Initial commit.

Not much here, mostly just equipment notes.

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto
+
+# Custom for Visual Studio
+*.cs     diff=csharp
+*.sln    merge=union
+*.csproj merge=union
+*.vbproj merge=union
+*.fsproj merge=union
+*.dbproj merge=union
+
+# Standard to msysgit
+*.doc	 diff=astextplain
+*.DOC	 diff=astextplain
+*.docx diff=astextplain
+*.DOCX diff=astextplain
+*.dot  diff=astextplain
+*.DOT  diff=astextplain
+*.pdf  diff=astextplain
+*.PDF	 diff=astextplain
+*.rtf	 diff=astextplain
+*.RTF	 diff=astextplain

.gitignore

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+#################
+## Eclipse
+#################
+
+*.pydevproject
+.project
+.metadata
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.classpath
+.settings/
+.loadpath
+
+# External tool builders
+.externalToolBuilders/
+
+# Locally stored "Eclipse launch configurations"
+*.launch
+
+# CDT-specific
+.cproject
+
+# PDT-specific
+.buildpath
+
+
+#################
+## Visual Studio
+#################
+
+## Ignore Visual Studio temporary files, build results, and
+## files generated by popular Visual Studio add-ons.
+
+# User-specific files
+*.suo
+*.user
+*.sln.docstates
+
+# Build results
+
+[Dd]ebug/
+[Rr]elease/
+x64/
+build/
+[Bb]in/
+[Oo]bj/
+
+# MSTest test Results
+[Tt]est[Rr]esult*/
+[Bb]uild[Ll]og.*
+
+*_i.c
+*_p.c
+*.ilk
+*.meta
+*.obj
+*.pch
+*.pdb
+*.pgc
+*.pgd
+*.rsp
+*.sbr
+*.tlb
+*.tli
+*.tlh
+*.tmp
+*.tmp_proj
+*.log
+*.vspscc
+*.vssscc
+.builds
+*.pidb
+*.log
+*.scc
+
+# Visual C++ cache files
+ipch/
+*.aps
+*.ncb
+*.opensdf
+*.sdf
+*.cachefile
+
+# Visual Studio profiler
+*.psess
+*.vsp
+*.vspx
+
+# Guidance Automation Toolkit
+*.gpState
+
+# ReSharper is a .NET coding add-in
+_ReSharper*/
+*.[Rr]e[Ss]harper
+
+# TeamCity is a build add-in
+_TeamCity*
+
+# DotCover is a Code Coverage Tool
+*.dotCover
+
+# NCrunch
+*.ncrunch*
+.*crunch*.local.xml
+
+# Installshield output folder
+[Ee]xpress/
+
+# DocProject is a documentation generator add-in
+DocProject/buildhelp/
+DocProject/Help/*.HxT
+DocProject/Help/*.HxC
+DocProject/Help/*.hhc
+DocProject/Help/*.hhk
+DocProject/Help/*.hhp
+DocProject/Help/Html2
+DocProject/Help/html
+
+# Click-Once directory
+publish/
+
+# Publish Web Output
+*.Publish.xml
+*.pubxml
+
+# NuGet Packages Directory
+## TODO: If you have NuGet Package Restore enabled, uncomment the next line
+#packages/
+
+# Windows Azure Build Output
+csx
+*.build.csdef
+
+# Windows Store app package directory
+AppPackages/
+
+# Others
+sql/
+*.Cache
+ClientBin/
+[Ss]tyle[Cc]op.*
+~$*
+*~
+*.dbmdl
+*.[Pp]ublish.xml
+*.pfx
+*.publishsettings
+
+# RIA/Silverlight projects
+Generated_Code/
+
+# Backup & report files from converting an old project file to a newer
+# Visual Studio version. Backup files are not needed, because we have git ;-)
+_UpgradeReport_Files/
+Backup*/
+UpgradeLog*.XML
+UpgradeLog*.htm
+
+# SQL Server files
+App_Data/*.mdf
+App_Data/*.ldf
+
+#############
+## Windows detritus
+#############
+
+# Windows image file caches
+Thumbs.db
+ehthumbs.db
+
+# Folder config file
+Desktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Mac crap
+.DS_Store
+
+
+#############
+## Python
+#############
+
+*.py[co]
+
+# Packages
+*.egg
+*.egg-info
+dist/
+build/
+eggs/
+parts/
+var/
+sdist/
+develop-eggs/
+.installed.cfg
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+
+#Translations
+*.mo
+
+#Mr Developer
+.mr.developer.cfg

