
-    function subchannelKey(operation) {
-        return channelKey + ':' + operation;
-    }
-    function receive(operation, handler) { // Record a handler for an operation on our channelKey
-        var subKey = subchannelKey(operation);
-        subchannelHandlers[subKey] = {receiver: handler, op: operation};
-        subchannelKeys[operation] = subKey;
-        messages.subscribe(subKey);
-    }
-    function sendHelper(subchannel, data) {
-        var message = JSON.stringify(data);
-        messages.sendMessage(subchannel, message);
-    }
-    function send1(operation, destination, data) { // Send data for an operation to just one destination on our channelKey.
-        debugSend(destination, operation, data);
-        sendHelper(subchannelKey(operation) + destination, data);
-    }
-    function send(operation, data) {  // Send data for an operation on our channelKey.
-        debugSend('-', operation, data);
-        sendHelper(subchannelKeys[operation], data);
-    }
-    function messageHandler(channel, messageString, senderID) {
-        var handler = subchannelHandlers[channel];
-        if (!handler) {
-            return;
-        }
-        var data = JSON.parse(messageString);
-        debugReceive(senderID, handler.op, data);
-        handler.receiver(data);
-    }
-    messages.messageReceived.connect(messageHandler);
-
-    var nPromises = 0, nAccepted = 0, electionWatchdog;
-
-    // It would be great if we had a way to know how many subscribers our channel has. Failing that...
-    var nNack = 0, previousNSubscribers = 0, lastGathering = 0, thisTimeout = electionTimeout;
-    function nSubscribers() { // Answer the number of subscribers.
-        // To find nQuorum, we need to know how many scripts are being run using this batonName, which isn't
-        // the same as the number of clients!
-        //
-        // If we overestimate by too much, we may fail to reach consensus, which triggers a new
-        // election proposal, so we take the number of acceptors to be the max(nPromises, nAccepted)
-        // + nNack reported in the previous round.
-        //
-        // If we understimate by too much, there can be different pockets on the Internet that each
-        // believe they have agreement on different holders of the baton, which is precisely what
-        // the virtualBaton is supposed to avoid. Therefore we need to allow 'nack' to gather stragglers.
-
-        var now = Date.now(), elapsed = now - lastGathering;
-        if (elapsed >= thisTimeout) {
-            previousNSubscribers = Math.max(nPromises, nAccepted) + nNack;
-            lastGathering = now;
-        } // ...otherwise we use the previous value unchanged.
-
-        // On startup, we do one proposal that we cannot possibly close, so that we'll
-        // lock things up for the full electionTimeout to gather responses.
-        if (!previousNSubscribers) {
-            var LARGE_INTEGER = Number.MAX_SAFE_INTEGER || (-1 >>> 1); // QT doesn't define the ECMA constant. Max int will do for our purposes.
-            previousNSubscribers = LARGE_INTEGER;
-        }
-        return previousNSubscribers;
-    }
-
-    // MAIN ALGORITHM
-    //
-    // Internally, this uses the Paxos algorith to hold elections.
-    // Alternatively, we could have the message server pick and maintain a winner, but it would
-    // still have to deal with the same issues of verification in the presence of lost/delayed/reordered messages.
-    // Paxos is known to be optimal under these circumstances, except that its best to have a dedicated proposer
-    // (such as the server).
-    function betterNumber(number, best) {
-        return (number.number || 0) > best.number;
-    }
-    // Paxos Proposer behavior
-    var proposalNumber = 0,
-        nQuorum = 0,
-        bestPromise = {number: 0},
-        claimCallback,
-        releaseCallback;
-    function propose() {  // Make a new proposal, so that we learn/update the proposalNumber and winner.
-        // Even though we send back a 'nack' if the proposal is obsolete, with network errors
-        // there's no way to know for certain that we've failed. The electionWatchdog will try a new
-        // proposal if we have not been accepted by a quorum after election Timeout.
-        if (electionWatchdog) {
-            // If we had a means of determining nSubscribers other than by counting, we could just
-            // timers.clearTimeout(electionWatchdog) and not return.
-            return;
-        }
-        thisTimeout = randomize(electionTimeout, 0.5); // Note use in nSubcribers.
-        electionWatchdog = timers.setTimeout(function () {
-            electionWatchdog = null;
-            propose();
-        }, thisTimeout);
-        var nAcceptors = nSubscribers();
-        nQuorum = Math.floor(nAcceptors / 2) + 1;
-
-        proposalNumber = Math.max(proposalNumber, bestPromise.number) + 1;
-        debugFlow('baton:', batonName, instanceId, 'propose', proposalNumber,
-                  'claim:', !!claimCallback, 'nAcceptors:', nAcceptors, nPromises, nAccepted, nNack);
-        nPromises = nAccepted = nNack = 0;
-        send('prepare!', {number: proposalNumber, proposerId: instanceId});
-    }
-    // We create a distinguished promise subchannel for our id, because promises need only be sent to the proposer.
-    receive('promise' + instanceId, function (data) {
-        if (betterNumber(data, bestPromise)) {
-            bestPromise = data;
-        }
-        if ((data.proposalNumber === proposalNumber) && (++nPromises >= nQuorum)) { // Note check for not being a previous round
-            var answer = {number: data.proposalNumber, proposerId: data.proposerId, winner: bestPromise.winner}; // Not data.number.
-            if (!answer.winner || (answer.winner === instanceId)) { // We get to pick.
-                answer.winner = claimCallback ? instanceId : null;
-            }
-            send('accept!', answer);
-        }
-    });
-    receive('nack' + instanceId, function (data) { // An acceptor reports more recent data...
-        if (data.proposalNumber === proposalNumber) {
-            nNack++;  // For updating nQuorum.
-            // IWBNI if we started our next proposal right now/here, but we need a decent nNack count.
-            // Lets save that optimization for another day...
-        }
-    });
-    // Paxos Acceptor behavior
-    var bestProposal = {number: 0}, accepted = {};
-    function acceptedId() {
-        return accepted && accepted.winner;
-    }
-    receive('prepare!', function (data) {
-        var response = {proposalNumber: data.number, proposerId: data.proposerId};
-        if (betterNumber(data, bestProposal)) {
-            bestProposal = data;
-            if (accepted.winner && connectionTest(accepted.winner)) {
-                response.number = accepted.number;
-                response.winner = accepted.winner;
-            }
-            send1('promise', data.proposerId, response);
-        } else {
-            send1('nack', data.proposerId, response);
-        }
-    });
-    receive('accept!', function (data) {
-        if (!betterNumber(bestProposal, data)) {
-            bestProposal = accepted = data; // Update both with current data. Might have missed the proposal earlier.
-            if (useOptimizations) {
-                // The Paxos literature describes every acceptor sending 'accepted' to
-                // every proposer and learner. In our case, these are the same nodes that received
-                // the 'accept!' message, so we can send to just the originating proposer and invoke
-                // our own accepted handler directly.
-                // Note that this optimization cannot be used with Byzantine Paxos (which needs another
-                // multi-broadcast to detect lying and collusion).
-                debugSend('/', 'accepted', data);
-                debugReceive(instanceId, 'accepted', data); // direct on next line, which doesn't get logging.
-                subchannelHandlers[subchannelKey('accepted') + instanceId].receiver(data);
-                if (data.proposerId !== instanceId) { // i.e., we didn't already do it directly on the line above.
-                    send1('accepted', data.proposerId, data);
-                }
-            } else {
-                send('accepted', data);
-            }
-        } else {
-            send1('nack', data.proposerId, {proposalNumber: data.number});
-        }
-    });
-    // Paxos Learner behavior.
-    function localRelease() {
-        var callback = releaseCallback;
-        debugFlow('baton:', batonName, 'localRelease', 'callback:', !!releaseCallback);
-        if (!releaseCallback) {
-            return;
-        } // Already released, but we might still receive a stale message. That's ok.
-        releaseCallback = undefined;
-        callback(batonName);  // Pass batonName so that clients may use the same handler for different batons.
-    }
-    receive('accepted' + (useOptimizations ? instanceId : ''), function (data) { // See note in 'accept!' regarding use of instanceId here.
-        if (betterNumber(accepted, data)) { // Especially when !useOptimizations, we can receive other acceptances late.
-            return;
-        }
-        var oldAccepted = accepted;
-        debugFlow('baton:', batonName, instanceId, 'accepted', data.number, data.winner);
-        accepted = data;
-        // If we are proposer, make sure we get a quorum of acceptances.
-        if ((data.proposerId === instanceId) && (data.number === proposalNumber) && (++nAccepted >= nQuorum)) {
-            if (electionWatchdog) {
-                timers.clearTimeout(electionWatchdog);
-                electionWatchdog = null;
-            }
-        }
-        // If we are the winner -- regardless of whether we were the proposer.
-        if (acceptedId() === instanceId) {
-            if (claimCallback) {
-                var callback = claimCallback;
-                claimCallback = undefined;
-                callback(batonName);
-            } else if (!releaseCallback) { // We won, but have been released and are no longer interested.
-                // Propose that someone else take the job.
-                timers.setTimeout(propose, 0); // Asynchronous to queue message handling if some are synchronous and others not.
-            }
-        } else if (releaseCallback && (oldAccepted.winner === instanceId)) { // We've been released by someone else!
-            localRelease(); // This can happen if enough people thought we'd disconnected.
-        }
-    });
-
-    // Public Interface
-    //
-    // Registers an intent to hold the baton:
-    // Calls onElection(batonName) once, if you are elected by the scripts
-    //    to be the unique holder of the baton, which may be never.
