Today while working on a project I needed to get access to the Gene Ontology hierarchy. While there a number of GO browsers such as Amigo, I needed access to the raw data to generate a graph that I could then slice and dice. A few minutes with Python led to a simple solution.
The program [...]
Posts Tagged ‘network’
Getting the GO into a Graph Data Structure
Posted in software, tagged go, network, python on January 31, 2009 | 3 Comments »
Annotating Bioassays
Posted in cheminformatics, text mining, visualization, tagged annotation, database, go, network, pubchem, text mining, visualization on January 25, 2009 | 1 Comment »
I’ve been working for some time with the PubChem Bioassay collection – a set of 1293 assays that cover a range of techniques (enzymatic, phenotypic etc.), targets and sizes (from 20 molecules to 200,000 molecules). In addition, some assays are primary, high-throughput assays whereas a number of them are smaller, confirmatory assays. While an extremely [...]
SALI Viewer Now on GitHub
Posted in cheminformatics, software, tagged graphviz, network, sali on January 16, 2009 | Leave a Comment »
Last year, John Van Drie and I published two papers (here and here) on the Structure Activity Landscape Index, (SALI) which is a way to view SAR data as a network of compounds. Along with the paper ,I put up a simple Java application (licensed under the LGPL) to generate and explore these networks. – [...]
Kinase Inhibitors and Polypharmacology
Posted in chemistry, research, tagged cancer, gleevec, kinase, network, polypharmacology on November 5, 2008 | Leave a Comment »
The Curious Wavefunction has a nice post on the issue of selective and non-selective kinase inhibitors. An interesting commentary, especially in the light of the recent paper on network polypharmcology. While there have been a number of papers on polypharmcology and the idea itself is very attractive, it has seemed to me that for this [...]
