Research and Teaching Blog
14 Posts with tag: programming
Serial communication demo
Demo code for connecting two computers using an Arduino-mediated serial connection. Needs fixing..
// An Arduino-mediated serial communication device // Kaustubh D. Bhalerao /* Device topology: Computer1--USB--Arduino1==Serial==Arduino2--USB--Computer2 We are going to try this.... Computer --TX0---> Arduino # <--RX0--- USART0 ## SWSerTX <===| | SWSerRX <===| The computer sends a packet over USART/USB to the Arduino The arduino relays it to the SWser transmit port which is received on the SWSer RX port, which relays it back to the computer */ // Pin Layout // Pins 2 and 3 ...Tags: ABE425 , programming
PID Control using the arduino
The Arduino comes with a beautiful contributed PID library. The following code demonstrates how to use the PID library to control the voltage level in a 'leaky' capacitor.
#include <PID_v1.h> // This file loads the PID_v1 library. // make sure the PID library is stored in // Path/to/Arduino/libraries/ folder // http://arduino.cc/playground/Code/PIDLibrary // PID library // http://arduino.cc/en/Reference/Libraries // How to install the library /* Tank filling PID controller. Kaustubh Bhalerao ABE 425 Demo In this ...Tags: ABE425 , programming
Digital IO with interrupts
Here is an improved version of the code. Note that the digital input pin is actually never even read! It is only used to detect the state changes (Here falling edges).
It is simple enough (and robust enough). As you can see my two-yr old can operate the circuit. It is unbelievable he has more fun with this switch than with an iPad!
/* A control system based on the Arduino microcontroller platform Copyright: Kaustubh D. Bhalerao. All rights reserved System ...Tags: ABE425 , Instrumentation , programming
Crowdsourced quantum computing
By now you've probably been hard at work trying to figure out what quantum computing is, and have been eager to share your findings with everyone.
After class on Monday I thought a little bit more about the nature of the 'experiment' we started, and figured that it was probably a better idea if everyone had a bit more time to work on the problem. So rather than have you bring your contribution to class on this Wednesday (today ...
Tags: ABE 446 , nanotechnology , programmingDIY thermal cycler
This post is way long overdue. In the Fall of 2008, (or was it 2007?) I taught a small module in the ABE 221 course dealing with automation in Biological Engineering. My hope was to create a home-made thermal cycler for less than $1000. Of course many people in the DIYBio community have constructed thermal cyclers for way less, and truly, you probably don't need to pay more than $300-400 (perhaps even less) to build a reasonably good quality ...
Tags: Do it yourself Biology , Instrumentation , labjack , programming , python , synthetic biologyStochastic kinetics solution
This post is related to the problem posed in the stochastic kinetics lecture. Attached here (link missing) is the solution to the problem (the .R code). To run the code, you will need this reaction.csv input file. The file is a text description of the reaction as a graph. The format is very simple: nodes are the reaction states, and are described by the line e.g. "node, Pyruvate" or "node, Pyruvate_PDC". State transitions are described by "edge, Pyruvate ...
Tags: BIOE504 posts , courses , programmingLabjack Sensors
Here are some resources on installing the drivers for Labjack on Windows, a prebuilt installer for Mac OS X as well as the python modules.
Steps required to install the LabJackPython module:
- Open a command prompt (Click on Start > Run and type cmd in the box. Should open a DOS window)
- Change directory to the folder where you have your LabJackPython files extracted (e.g. 'cd \Downloads\LabJackPython\)
- type the command 'python setup.py install' in the folder where the ...
Temperature and RH in 376A
Here's an experiment. I have a script uploading hourly temperature and humidity data to a spreadsheet. Here's the visualization of the temperature and humidity data in my office.
Tags: Instrumentation , labjack , miscellaneous , programming , pythonResistor codes
Here is a program to find the value of a resistor based on its color coding.
Tags: miscellaneous , programming , tsm435Particle aggregation
Particle aggregation is a fascinating area, important for all kinds of applications, from computer graphics to biotechnology and bioprocessing. Here's a particle aggregation simulation app I wrote a while back to study the emergence of particle size distributions as a result of entropic considerations in the aggregation process. Here's a link to the application. Watch how the particles dissociate / aggregate when you toggle the surfactant.
Tags: Java , particles , programmingWeb interface for the LabJack
One of the things I've always wanted to do is to create a web-based controller for the LabJack family of devices. This is not exactly the same thing I've written about in the past, but it is not unrelated either. U3OverIP provides a good framework to build the web interface, but writing the actual interface is non-trivial - at least for me. Any way. Here's a simple implementation. Look at the "Announcements" section of the index page of ...
Tags: Instrumentation , labjack , programming , pythonNetwork graphs for KEGG
Here's a graph of all the compounds connected by various reactions in the KEGG database. I used the flat file provided at the KEGG FTP site which lists the reactions including their reversibility (or lack thereof). The file was parsed with Python, networkx and pydot, and the graph was generated using Graphviz using the neato algorithm. Here's the link
Tags: programming , synthetic biology
U3OverIP
Joshua Sander, our student in ABE is currently finishing up his MS working on a a high channel DAQ system as shown in the figure. Briefly, the system is constructed as follows:
First the hardware:
We have a standard LAMP server with the labjack u3 connected to it. We built our own MUX boards capable of doing analog or frequency (RH) signals using an Analog Devices (I believe ADG506) with basic RC filtering. The sensors are standard chip-based temperature / RH ... Tags: Instrumentation , labjack , programming , pythonFirst Post
About time I created the research page for my website. Figured I'd make a blog instead, where I can blog about the research. So here it is: "Hello World!".
I used the basic blog structure provided by Ross P (www.rossp.org) and used it to integrate it into the website.