Research and Teaching Blog

3 Posts in June Archive

Web 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 ...

Posted on June 10, 2009 1 Comment

DNA Counters

In order to 'program' biology, do we need a different programming paradigm? Or can we co-opt programming paradigms from computer sciences?
The recent issue of Science features an article by Friedland et al., outlines two different synthetic gene network counters, one based on the delay inherent in the process of gene expression, while the other based on cascaded FLP-FRT recombinase pattern. In doing so, they have shown a viable implementation of a more reliable 'kill switch' for synthetic gene networks ...

Posted on June 8, 2009 0 Comments

Network 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

Posted on June 3, 2009 0 Comments