-    // Calls onRelease(batonName) once, if the baton held by you is released,
-    //    whether this is by you calling release(), or by losing
-    //    an election when you become disconnected.
-    // You may claim again at any time after the start of onRelease
-    // being called.
-    exports.claim = function claim(onElection, onRelease) {
-        debugFlow('baton:', batonName, instanceId, 'claim');
-        if (claimCallback) {
-            log("Ignoring attempt to claim virtualBaton " + batonName + ", which is already waiting for claim.");
-            return;
-        }
-        if (releaseCallback) {
-            log("Ignoring attempt to claim virtualBaton " + batonName + ", which is somehow incorrect released, and that should not happen.");
-            return;
-        }
-        claimCallback = onElection;
-        releaseCallback = onRelease;
-        propose();
-        return exports; // Allows chaining. e.g., var baton = virtualBaton({batonName: 'foo'}.claim(onClaim, onRelease);
-    };
-    // Release the baton you hold, or just log that you are not holding it.
-    exports.release = function release(optionalReplacementOnRelease) {
-        debugFlow('baton:', batonName, instanceId, 'release');
-        if (optionalReplacementOnRelease) { // If you want to change.
-            releaseCallback = optionalReplacementOnRelease;
-        }
-        if (acceptedId() !== instanceId) {
-            log("Ignoring attempt to release virtualBaton " + batonName + ", which is not being held.");
-            return;
-        }
-        localRelease();
-        if (!claimCallback) { // No claim set in release callback.
-            propose();
-        }
-        return exports;
-    };
-    exports.recheckWatchdog = timers.setInterval(function recheck() {
-        var holder = acceptedId();  // If we're waiting and we notice the holder is gone, ...
-        if (holder && claimCallback && !electionWatchdog && !connectionTest(holder)) {
-            bestPromise.winner = null; // used if the quorum agrees that old winner is not there
-            propose();  // ... propose an election.
-        }
-    }, recheckInterval);
-    exports.unload = function unload() { // Disconnect from everything.
-        messages.messageReceived.disconnect(messageHandler);
-        timers.clearInterval(exports.recheckWatchdog);
-        if (electionWatchdog) {
-            timers.clearTimeout(electionWatchdog);
-        }
-        electionWatchdog = claimCallback = releaseCallback = null;
-        Object.keys(subchannelHandlers).forEach(messages.unsubscribe);
-        debugFlow('baton:', batonName, instanceId, 'unload');
-        return exports;
-    };
-
-    // Gather nAcceptors by making two proposals with some gathering time, even without a claim.
-    propose();
-    return exports;
-}
-if (typeof module !== 'undefined') { // Allow testing in nodejs.
-    module.exports = virtualBatonf;
-} else {
-    virtualBaton = virtualBatonf;
-}
diff --git a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js b/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
deleted file mode 100644
index dd6a48c617..0000000000
--- a/unpublishedScripts/DomainContent/CellScience/Scripts/zoomAndMoveRandomly.js
+++ /dev/null
@@ -1,164 +0,0 @@
-//  Copyright 2016 High Fidelity, Inc.
-//
-//
-//  Distributed under the Apache License, Version 2.0.
-//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
-//
-
-(function() {
-    var teleport;
-    var portalDestination;
-    var animationURL;
-
-    this.entered = true;
-    Script.include('virtualBaton.js');
-
-    var self = this;
-    var baton;
-
-    this.iOwn = false;
-    var currentInterval;
-    var _entityId;
-
-    function startUpdate() {
-        self.iOwn = true;
-        print('i am the owner ' + _entityId)
-    }
-
-    function stopUpdateAndReclaim() {
-        print('i released the object ' + _entityId)
-        self.iOwn = false;
-        baton.claim(startUpdate, stopUpdateAndReclaim);
-    }
-
-    this.preload = function(entityID) {
-        this.entityId = entityID;
-        _entityId = entityID;
-        this.initialize(entityID);
-        this.initTimeout = null;
-        this.minVelocity = 1;
-        this.maxVelocity = 5;
-        this.minAngularVelocity = 0.03;
-        this.maxAngularVelocity = 0.10;
-        baton = virtualBaton({
-            batonName: 'io.highfidelity.cells:' + entityID, // One winner for each entity
-        });
-        stopUpdateAndReclaim();
-        currentInterval = Script.setInterval(self.move, self.getTotalWait())
-
-    }
-
-    this.initialize = function(entityID) {
-        // print(' should initialize')
-        var properties = Entities.getEntityProperties(entityID);
-        if (properties.userData.length === 0 || properties.hasOwnProperty('userData') === false) {
-            self.initTimeout = Script.setTimeout(function() {
-                // print(' no user data yet, try again in one second')
-                self.initialize(entityID);
-            }, 1000)
-        } else {
-            // print(' has userData')
-            self.portalDestination = properties.userData;
-            animationURL = properties.modelURL;
-            self.soundOptions = {
-                stereo: true,
-                loop: false,
-                localOnly: false,
-                position: properties.position,
-                volume: 0.5
-            };
-
-            self.teleportSound = SoundCache.getSound("https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/Audio/whoosh.wav");
-
-        }
-    }
-
-    this.enterEntity = function(entityID) {
-        //print('ENTERED A BOUNDARY ENTITY, SHOULD ZOOM', entityID)
-        var data = JSON.parse(Entities.getEntityProperties(this.entityId).userData);
-        //print('DATA IS::' + data)
-        if (data != null) {
-            print("Teleporting to (" + data.location.x + ", " + data.location.y + ", " + data.location.z + ")");
-
-            MyAvatar.position = data.location;
-        }
-
-    }
-
-    this.lookAtTarget = function(entryPoint, target) {
-        //print('SHOULD LOOK AT TARGET')
-        var direction = Vec3.normalize(Vec3.subtract(entryPoint, target));
-        var pitch = Quat.angleAxis(Math.asin(-direction.y) * 180.0 / Math.PI, {
-            x: 1,
-            y: 0,
-            z: 0
-        });
-        var yaw = Quat.angleAxis(Math.atan2(direction.x, direction.z) * 180.0 / Math.PI, {
-            x: 0,
-            y: 1,
-            z: 0
-        });
-
-        MyAvatar.goToLocation(entryPoint, true, yaw);
-
-        MyAvatar.headYaw = 0;
-
-    }
-
-    this.leaveEntity = function(entityID) {
-        Entities.editEntity(entityID, {
-            animationURL: animationURL,
-            animationSettings: '{ "frameIndex": 1, "running": false }'
-        });
-        this.entered = false;
-        if (this.initTimeout !== null) {
-            Script.clearTimeout(this.initTimeout);
-        }
-        //playSound();
-    }
-
-    this.unload = function() {
-        if (this.initTimeout !== null) {
-            Script.clearTimeout(this.initTimeout);
-        }
-        if (baton) {
-            baton.release(function() {});
-        }
-
-        Script.clearInterval(currentInterval);
-    }
-
-    this.hoverEnterEntity = function(entityID) {
-        Entities.editEntity(entityID, {
-            animationURL: animationURL,
-            animationSettings: '{ "fps": 24, "firstFrame": 1, "lastFrame": 25, "frameIndex": 1, "running": true, "hold": true }'
-        });
-    }
-
-    this.getTotalWait = function() {
-        return (Math.random() * 5000) * 3;
-    }
-
-    this.move = function() {
-        if (self.iOwn === false) {
-            print('cell is not owned by me...')
-            return;
-        }
-
-        var magnitudeAV = self.maxAngularVelocity;
-
-        var directionAV = {
-            x: Math.random() - 0.5,
-            y: Math.random() - 0.5,
-            z: Math.random() - 0.5
-        };
-        // print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
-        Entities.editEntity(self.entityId, {
-            angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
-
-        });
-
-
-    }
-
-})
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index 25323495d1..55b09cd4a7 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -120,7 +120,7 @@ var scenes = [{
             location: locations.cellLayout[1],
             baseURL: baseLocation
         }),
-        script: "zoomAndMoveRandomly.js?" + version,
+        script: "zoom.js?" + version,
         visible: true
     }],
     boundary: {
@@ -194,7 +194,6 @@ var scenes = [{
                     grabbable: false
                 }
             }),
-            script: "moveRandomly2.js?" + version,
             visible: true
         }, { //golgi vesicles
             model: "vesicle",
@@ -238,7 +237,6 @@ var scenes = [{
                     grabbable: false
                 }
             }),
-            script: "moveRandomly2.js?" + version,
             visible: true
         }, {
             model: "vesicle",
@@ -304,7 +302,6 @@ var scenes = [{
                     grabbable: false
                 }
             }),
-            script: "moveRandomly2.js?" + version,
             visible: true
         }, { //outer vesicles
             model: "vesicle",
@@ -326,32 +323,8 @@ var scenes = [{
                     grabbable: false
                 }
             }),
-            script: "moveRandomly2.js?" + version,
             visible: true
-        },
-        //          {//wigglies
-        //              model:"wiggly",
-        //              dimensions:{x:320,y:40,z:160},
-        //              randomSize: 10,
-        //              offset:{x:0,y:0,z:0},
-        //              radius:1800,
-        //              number:50,
-        //              userData:"",
-        //              script:"moveRandomly",
-        //              visible:true
-        //          },
-        ////            {//wigglies
-        //              model:"wiggly",
-        //              dimensions:{x:640,y:80,z:320},
-        //              randomSize: 10,
-        //              offset:{x:0,y:0,z:0},
-        //              radius:2100,
-        //              number:50,
-        //              userData:"",
-        //              script:"moveRandomly",
-        //              visible:true
-        //          },
-        {
+        }, {
             model: "hexokinase",
             dimensions: {
                 x: 3,
@@ -813,7 +786,7 @@ function CreateInstances(scene) {
                     x: 0,
                     y: 0,
                     z: 0
-                }, idBounds, 150);
+                }, idBounds, 150, scene.instances[i]);
 