arduino_motor_shield_drive/arduino_motor_shield_drive.ino

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+// Amber Fechko, quick and dirty motor/button solution for peristaltic pump driver.
+// amber@kelpforest.org
+
+int buttonPin = 5;              // which pin is the button switch connected to?
+int pinI1 = 8;                  // motor shield interface I1
+int pinI2 = 11;                 // motor shield interface I2
+int speedpinA=9;                // enable motor A
+int pwmSpeed = 1000;            // define the pwmSpeed of motor
+int buttonState = 0;            // tracking whether button is pressed or not
+ 
+void setup() {
+    pinMode(pinI1,OUTPUT);      // configure pinI1 as output
+    pinMode(pinI2,OUTPUT);      // configure pinI2 as output
+    pinMode(speedpinA,OUTPUT);  // enable motor pin as output
+    pinMode(buttonPin, INPUT);  // enable buttonPin as input
+}
+ 
+void forward() {
+     analogWrite(speedpinA,pwmSpeed);      // input a simulation value to set the speed
+     digitalWrite(pinI2,LOW);              // turn DC Motor clockwise
+     digitalWrite(pinI1,HIGH);
+}
+void backward() {
+     analogWrite(speedpinA,pwmSpeed);      // input a simulation value to set the speed
+     digitalWrite(pinI2,HIGH);             // turn DC Motor counterclockwise
+     digitalWrite(pinI1,LOW);
+}
+void stop() {
+     digitalWrite(speedpinA,LOW);          // disable the pin to stop the motor -- this should be done to avid damaging the motor. 
+     delay(1000);
+}
+
+void loop() {
+    buttonState = digitalRead(buttonPin);  // check button pin for pressed button
+    if (buttonState == HIGH) {             // if button is being pressed..
+        forward();                         // move forward for ...
+        delay(6000);                       // .. six seconds ..
+        stop();                            // .. then stop the motor...
+        delay(500);                        // .. and hold everything for a half second.
+    } else {    
+      delay(500);
+    }
+}

ps pump equipment list and notes.txt

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+Most commercial water/fluid reward systems used in research settings cost a few hundred dollars (or more) and aren't easily modified. This is a fairly quick hack, but it does the job well and won't cost you >$100.. much less if you already have some of the components sitting around. Using a peristaltic pump is preferred, as the motor never actually comes into contact with the fluid itself.
+
+---------------------------------------------
+---------------EQUIPMENT---------------------
+---------------------------------------------
+Common Equipment (All Versions):
+- Peristaltic Liquid Pump (12VDC / 300mA) with Silicone Tubing (max flow 100mL/min) [ http://www.adafruit.com/products/1150 ]
+- 12VDC Adapter (old D-Link wall adapter in my case) to power the motor
+- Momentary Push Button/Switch for manual fluid delivery (optional)
+
+Equipment Used for Raspberry Pi Version:
+- Raspberry Pi Model B [ http://www.newark.com/jsp/search/productdetail.jsp?sku=43W5302 ]
+- Gertboard [ http://www.newark.com/jsp/search/productdetail.jsp?sku=46W9829 ]
+
+Equipment Used for Arduino Version:
+- Arduino Duemilanova w/ATMEGA328 [ http://arduino.cc/en/Main/arduinoBoardDuemilanove ]
+- Seeed Studio Motor Shield [ http://www.seeedstudio.com/depot/motor-shield-p-913.html ] 
+
+*** If you're not using a gertboard or motor shield of some sort, you'll need either a power transistor (basic on/off) or a motor driver chip such as the L293D to work with the DC motor which drives the peristaltic pump. [ http://www.ti.com/lit/ds/symlink/l293d.pdf ]
+
+
+
+---------------------------------------------
+------------ARDUINO VERSION------------------
+---------------------------------------------
+I used an older arduino (duemilanova) I had sitting around, but any version should be fine. If you use the Seeed motor shield you'll need a compatible pinout -- the duemilanova or the uno both work well. I wouldn't specifically recommend the motor shield, it's overkill for this, but it's cheap/simple and if you have one laying around it works fine. If you do go for this particular motor shield, the wiki has good information: [ http://www.seeedstudio.com/wiki/Motor_Shield_V1.0 ].
+
+Connect your DC power adapter to the motor shield Vs / Gnd pins, and connect the motor to the M1+ / M1- pins. Connect the motor shield to the arduino. Upload arduino code via USB. If you leave the J6 jumper connected, you don't need to provide a separate power source to the arduino -- it will pull power from the motor shield. If you want a manual "push button to dispense fluid" feature, you can pick up a button module from Seeed and connect it via their Grove system to make life easy, but I used a 10kOhm resistor and an old button switch I had laying around.
+
+			Switch
+			  |
+			  |------------
+			  |			  |
+			  |			  |
+			  |          / \
+			 5V		    /	\
+				   10kOhm	 Arduino Pin #5			
+				  Resistor
+					 |
+					 |
+					Gnd
+
+The physical assembly was done using odd metal pieces I had laying around. I'm not particularly proud of it, but it works fine (it doesn't really need a physical assembly to be functional).
+					
+---------------------------------------------
+-----------RASPBERRY PI VERSION--------------
+---------------------------------------------
+A gertboard is overkill for this, but again, I already had it sitting around. :) I used a raspberry pi model B, with a pre-assembled gertboard to drive the motor. If you go the gertboard route, their manual is valuable: [  ]. 
+
+
+
+---------------------------------------------
+--------------GENERAL NOTES------------------
+---------------------------------------------
+You can use pulse width modulation w/the motor to speed up or slow down the flow rate; if you connect the motor the other way it will move fluid the other direction. It uses 3/16″ (4.7mm) outer diameter silicone tubing, which connects nicely to a metal drinking tube pulled out of a rodent water bottle.
+
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