             }
             //print('SCRIPT AT CREATE ENTITY: ' + script)
@@ -824,8 +797,11 @@ function CreateInstances(scene) {
 
 
 
-function CreateIdentification(name, position, rotation, dimensions, showDistance) {
+function CreateIdentification(name, position, rotation, dimensions, showDistance, parentID) {
     //print ("creating ID for " + name);
+    if (parentID === undefined) {
+        parentID = "{00000000-0000-0000-0000-000000000000}";
+    }
     Entities.addEntity({
         type: "Sphere",
         name: "ID for " + name,
@@ -834,6 +810,7 @@ function CreateIdentification(name, position, rotation, dimensions, showDistance
             green: 0,
             blue: 0
         },
+        parentID: parentID,
         dimensions: dimensions,
         position: position,
         rotation: rotation,
@@ -9042,7 +9019,7 @@ Script.scriptEnding.connect(function() {
     Entities.addingEntity.disconnect(makeUngrabbable);
 });
 
-Script.setTimeout(function(){
+Script.setTimeout(function() {
     print('JBP stopping cell science import');
     Script.stop();
-},30000)
\ No newline at end of file
+}, 30000)
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js b/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js
new file mode 100644
index 0000000000..30e83108d6
--- /dev/null
+++ b/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js
@@ -0,0 +1,96 @@
+var basePosition = {
+    x: 3000,
+    y: 13500,
+    z: 3000
+};
+
+var initialized = false;
+
+EntityViewer.setPosition(basePosition);
+EntityViewer.setKeyholeRadius(60000);
+var octreeQueryInterval = Script.setInterval(function() {
+    EntityViewer.queryOctree();
+}, 200);
+
+var THROTTLE = true;
+var THROTTLE_RATE = 5000;
+
+var sinceLastUpdate = 0;
+
+print('cells script')
+
+function findCells() {
+    var results = Entities.findEntities(basePosition, 60000);
+
+    if (results.length === 0) {
+        print('no entities found')
+        return;
+    }
+
+    results.forEach(function(v) {
+        var name = Entities.getEntityProperties(v, 'name').name;
+        print('name is:: ' + name)
+        if (name === 'Cell') {
+            print('found a cell!!' + v)
+            Script.setTimeout(function() {
+                moveCell(v);
+            }, Math.random() * THROTTLE_RATE)
+        }
+    });
+}
+
+
+var minAngularVelocity = 0.01;
+var maxAngularVelocity = 0.03;
+
+function moveCell(entityId) {
+    print('moving a cell! ' + entityId)
+
+    var magnitudeAV = maxAngularVelocity;
+
+    var directionAV = {
+        x: Math.random() - 0.5,
+        y: Math.random() - 0.5,
+        z: Math.random() - 0.5
+    };
+    print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
+    Entities.editEntity(entityId, {
+        angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
+    });
+
+}
+
+function update(deltaTime) {
+
+    // print('deltaTime',deltaTime)
+    if (!initialized) {
+        print("checking for servers...");
+        if (Entities.serversExist() && Entities.canRez()) {
+            print("servers exist -- makeAll...");
+            Entities.setPacketsPerSecond(6000);
+            print("PPS:" + Entities.getPacketsPerSecond());
+            initialized = true;
+        }
+        return;
+    }
+
+    if (THROTTLE === true) {
+        sinceLastUpdate = sinceLastUpdate + deltaTime * 1000;
+        if (sinceLastUpdate > THROTTLE_RATE) {
+            print('SHOULD FIND CELLS!!!')
+            sinceLastUpdate = 0;
+            findCells();
+        } else {
+            // print('returning in update ' + sinceLastUpdate)
+            return;
+        }
+    }
+
+}
+
+function unload() {
+    Script.update.disconnect(update);
+}
+
+Script.update.connect(update);
+Script.scriptEnding.connect(unload);
\ No newline at end of file
diff --git a/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js b/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js
new file mode 100644
index 0000000000..ce8da54eb2
--- /dev/null
+++ b/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js
@@ -0,0 +1,106 @@
+var basePosition = {
+    x: 3000,
+    y: 13500,
+    z: 3000
+};
+
+var initialized = false;
+
+EntityViewer.setPosition(basePosition);
+EntityViewer.setKeyholeRadius(60000);
+var octreeQueryInterval = Script.setInterval(function() {
+    EntityViewer.queryOctree();
+}, 200);
+
+var THROTTLE = true;
+var THROTTLE_RATE = 5000;
+
+var sinceLastUpdate = 0;
+
+print('vesicle script')
+
+function findVesicles() {
+    var results = Entities.findEntities(basePosition, 60000);
+
+    if (results.length === 0) {
+        print('no entities found')
+        return;
+    }
+
+    results.forEach(function(v) {
+        var name = Entities.getEntityProperties(v, 'name').name;
+        print('name is:: ' + name)
+        if (name === 'vesicle') {
+            print('found a vesicle!!' + v)
+            Script.setTimeout(function() {
+                moveVesicle(v);
+            }, Math.random() * THROTTLE_RATE)
+        }
+    });
+}
+
+var minVelocity = 1;
+var maxVelocity = 5;
+var minAngularVelocity = 0.01;
+var maxAngularVelocity = 0.03;
+
+function moveVesicle(entityId) {
+    print('moving a vesicle! ' + entityId)
+    var magnitudeV = maxVelocity;
+    var directionV = {
+        x: Math.random() - 0.5,
+        y: Math.random() - 0.5,
+        z: Math.random() - 0.5
+    };
+
+    print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
+
+    var magnitudeAV = maxAngularVelocity;
+
+    var directionAV = {
+        x: Math.random() - 0.5,
+        y: Math.random() - 0.5,
+        z: Math.random() - 0.5
+    };
+    print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
+    Entities.editEntity(entityId, {
+        velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV)),
+        angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
+    });
+
+}
+
+function update(deltaTime) {
+
+    // print('deltaTime',deltaTime)
+    if (!initialized) {
+        print("checking for servers...");
+        if (Entities.serversExist() && Entities.canRez()) {
+            print("servers exist -- makeAll...");
+            Entities.setPacketsPerSecond(6000);
+            print("PPS:" + Entities.getPacketsPerSecond());
+            initialized = true;
+        }
+        return;
+    }
+
+    if (THROTTLE === true) {
+        sinceLastUpdate = sinceLastUpdate + deltaTime * 1000;
+        if (sinceLastUpdate > THROTTLE_RATE) {
+            print('SHOULD FIND VESICLES!!!')
+            sinceLastUpdate = 0;
+            findVesicles();
+        } else {
+            // print('returning in update ' + sinceLastUpdate)
+            return;
+        }
+    }
+
+}
+
+function unload() {
+    Script.update.disconnect(update);
+}
+
+Script.update.connect(update);
+Script.scriptEnding.connect(unload);
\ No newline at end of file

From baa030b7b07a24612953807d5a116398e8354f17 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Wed, 24 Feb 2016 13:18:01 -0800
Subject: [PATCH 11/19] cleanup and submit

---
 .../CellScience/importCellScience.js          |  2 +-
 .../DomainContent/CellScience/moveCellsAC.js  | 21 ++++++++++++-------
 .../CellScience/moveVesiclesAC.js             | 20 +++++++++++-------
 3 files changed, 28 insertions(+), 15 deletions(-)

diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index 55b09cd4a7..6a6de23f4e 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -5,7 +5,7 @@
 //  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
 //
 
-var version = 1057;
+var version = 1100;
 var cellLayout;
 var baseLocation = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 
diff --git a/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js b/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js
index 30e83108d6..881f8e981c 100644
--- a/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js
+++ b/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js
@@ -1,3 +1,10 @@
+//  Copyright 2016 High Fidelity, Inc.
+//
+//
+//  Distributed under the Apache License, Version 2.0.
+//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
+//
+
 var basePosition = {
     x: 3000,
     y: 13500,
@@ -17,21 +24,21 @@ var THROTTLE_RATE = 5000;
 
 var sinceLastUpdate = 0;
 
-print('cells script')
+//print('cells script')
 
 function findCells() {
     var results = Entities.findEntities(basePosition, 60000);
 
     if (results.length === 0) {
-        print('no entities found')
+    //    print('no entities found')
         return;
     }
 
     results.forEach(function(v) {
         var name = Entities.getEntityProperties(v, 'name').name;
-        print('name is:: ' + name)
+      //  print('name is:: ' + name)
         if (name === 'Cell') {
-            print('found a cell!!' + v)
+         //   print('found a cell!!' + v)
             Script.setTimeout(function() {
                 moveCell(v);
             }, Math.random() * THROTTLE_RATE)
@@ -44,7 +51,7 @@ var minAngularVelocity = 0.01;
 var maxAngularVelocity = 0.03;
 
 function moveCell(entityId) {
-    print('moving a cell! ' + entityId)
+  //  print('moving a cell! ' + entityId)
 
     var magnitudeAV = maxAngularVelocity;
 
@@ -53,7 +60,7 @@ function moveCell(entityId) {
         y: Math.random() - 0.5,
         z: Math.random() - 0.5
     };
-    print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
+  //  print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
     Entities.editEntity(entityId, {
         angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
     });
@@ -77,7 +84,7 @@ function update(deltaTime) {
     if (THROTTLE === true) {
         sinceLastUpdate = sinceLastUpdate + deltaTime * 1000;
         if (sinceLastUpdate > THROTTLE_RATE) {
-            print('SHOULD FIND CELLS!!!')
+       //     print('SHOULD FIND CELLS!!!')
             sinceLastUpdate = 0;
             findCells();
         } else {
diff --git a/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js b/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js
index ce8da54eb2..3e70934cba 100644
--- a/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js
+++ b/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js
@@ -1,3 +1,10 @@
+//  Copyright 2016 High Fidelity, Inc.
+//
+//
+//  Distributed under the Apache License, Version 2.0.
+//  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
+//
+
 var basePosition = {
     x: 3000,
     y: 13500,
@@ -17,7 +24,7 @@ var THROTTLE_RATE = 5000;
 
 var sinceLastUpdate = 0;
 
-print('vesicle script')
+//print('vesicle script')
 
 function findVesicles() {
     var results = Entities.findEntities(basePosition, 60000);
@@ -31,7 +38,7 @@ function findVesicles() {
         var name = Entities.getEntityProperties(v, 'name').name;
         print('name is:: ' + name)
         if (name === 'vesicle') {
-            print('found a vesicle!!' + v)
+            //    print('found a vesicle!!' + v)
             Script.setTimeout(function() {
                 moveVesicle(v);
             }, Math.random() * THROTTLE_RATE)
@@ -45,7 +52,7 @@ var minAngularVelocity = 0.01;
 var maxAngularVelocity = 0.03;
 
 function moveVesicle(entityId) {
-    print('moving a vesicle! ' + entityId)
+    // print('moving a vesicle! ' + entityId)
     var magnitudeV = maxVelocity;
     var directionV = {
         x: Math.random() - 0.5,
@@ -53,7 +60,7 @@ function moveVesicle(entityId) {
         z: Math.random() - 0.5
     };
 
-    print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
+    // print("POS magnitude is " + magnitudeV + " and direction is " + directionV.x);
 
     var magnitudeAV = maxAngularVelocity;
 
@@ -62,7 +69,7 @@ function moveVesicle(entityId) {
         y: Math.random() - 0.5,
         z: Math.random() - 0.5
     };
-    print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
+    // print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
     Entities.editEntity(entityId, {
         velocity: Vec3.multiply(magnitudeV, Vec3.normalize(directionV)),
         angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
@@ -71,7 +78,6 @@ function moveVesicle(entityId) {
 }
 
 function update(deltaTime) {
-
     // print('deltaTime',deltaTime)
     if (!initialized) {
         print("checking for servers...");
@@ -87,7 +93,7 @@ function update(deltaTime) {
     if (THROTTLE === true) {
         sinceLastUpdate = sinceLastUpdate + deltaTime * 1000;
         if (sinceLastUpdate > THROTTLE_RATE) {
-            print('SHOULD FIND VESICLES!!!')
+            //      print('SHOULD FIND VESICLES!!!')
             sinceLastUpdate = 0;
             findVesicles();
         } else {

From b4edfe2390d5821d13e76aae5e9c77af8bc3324a Mon Sep 17 00:00:00 2001
From: Andrew Meadows <andrew@highfidelity.io>
Date: Thu, 25 Feb 2016 12:06:22 -0800
Subject: [PATCH 12/19] no expiry for simulation ownership

---
 .../src/entities/EntityServer.cpp             |  11 +-
 assignment-client/src/entities/EntityServer.h |   8 +-
 .../entities/src/SimpleEntitySimulation.cpp   | 122 ++++++++++++------
 .../entities/src/SimpleEntitySimulation.h     |   7 +-
 libraries/physics/src/EntityMotionState.cpp   |  23 ++--
 5 files changed, 106 insertions(+), 65 deletions(-)

diff --git a/assignment-client/src/entities/EntityServer.cpp b/assignment-client/src/entities/EntityServer.cpp
index b6223497e6..b177d2a9a0 100644
--- a/assignment-client/src/entities/EntityServer.cpp
+++ b/assignment-client/src/entities/EntityServer.cpp
@@ -277,14 +277,17 @@ void EntityServer::readAdditionalConfiguration(const QJsonObject& settingsSectio
 // set of stats to have, but we'd probably want a different data structure if we keep it very long.
 // Since this version uses a single shared QMap for all senders, there could be some lock contention 
 // on this QWriteLocker
-void EntityServer::trackSend(const QUuid& dataID, quint64 dataLastEdited, const QUuid& viewerNode) {
+void EntityServer::trackSend(const QUuid& dataID, quint64 dataLastEdited, const QUuid& sessionID) {
     QWriteLocker locker(&_viewerSendingStatsLock);
-    _viewerSendingStats[viewerNode][dataID] = { usecTimestampNow(), dataLastEdited };
+    _viewerSendingStats[sessionID][dataID] = { usecTimestampNow(), dataLastEdited };
 }
 
-void EntityServer::trackViewerGone(const QUuid& viewerNode) {
+void EntityServer::trackViewerGone(const QUuid& sessionID) {
     QWriteLocker locker(&_viewerSendingStatsLock);
-    _viewerSendingStats.remove(viewerNode);
+    _viewerSendingStats.remove(sessionID);
+    if (_entitySimulation) {
+        _entitySimulation->clearOwnership(sessionID);
+    }
 }
 
 QString EntityServer::serverSubclassStats() {
diff --git a/assignment-client/src/entities/EntityServer.h b/assignment-client/src/entities/EntityServer.h
index cd603f44d8..74057bfa5d 100644
--- a/assignment-client/src/entities/EntityServer.h
+++ b/assignment-client/src/entities/EntityServer.h
@@ -27,6 +27,8 @@ struct ViewerSendingStats {
     quint64 lastEdited;
 };
 
+class SimpleEntitySimulation;
+
 class EntityServer : public OctreeServer, public NewlyCreatedEntityHook {
     Q_OBJECT
 public:
@@ -52,8 +54,8 @@ public:
     virtual void readAdditionalConfiguration(const QJsonObject& settingsSectionObject) override;
     virtual QString serverSubclassStats() override;
 
-    virtual void trackSend(const QUuid& dataID, quint64 dataLastEdited, const QUuid& viewerNode) override;
-    virtual void trackViewerGone(const QUuid& viewerNode) override;
+    virtual void trackSend(const QUuid& dataID, quint64 dataLastEdited, const QUuid& sessionID) override;
+    virtual void trackViewerGone(const QUuid& sessionID) override;
 
 public slots:
     void pruneDeletedEntities();
@@ -65,7 +67,7 @@ private slots:
     void handleEntityPacket(QSharedPointer<ReceivedMessage> message, SharedNodePointer senderNode);
 
 private:
-    EntitySimulation* _entitySimulation;
+    SimpleEntitySimulation* _entitySimulation;
     QTimer* _pruneDeletedEntitiesTimer = nullptr;
 
     QReadWriteLock _viewerSendingStatsLock;
diff --git a/libraries/entities/src/SimpleEntitySimulation.cpp b/libraries/entities/src/SimpleEntitySimulation.cpp
index bdf27f4440..693d80b27d 100644
--- a/libraries/entities/src/SimpleEntitySimulation.cpp
+++ b/libraries/entities/src/SimpleEntitySimulation.cpp
@@ -18,51 +18,69 @@
 #include "EntityItem.h"
 #include "EntitiesLogging.h"
 
-const quint64 MIN_SIMULATION_OWNERSHIP_UPDATE_PERIOD = 2 * USECS_PER_SECOND;
-
-void SimpleEntitySimulation::updateEntitiesInternal(const quint64& now) {
-    if (_entitiesWithSimulator.size() == 0) {
-        return;
-    }
-
-    if (now < _nextSimulationExpiry) {
-        // nothing has expired yet
-        return;
-    }
-
-    // If an Entity has a simulation owner but there has been no update for a while: clear the owner.
-    // If an Entity goes ownerless for too long: zero velocity and remove from _entitiesWithSimulator.
-    _nextSimulationExpiry = now + MIN_SIMULATION_OWNERSHIP_UPDATE_PERIOD;
+const quint64 MAX_OWNERLESS_PERIOD = 2 * USECS_PER_SECOND;
 
+void SimpleEntitySimulation::clearOwnership(const QUuid& ownerID) {
     QMutexLocker lock(&_mutex);
-    SetOfEntities::iterator itemItr = _entitiesWithSimulator.begin();
-    while (itemItr != _entitiesWithSimulator.end()) {
+    SetOfEntities::iterator itemItr = _entitiesWithSimulationOwner.begin();
+    while (itemItr != _entitiesWithSimulationOwner.end()) {
         EntityItemPointer entity = *itemItr;
-        quint64 expiry = entity->getLastChangedOnServer() + MIN_SIMULATION_OWNERSHIP_UPDATE_PERIOD;
-        if (expiry < now) {
-            if (entity->getSimulatorID().isNull()) {
-                // no simulators are volunteering
-                // zero the velocity on this entity so that it doesn't drift far away
-                entity->setVelocity(Vectors::ZERO);
-                entity->setAngularVelocity(Vectors::ZERO);
-                entity->setAcceleration(Vectors::ZERO);
-                // remove from list
-                itemItr = _entitiesWithSimulator.erase(itemItr);
-                continue;
-            } else {
-                // the simulator has stopped updating this object
-                // clear ownership and restart timer, giving nearby simulators time to volunteer
-                qCDebug(entities) << "auto-removing simulation owner " << entity->getSimulatorID();
-                entity->clearSimulationOwnership();
+        if (entity->getSimulatorID() == ownerID) {
+            // the simulator has abandonded this object --> remove from owned list
+            qCDebug(entities) << "auto-removing simulation owner " << entity->getSimulatorID();
+            itemItr = _entitiesWithSimulationOwner.erase(itemItr);
+
+            if (entity->getDynamic() && entity->hasLocalVelocity()) {
+                // it is still moving dynamically --> add to orphaned list
+                _entitiesThatNeedSimulationOwner.insert(entity);
+                quint64 expiry = entity->getLastChangedOnServer() + MAX_OWNERLESS_PERIOD;
+                if (expiry < _nextOwnerlessExpiry) {
+                    _nextOwnerlessExpiry = expiry;
+                }
             }
+
+            // remove ownership and dirty all the tree elements that contain the it
+            entity->clearSimulationOwnership();
             entity->markAsChangedOnServer();
-            // dirty all the tree elements that contain the entity
             DirtyOctreeElementOperator op(entity->getElement());
             getEntityTree()->recurseTreeWithOperator(&op);
-        } else if (expiry < _nextSimulationExpiry) {
-            _nextSimulationExpiry = expiry;
+        } else {
+            ++itemItr;
+        }
+    }
+}
+
+void SimpleEntitySimulation::updateEntitiesInternal(const quint64& now) {
+    if (now > _nextOwnerlessExpiry) {
+        // search for ownerless objects that have expired
+        QMutexLocker lock(&_mutex);
+        _nextOwnerlessExpiry = -1;
+        SetOfEntities::iterator itemItr = _entitiesThatNeedSimulationOwner.begin();
+        while (itemItr != _entitiesThatNeedSimulationOwner.end()) {
+            EntityItemPointer entity = *itemItr;
+            quint64 expiry = entity->getLastChangedOnServer() + MAX_OWNERLESS_PERIOD;
+            if (expiry < now) {
+                // no simulators have volunteered ownership --> remove from list
+                itemItr = _entitiesThatNeedSimulationOwner.erase(itemItr);
+
+                if (entity->getSimulatorID().isNull() && entity->getDynamic() && entity->hasLocalVelocity()) {
+                    // zero the derivatives
+                    entity->setVelocity(Vectors::ZERO);
+                    entity->setAngularVelocity(Vectors::ZERO);
+                    entity->setAcceleration(Vectors::ZERO);
+
+                    // dirty all the tree elements that contain it
+                    entity->markAsChangedOnServer();
+                    DirtyOctreeElementOperator op(entity->getElement());
+                    getEntityTree()->recurseTreeWithOperator(&op);
+                }
+            } else {
+                ++itemItr;
+                if (expiry < _nextOwnerlessExpiry) {
+                    _nextOwnerlessExpiry = expiry;
+                }
+            }
         }
-        ++itemItr;
     }
 }
 
@@ -70,26 +88,46 @@ void SimpleEntitySimulation::addEntityInternal(EntityItemPointer entity) {
     EntitySimulation::addEntityInternal(entity);
     if (!entity->getSimulatorID().isNull()) {
         QMutexLocker lock(&_mutex);
-        _entitiesWithSimulator.insert(entity);
+        _entitiesWithSimulationOwner.insert(entity);
+    } else if (entity->getDynamic() && entity->hasLocalVelocity()) {
+        QMutexLocker lock(&_mutex);
+        _entitiesThatNeedSimulationOwner.insert(entity);
+        quint64 expiry = entity->getLastChangedOnServer() + MAX_OWNERLESS_PERIOD;
+        if (expiry < _nextOwnerlessExpiry) {
+            _nextOwnerlessExpiry = expiry;
+        }
     }
 }
 
 void SimpleEntitySimulation::removeEntityInternal(EntityItemPointer entity) {
     EntitySimulation::removeEntityInternal(entity);
     QMutexLocker lock(&_mutex);
-    _entitiesWithSimulator.remove(entity);
+    _entitiesWithSimulationOwner.remove(entity);
+    _entitiesThatNeedSimulationOwner.remove(entity);
 }
 
 void SimpleEntitySimulation::changeEntityInternal(EntityItemPointer entity) {
     EntitySimulation::changeEntityInternal(entity);
-    if (!entity->getSimulatorID().isNull()) {
+    if (entity->getSimulatorID().isNull()) {
         QMutexLocker lock(&_mutex);
-        _entitiesWithSimulator.insert(entity);
+        _entitiesWithSimulationOwner.remove(entity);
+        if (entity->getDynamic() && entity->hasLocalVelocity()) {
+            _entitiesThatNeedSimulationOwner.insert(entity);
+            quint64 expiry = entity->getLastChangedOnServer() + MAX_OWNERLESS_PERIOD;
+            if (expiry < _nextOwnerlessExpiry) {
+                _nextOwnerlessExpiry = expiry;
+            }
+        }
+    } else {
+        QMutexLocker lock(&_mutex);
+        _entitiesWithSimulationOwner.insert(entity);
+        _entitiesThatNeedSimulationOwner.remove(entity);
     }
     entity->clearDirtyFlags();
 }
 
 void SimpleEntitySimulation::clearEntitiesInternal() {
-    _entitiesWithSimulator.clear();
+    _entitiesWithSimulationOwner.clear();
+    _entitiesThatNeedSimulationOwner.clear();
 }
 
diff --git a/libraries/entities/src/SimpleEntitySimulation.h b/libraries/entities/src/SimpleEntitySimulation.h
index 53a7574bf2..d9c04fdcf9 100644
--- a/libraries/entities/src/SimpleEntitySimulation.h
+++ b/libraries/entities/src/SimpleEntitySimulation.h
@@ -21,6 +21,8 @@ public:
     SimpleEntitySimulation() : EntitySimulation() { }
     virtual ~SimpleEntitySimulation() { clearEntitiesInternal(); }
 
+    void clearOwnership(const QUuid& ownerID);
+
 protected:
     virtual void updateEntitiesInternal(const quint64& now) override;
     virtual void addEntityInternal(EntityItemPointer entity) override;
@@ -28,8 +30,9 @@ protected:
     virtual void changeEntityInternal(EntityItemPointer entity) override;
     virtual void clearEntitiesInternal() override;
 
-    SetOfEntities _entitiesWithSimulator;
-    quint64 _nextSimulationExpiry { 0 };
+    SetOfEntities _entitiesWithSimulationOwner;
+    SetOfEntities _entitiesThatNeedSimulationOwner;
+    quint64 _nextOwnerlessExpiry { 0 };
 };
 
 #endif // hifi_SimpleEntitySimulation_h
diff --git a/libraries/physics/src/EntityMotionState.cpp b/libraries/physics/src/EntityMotionState.cpp
index 8c0dab98db..6a818a1972 100644
--- a/libraries/physics/src/EntityMotionState.cpp
+++ b/libraries/physics/src/EntityMotionState.cpp
@@ -272,7 +272,7 @@ bool EntityMotionState::remoteSimulationOutOfSync(uint32_t simulationStep) {
     float dt = (float)(numSteps) * PHYSICS_ENGINE_FIXED_SUBSTEP;
 
     if (_numInactiveUpdates > 0) {
-        const uint8_t MAX_NUM_INACTIVE_UPDATES = 3;
+        const uint8_t MAX_NUM_INACTIVE_UPDATES = 20;
         if (_numInactiveUpdates > MAX_NUM_INACTIVE_UPDATES) {
             // clear local ownership (stop sending updates) and let the server clear itself
             _entity->clearSimulationOwnership();
@@ -282,7 +282,7 @@ bool EntityMotionState::remoteSimulationOutOfSync(uint32_t simulationStep) {
         // until it is removed from the outgoing updates
         // (which happens when we don't own the simulation and it isn't touching our simulation)
         const float INACTIVE_UPDATE_PERIOD = 0.5f;
-        return (dt > INACTIVE_UPDATE_PERIOD);
+        return (dt > INACTIVE_UPDATE_PERIOD * (float)_numInactiveUpdates);
     }
 
     if (!_body->isActive()) {
@@ -404,8 +404,7 @@ void EntityMotionState::sendUpdate(OctreeEditPacketSender* packetSender, const Q
     assert(_entity);
     assert(entityTreeIsLocked());
 
-    bool active = _body->isActive();
-    if (!active) {
+    if (!_body->isActive()) {
         // make sure all derivatives are zero
         glm::vec3 zero(0.0f);
         _entity->setVelocity(zero);
@@ -495,16 +494,12 @@ void EntityMotionState::sendUpdate(OctreeEditPacketSender* packetSender, const Q
         qCDebug(physics) << "       lastSimulated:" << debugTime(lastSimulated, now);
     #endif //def WANT_DEBUG
 
-    if (sessionID == _entity->getSimulatorID()) {
-        // we think we own the simulation
-        if (!active) {
-            // we own the simulation but the entity has stopped, so we tell the server that we're clearing simulatorID
-            // but we remember that we do still own it...  and rely on the server to tell us that we don't
-            properties.clearSimulationOwner();
-            _outgoingPriority = ZERO_SIMULATION_PRIORITY;
-        }
-        // else the ownership is not changing so we don't bother to pack it
-    } else {
+    if (_numInactiveUpdates > 0) {
+        // we own the simulation but the entity has stopped, so we tell the server that we're clearing simulatorID
+        // but we remember that we do still own it...  and rely on the server to tell us that we don't
+        properties.clearSimulationOwner();
+        _outgoingPriority = ZERO_SIMULATION_PRIORITY;
+    } else if (sessionID != _entity->getSimulatorID()) {
         // we don't own the simulation for this entity yet, but we're sending a bid for it
         properties.setSimulationOwner(sessionID, glm::max<uint8_t>(_outgoingPriority, VOLUNTEER_SIMULATION_PRIORITY));
         _nextOwnershipBid = now + USECS_BETWEEN_OWNERSHIP_BIDS;

From b0cb4b719994a2e825c7b56f0bf515544e8ef61f Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Fri, 26 Feb 2016 10:26:02 -0800
Subject: [PATCH 13/19] disable boundaries

---
 .../CellScience/importCellScience.js          | 513 +++++++++---------
 1 file changed, 248 insertions(+), 265 deletions(-)

diff --git a/unpublishedScripts/DomainContent/CellScience/importCellScience.js b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
index 6a6de23f4e..876df8adb1 100644
--- a/unpublishedScripts/DomainContent/CellScience/importCellScience.js
+++ b/unpublishedScripts/DomainContent/CellScience/importCellScience.js
@@ -5,7 +5,7 @@
 //  See the accompanying file LICENSE or http://www.apache.org/licenses/LICENSE-2.0.html
 //
 
-var version = 1100;
+var version = 1112;
 var cellLayout;
 var baseLocation = "https://hifi-content.s3.amazonaws.com/DomainContent/CellScience/";
 
@@ -112,7 +112,7 @@ var scenes = [{
             y: 0,
             z: 0
         },
-        radius: 450,
+        radius: 500,
         number: 10,
         userData: JSON.stringify({
             entryPoint: locations.cellLayout[1],
@@ -151,267 +151,253 @@ var scenes = [{
         skybox: "cosmos_skybox_blurred"
     },
     instances: [{
-            model: "translation",
-            dimensions: {
-                x: 10,
-                y: 16,
-                z: 10
+        model: "translation",
+        dimensions: {
+            x: 10,
+            y: 16,
+            z: 10
+        },
+        offset: {
+            x: 0,
+            y: 0,
+            z: 0
+        },
+        radius: 300,
+        number: 7,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
             },
-            offset: {
-                x: 0,
-                y: 0,
-                z: 0
+            target: locations.ribosome[1],
+            location: locations.ribosome[0],
+            baseURL: baseLocation
+        }),
+        script: "zoom.js?" + version,
+        visible: true
+    }, {
+        model: "vesicle",
+        dimensions: {
+            x: 60,
+            y: 60,
+            z: 60
+        },
+        randomSize: 10,
+        offset: {
+            x: 0,
+            y: 0,
+            z: 0
+        },
+        radius: 1000,
+        number: 22,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
+            }
+        }),
+        visible: true
+    }, { //golgi vesicles
+        model: "vesicle",
+        dimensions: {
+            x: 10,
+            y: 10,
+            z: 10
+        },
+        randomSize: 10,
+        offset: {
+            x: -319,
+            y: 66,
+            z: 976
+        },
+        radius: 140,
+        number: 10,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
+            }
+        }),
+        script: "",
+        visible: true
+    }, { //golgi vesicles
+        model: "vesicle",
+        dimensions: {
+            x: 15,
+            y: 15,
+            z: 15
+        },
+        randomSize: 10,
+        offset: {
+            x: -319,
+            y: 66,
+            z: 976
+        },
+        radius: 115,
+        number: 7,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
+            }
+        }),
+        visible: true
+    }, {
+        model: "vesicle",
+        dimensions: {
+            x: 50,
+            y: 50,
+            z: 50
+        },
+        randomSize: 10,
+        offset: {
+            x: 0,
+            y: 0,
+            z: 0
+        },
+        radius: 600,
+        number: 15,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
+            }
+        }),
+        script: "",
+        visible: true
+    }, { //outer vesicles
+        model: "vesicle",
+        dimensions: {
+            x: 60,
+            y: 60,
+            z: 60
+        },
+        randomSize: 10,
+        offset: {
+            x: 0,
+            y: 0,
+            z: 0
+        },
+        radius: 1600,
+        number: 22,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
+            }
+        }),
+        script: "",
+        visible: true
+    }, { //outer vesicles
+        model: "vesicle",
+        dimensions: {
+            x: 40,
+            y: 40,
+            z: 40
+        },
+        randomSize: 10,
+        offset: {
+            x: 0,
+            y: 0,
+            z: 0
+        },
+        radius: 1400,
+        number: 22,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
+            }
+        }),
+        visible: true
+    }, { //outer vesicles
+        model: "vesicle",
+        dimensions: {
+            x: 80,
+            y: 80,
+            z: 80
+        },
+        randomSize: 10,
+        offset: {
+            x: 0,
+            y: 0,
+            z: 0
+        },
+        radius: 1800,
+        number: 22,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
+            }
+        }),
+        visible: true
+    }, {
+        model: "hexokinase",
+        dimensions: {
+            x: 3,
+            y: 4,
+            z: 3
+        },
+        randomSize: 10,
+        offset: {
+            x: 236,
+            y: 8,
+            z: 771
+        },
+        radius: 80,
+        number: 7,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
             },
-            radius: 300,
-            number: 7,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                },
-                target: locations.ribosome[1],
-                location: locations.ribosome[0],
-                baseURL: baseLocation
-            }),
-            script: "zoom.js?" + version,
-            visible: true
-        }, {
-            model: "vesicle",
-            dimensions: {
-                x: 60,
-                y: 60,
-                z: 60
+            target: locations.hexokinase[1],
+            location: locations.hexokinase[0],
+            baseURL: baseLocation
+        }),
+        script: "zoom.js?" + version,
+        visible: true
+    }, {
+        model: "pfructo_kinase",
+        dimensions: {
+            x: 3,
+            y: 4,
+            z: 3
+        },
+        randomSize: 10,
+        offset: {
+            x: 236,
+            y: 8,
+            z: 771
+        },
+        radius: 60,
+        number: 7,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
             },
-            randomSize: 10,
-            offset: {
-                x: 0,
-                y: 0,
-                z: 0
+            target: locations.hexokinase[1],
+            location: locations.hexokinase[0],
+        }),
+        script: "zoom.js?" + version,
+        visible: true
+    }, {
+        model: "glucose_isomerase",
+        dimensions: {
+            x: 3,
+            y: 4,
+            z: 3
+        },
+        randomSize: 10,
+        offset: {
+            x: 236,
+            y: 8,
+            z: 771
+        },
+        radius: 70,
+        number: 7,
+        userData: JSON.stringify({
+            grabbableKey: {
+                grabbable: false
             },
-            radius: 1000,
-            number: 22,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                }
-            }),
-            visible: true
-        }, { //golgi vesicles
-            model: "vesicle",
-            dimensions: {
-                x: 10,
-                y: 10,
-                z: 10
-            },
-            randomSize: 10,
-            offset: {
-                x: -319,
-                y: 66,
-                z: 976
-            },
-            radius: 140,
-            number: 10,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                }
-            }),
-            script: "",
-            visible: true
-        }, { //golgi vesicles
-            model: "vesicle",
-            dimensions: {
-                x: 15,
-                y: 15,
-                z: 15
-            },
-            randomSize: 10,
-            offset: {
-                x: -319,
-                y: 66,
-                z: 976
-            },
-            radius: 115,
-            number: 7,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                }
-            }),
-            visible: true
-        }, {
-            model: "vesicle",
-            dimensions: {
-                x: 50,
-                y: 50,
-                z: 50
-            },
-            randomSize: 10,
-            offset: {
-                x: 0,
-                y: 0,
-                z: 0
-            },
-            radius: 600,
-            number: 15,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                }
-            }),
-            script: "",
-            visible: true
-        }, { //outer vesicles
-            model: "vesicle",
-            dimensions: {
-                x: 60,
-                y: 60,
-                z: 60
-            },
-            randomSize: 10,
-            offset: {
-                x: 0,
-                y: 0,
-                z: 0
-            },
-            radius: 1600,
-            number: 22,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                }
-            }),
-            script: "",
-            visible: true
-        }, { //outer vesicles
-            model: "vesicle",
-            dimensions: {
-                x: 40,
-                y: 40,
-                z: 40
-            },
-            randomSize: 10,
-            offset: {
-                x: 0,
-                y: 0,
-                z: 0
-            },
-            radius: 1400,
-            number: 22,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                }
-            }),
-            visible: true
-        }, { //outer vesicles
-            model: "vesicle",
-            dimensions: {
-                x: 80,
-                y: 80,
-                z: 80
-            },
-            randomSize: 10,
-            offset: {
-                x: 0,
-                y: 0,
-                z: 0
-            },
-            radius: 1800,
-            number: 22,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                }
-            }),
-            visible: true
-        }, {
-            model: "hexokinase",
-            dimensions: {
-                x: 3,
-                y: 4,
-                z: 3
-            },
-            randomSize: 10,
-            offset: {
-                x: 236,
-                y: 8,
-                z: 771
-            },
-            radius: 80,
-            number: 7,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                },
-                target: locations.hexokinase[1],
-                location: locations.hexokinase[0],
-                baseURL: baseLocation
-            }),
-            script: "zoom.js?" + version,
-            visible: true
-        }, {
-            model: "pfructo_kinase",
-            dimensions: {
-                x: 3,
-                y: 4,
-                z: 3
-            },
-            randomSize: 10,
-            offset: {
-                x: 236,
-                y: 8,
-                z: 771
-            },
-            radius: 60,
-            number: 7,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                },
-                target: locations.hexokinase[1],
-                location: locations.hexokinase[0],
-            }),
-            script: "zoom.js?" + version,
-            visible: true
-        }, {
-            model: "glucose_isomerase",
-            dimensions: {
-                x: 3,
-                y: 4,
-                z: 3
-            },
-            randomSize: 10,
-            offset: {
-                x: 236,
-                y: 8,
-                z: 771
-            },
-            radius: 70,
-            number: 7,
-            userData: JSON.stringify({
-                grabbableKey: {
-                    grabbable: false
-                },
-                target: locations.hexokinase[1],
-                location: locations.hexokinase[0],
-            }),
-            script: "zoom.js?" + version,
-            visible: true
-        }
-        //          {
-        //              model:"NPC",
-        //              dimensions:{x:20,y:20,z:20},
-        //              randomSize: 10,
-        //              offset:{x:208.593693,y:6.113100222,z:153.3202277},
-        //              radius:520,
-        //              number:25,
-        //              userData: "",
-        //              script:"",
-        //              visible:true
-        //          }
-
-
-    ],
+            target: locations.hexokinase[1],
+            location: locations.hexokinase[0],
+        }),
+        script: "zoom.js?" + version,
+        visible: true
+    }],
     boundary: {
         radius: locations.cellLayout[2],
         center: locations.cellLayout[0],
@@ -573,7 +559,7 @@ function ImportScene(scene) {
 
     CreateZone(scene);
     CreateInstances(scene);
-    CreateBoundary(scene);
+    // CreateBoundary(scene);
 
     // print("done " + scene.name);
 
@@ -797,11 +783,9 @@ function CreateInstances(scene) {
 
 
 
-function CreateIdentification(name, position, rotation, dimensions, showDistance, parentID) {
+function CreateIdentification(name, position, rotation, dimensions, showDistance) {
     //print ("creating ID for " + name);
-    if (parentID === undefined) {
-        parentID = "{00000000-0000-0000-0000-000000000000}";
-    }
+
     Entities.addEntity({
         type: "Sphere",
         name: "ID for " + name,
@@ -810,7 +794,6 @@ function CreateIdentification(name, position, rotation, dimensions, showDistance
             green: 0,
             blue: 0
         },
-        parentID: parentID,
         dimensions: dimensions,
         position: position,
         rotation: rotation,

From 6c6ea3f0a76ce9bdc433216f3e3bcb6ad5d678e0 Mon Sep 17 00:00:00 2001
From: "James B. Pollack" <jamesbradenpollack@gmail.com>
Date: Fri, 26 Feb 2016 10:42:45 -0800
Subject: [PATCH 14/19] code cleanup

---
 .../DomainContent/CellScience/moveCellsAC.js       | 14 +++++++-------
 .../DomainContent/CellScience/moveVesiclesAC.js    | 10 +++-------
 2 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js b/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js
index 881f8e981c..cf35e081e0 100644
--- a/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js
+++ b/unpublishedScripts/DomainContent/CellScience/moveCellsAC.js
@@ -30,18 +30,18 @@ function findCells() {
     var results = Entities.findEntities(basePosition, 60000);
 
     if (results.length === 0) {
-    //    print('no entities found')
+        //    print('no entities found')
         return;
     }
 
     results.forEach(function(v) {
         var name = Entities.getEntityProperties(v, 'name').name;
-      //  print('name is:: ' + name)
+        //  print('name is:: ' + name)
         if (name === 'Cell') {
-         //   print('found a cell!!' + v)
+            //   print('found a cell!!' + v)
             Script.setTimeout(function() {
                 moveCell(v);
-            }, Math.random() * THROTTLE_RATE)
+            }, Math.random() * THROTTLE_RATE);
         }
     });
 }
@@ -51,7 +51,7 @@ var minAngularVelocity = 0.01;
 var maxAngularVelocity = 0.03;
 
 function moveCell(entityId) {
-  //  print('moving a cell! ' + entityId)
+    //  print('moving a cell! ' + entityId)
 
     var magnitudeAV = maxAngularVelocity;
 
@@ -60,7 +60,7 @@ function moveCell(entityId) {
         y: Math.random() - 0.5,
         z: Math.random() - 0.5
     };
-  //  print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
+    //  print("ROT magnitude is " + magnitudeAV + " and direction is " + directionAV.x);
     Entities.editEntity(entityId, {
         angularVelocity: Vec3.multiply(magnitudeAV, Vec3.normalize(directionAV))
     });
@@ -84,7 +84,7 @@ function update(deltaTime) {
     if (THROTTLE === true) {
         sinceLastUpdate = sinceLastUpdate + deltaTime * 1000;
         if (sinceLastUpdate > THROTTLE_RATE) {
-       //     print('SHOULD FIND CELLS!!!')
+            //     print('SHOULD FIND CELLS!!!')
             sinceLastUpdate = 0;
             findCells();
         } else {
diff --git a/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js b/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js
index 3e70934cba..922f0d94cf 100644
--- a/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js
+++ b/unpublishedScripts/DomainContent/CellScience/moveVesiclesAC.js
@@ -30,18 +30,17 @@ function findVesicles() {
     var results = Entities.findEntities(basePosition, 60000);
 
     if (results.length === 0) {
-        print('no entities found')
+        // print('no entities found');
         return;
     }
 
     results.forEach(function(v) {
         var name = Entities.getEntityProperties(v, 'name').name;
-        print('name is:: ' + name)
         if (name === 'vesicle') {
-            //    print('found a vesicle!!' + v)
+            //print('found a vesicle!!' + v)
             Script.setTimeout(function() {
                 moveVesicle(v);
-            }, Math.random() * THROTTLE_RATE)
+            }, Math.random() * THROTTLE_RATE);
         }
     });
 }
@@ -78,7 +77,6 @@ function moveVesicle(entityId) {
 }
 
 function update(deltaTime) {
-    // print('deltaTime',deltaTime)
     if (!initialized) {
         print("checking for servers...");
         if (Entities.serversExist() && Entities.canRez()) {
@@ -93,11 +91,9 @@ function update(deltaTime) {
     if (THROTTLE === true) {
         sinceLastUpdate = sinceLastUpdate + deltaTime * 1000;
         if (sinceLastUpdate > THROTTLE_RATE) {
-            //      print('SHOULD FIND VESICLES!!!')
             sinceLastUpdate = 0;
             findVesicles();
         } else {
-            // print('returning in update ' + sinceLastUpdate)
             return;
         }
     }

From 6d9c5856041ffd26eb1f06bbe03a463fb6fecb47 Mon Sep 17 00:00:00 2001
From: Brad Hefta-Gaub <brad@highfidelity.io>
Date: Fri, 26 Feb 2016 12:01:59 -0800
Subject: [PATCH 15/19] add fade between depths in depth reticle

---
 examples/depthReticle.js | 47 +++++++++++++++++++++++++++++++++++-----
 1 file changed, 41 insertions(+), 6 deletions(-)

diff --git a/examples/depthReticle.js b/examples/depthReticle.js
index a60e61d07c..a8afb80df2 100644
--- a/examples/depthReticle.js
+++ b/examples/depthReticle.js
@@ -12,17 +12,24 @@
 
 var APPARENT_2D_OVERLAY_DEPTH = 1.0;
 var APPARENT_MAXIMUM_DEPTH = 100.0; // this is a depth at which things all seem sufficiently distant
-var lastDepthCheckTime = 0;
+var lastDepthCheckTime = Date.now();
+var desiredDepth = APPARENT_2D_OVERLAY_DEPTH;
+var wasDepth = Reticle.depth; // depth at the time we changed our desired depth
+var desiredDepthLastSet = lastDepthCheckTime; // time we changed our desired depth
+var TIME_BETWEEN_DEPTH_CHECKS = 100;
+var TIME_TO_FADE_DEPTH = 50;
 
 Script.update.connect(function(deltaTime) {
-    var TIME_BETWEEN_DEPTH_CHECKS = 100;
-    var timeSinceLastDepthCheck = Date.now() - lastDepthCheckTime;
+    var now = Date.now();
+    var timeSinceLastDepthCheck = now - lastDepthCheckTime;
     if (timeSinceLastDepthCheck > TIME_BETWEEN_DEPTH_CHECKS) {
+        var newDesiredDepth = desiredDepth;
+        lastDepthCheckTime = now;
         var reticlePosition = Reticle.position;
 
         // first check the 2D Overlays
         if (Reticle.pointingAtSystemOverlay || Overlays.getOverlayAtPoint(reticlePosition)) {
-            Reticle.setDepth(APPARENT_2D_OVERLAY_DEPTH);
+            newDesiredDepth = APPARENT_2D_OVERLAY_DEPTH;
         } else {
             var pickRay = Camera.computePickRay(reticlePosition.x, reticlePosition.y);
 
@@ -37,11 +44,39 @@ Script.update.connect(function(deltaTime) {
             // If either the overlays or entities intersect, then set the reticle depth to 
             // the distance of intersection
             if (result.intersects) {
-                Reticle.setDepth(result.distance);
+                newDesiredDepth = result.distance;
             } else {
                 // if nothing intersects... set the depth to some sufficiently large depth
-                Reticle.setDepth(APPARENT_MAXIMUM_DEPTH);
+                newDesiredDepth = APPARENT_MAXIMUM_DEPTH;
             }
         }
+
+        // If the desired depth has changed, reset our fade start time
+        if (desiredDepth != newDesiredDepth) {
+            desiredDepthLastSet = now;
+            desiredDepth = newDesiredDepth;
+            wasDepth = Reticle.depth;
+        }
+    }
+
+    // move the reticle toward the desired depth
+    if (desiredDepth != Reticle.depth) {
+
+        // determine the time between now, and when we set our determined our desiredDepth
+        var elapsed = now - desiredDepthLastSet;
+        var distanceToFade = desiredDepth - wasDepth;
+        var percentElapsed = Math.min(1, elapsed / TIME_TO_FADE_DEPTH);
+
+        // special case to handle no fade settings
+        if (TIME_TO_FADE_DEPTH == 0) {
+            percentElapsed = 1;
+        }
+        var depthDelta = distanceToFade * percentElapsed;
+
+        var newDepth = wasDepth + depthDelta;
+        if (percentElapsed == 1) {
+            newDepth = desiredDepth;
+        }
+        Reticle.setDepth(newDepth);
     }
 });

From 9a01c933221c5a65499e75442668adc08c804474 Mon Sep 17 00:00:00 2001
From: "Anthony J. Thibault" <tony@highfidelity.io>
Date: Fri, 26 Feb 2016 14:28:27 -0800
Subject: [PATCH 16/19] Avatar: fix for rendering avatar attachments

---
 interface/src/avatar/Avatar.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interface/src/avatar/Avatar.cpp b/interface/src/avatar/Avatar.cpp
index 83351d5188..0bd134bef5 100644
--- a/interface/src/avatar/Avatar.cpp
+++ b/interface/src/avatar/Avatar.cpp
@@ -400,7 +400,7 @@ void Avatar::render(RenderArgs* renderArgs, const glm::vec3& cameraPosition) {
         frustum = qApp->getDisplayViewFrustum();
     }
 
-    if (frustum->sphereIntersectsFrustum(getPosition(), boundingRadius)) {
+    if (!frustum->sphereIntersectsFrustum(getPosition(), boundingRadius)) {
         endRender();
         return;
     }

From e403c990d96f8c174ecb97b82e0ed906b7ed5159 Mon Sep 17 00:00:00 2001
From: Brad Hefta-Gaub <brad@highfidelity.io>
Date: Sat, 27 Feb 2016 17:13:09 -0800
Subject: [PATCH 17/19] make fade non-linear

---
 examples/depthReticle.js | 26 ++++++++------------------
 1 file changed, 8 insertions(+), 18 deletions(-)

diff --git a/examples/depthReticle.js b/examples/depthReticle.js
index a8afb80df2..4b649f49b6 100644
--- a/examples/depthReticle.js
+++ b/examples/depthReticle.js
@@ -14,10 +14,9 @@ var APPARENT_2D_OVERLAY_DEPTH = 1.0;
 var APPARENT_MAXIMUM_DEPTH = 100.0; // this is a depth at which things all seem sufficiently distant
 var lastDepthCheckTime = Date.now();
 var desiredDepth = APPARENT_2D_OVERLAY_DEPTH;
-var wasDepth = Reticle.depth; // depth at the time we changed our desired depth
-var desiredDepthLastSet = lastDepthCheckTime; // time we changed our desired depth
 var TIME_BETWEEN_DEPTH_CHECKS = 100;
-var TIME_TO_FADE_DEPTH = 50;
+var MINIMUM_DEPTH_ADJUST = 0.01;
+var NON_LINEAR_DIVISOR = 2;
 
 Script.update.connect(function(deltaTime) {
     var now = Date.now();
@@ -53,30 +52,21 @@ Script.update.connect(function(deltaTime) {
 
         // If the desired depth has changed, reset our fade start time
         if (desiredDepth != newDesiredDepth) {
-            desiredDepthLastSet = now;
             desiredDepth = newDesiredDepth;
-            wasDepth = Reticle.depth;
         }
     }
 
     // move the reticle toward the desired depth
     if (desiredDepth != Reticle.depth) {
 
-        // determine the time between now, and when we set our determined our desiredDepth
-        var elapsed = now - desiredDepthLastSet;
-        var distanceToFade = desiredDepth - wasDepth;
-        var percentElapsed = Math.min(1, elapsed / TIME_TO_FADE_DEPTH);
-
-        // special case to handle no fade settings
-        if (TIME_TO_FADE_DEPTH == 0) {
-            percentElapsed = 1;
-        }
-        var depthDelta = distanceToFade * percentElapsed;
-
-        var newDepth = wasDepth + depthDelta;
-        if (percentElapsed == 1) {
+        // cut distance between desiredDepth and current depth in half until we're close enough
+        var distanceToAdjustThisCycle = (desiredDepth - Reticle.depth) / NON_LINEAR_DIVISOR;
+        if (Math.abs(distanceToAdjustThisCycle) < MINIMUM_DEPTH_ADJUST) {
             newDepth = desiredDepth;
+        } else {
+            newDepth = Reticle.depth + distanceToAdjustThisCycle;
         }
+
         Reticle.setDepth(newDepth);
     }
 });

From 188cf3694b83f36a6808bac3659ff7f1958f2f99 Mon Sep 17 00:00:00 2001
From: Brad Hefta-Gaub <brad@highfidelity.io>
Date: Sat, 27 Feb 2016 17:31:35 -0800
Subject: [PATCH 18/19] fix rotation of depth reticle

---
 interface/src/ui/ApplicationCompositor.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/interface/src/ui/ApplicationCompositor.cpp b/interface/src/ui/ApplicationCompositor.cpp
index 99f0b4fdc4..59d794d7cb 100644
--- a/interface/src/ui/ApplicationCompositor.cpp
+++ b/interface/src/ui/ApplicationCompositor.cpp
@@ -301,7 +301,7 @@ void ApplicationCompositor::displayOverlayTextureHmd(RenderArgs* renderArgs, int
                 // look at borrowed from overlays
                 float elevation = -asinf(relativePosition.y / glm::length(relativePosition));
                 float azimuth = atan2f(relativePosition.x, relativePosition.z);
-                glm::quat faceCamera = glm::quat(glm::vec3(elevation, azimuth, 0)) * quat(vec3(0, 0, -1)); // this extra *quat(vec3(0,0,-1)) was required to get the quad to flip this seems like we could optimize
+                glm::quat faceCamera = glm::quat(glm::vec3(elevation, azimuth, 0)) * quat(vec3(0, -PI, 0)); // this extra *quat(vec3(0,-PI,0)) was required to get the quad to flip this seems like we could optimize
 
                 Transform transform;
                 transform.setTranslation(relativePosition);

From a933935e2d6af70dea252a2707efa2d3ce8d7675 Mon Sep 17 00:00:00 2001
From: Andrew Meadows <andrew@highfidelity.io>
Date: Sun, 28 Feb 2016 15:13:49 -0800
Subject: [PATCH 19/19] lock mutex in clearEntitiesInernal()

---
 libraries/entities/src/SimpleEntitySimulation.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/libraries/entities/src/SimpleEntitySimulation.cpp b/libraries/entities/src/SimpleEntitySimulation.cpp
index 693d80b27d..6bf25f767d 100644
--- a/libraries/entities/src/SimpleEntitySimulation.cpp
+++ b/libraries/entities/src/SimpleEntitySimulation.cpp
@@ -127,6 +127,7 @@ void SimpleEntitySimulation::changeEntityInternal(EntityItemPointer entity) {
 }
 
 void SimpleEntitySimulation::clearEntitiesInternal() {
+    QMutexLocker lock(&_mutex);
     _entitiesWithSimulationOwner.clear();
     _entitiesThatNeedSimulationOwner.clear();
 }