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 ‘python’
Getting the GO into a Graph Data Structure
Posted in software, tagged go, network, python on January 31, 2009 | 3 Comments »
Deploying Predictive Models
Posted in cheminformatics, tagged cdk, python, qsar, R, REST, rpy2, solubility, web service on January 14, 2009 | 1 Comment »
Over the past few days I’ve been developing some predictive models in R, for the solubility data being generated as part of the ONS Solubility Challenge. As I develop the models I put up a brief summary of the results on the wiki. In the end however, we’d like to use these models to predict [...]
Update to the REST Descriptor Services
Posted in cheminformatics, software, tagged base64, descriptors, python, REST, web service on January 11, 2009 | 3 Comments »
The current version of the REST interface to the CDK descriptors allowed one to access descriptor values for a SMILES string by simply appending it to an URL, resulting in something like
http://rguha.ath.cx/~rguha/cicc/rest/desc/descriptors/
org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor/c1ccccc1COCC
This type of URL is pretty handy to construct by hand. However, as Pat Walters pointed out in the comments to that post, SMILES [...]
Quick Comments on an Analysis of Antithrombotics
Posted in cheminformatics, tagged database, factor Xa, inchikey, performance, pubchem, python, REST on January 5, 2009 | Leave a Comment »
Joerg has made a nice blog post on the use of Open Source software and data to analyse the occurence of antithrombotics. More specifically he was trying to answer the question
Which XRay ligands are closest to the Fontaine et al. structure-activity relationship data for allowing structure-based drug design?
using Blue Obelisk tools and ChemSpider and where [...]
Extending the REST PCA Service
Posted in cheminformatics, software, tagged python, mod_python, REST, pca, numpy on January 3, 2009 | 12 Comments »
I recently described a REST based service for performing PCA-based visualization of chemical spaces. By visiting a URL of the form
http://rguha.ath.cx/~rguha/cicc/rest/chemspace/default/
c1ccccc1,c1ccccc1CC,c1ccccc1CCC,C(=O)C(=O),CC(=O)O
one would get a HTML, plain text or JSON page containing the first two principal components for the molecules specified. With this data one can generate a simple 2D plot of the distributions of molecules [...]
The ONS Challenge & Visualizing Chemical Space
Posted in cheminformatics, visualization, tagged diversity, numpy, pca, python on December 30, 2008 | 7 Comments »
The ONSChallenge has been running for some time now and the simple web query form that tied in the data from Google Docs along with web services from IU has turned out to be pretty handy. With more and more data becoming available, I had done some initial exploratory analysis of the measured solubilities. One [...]
Getting a CAS Number from a PubChem CID
Posted in software, tagged cas, postgres, pubchem, python on December 12, 2008 | 1 Comment »
A few days back, Hari on FriendFeed had asked how one could get a a CAS number from a PubChem compound ID (CID). The reverse, that is finding a CID for a given CAS number is generally quite easy as shown by Rich here and here. Since I was trying to get some writing done, [...]
Multi-threaded Database Access with Python
Posted in software, tagged database, parallel, performance, postgres, python, threads on November 14, 2008 | 8 Comments »
Pub3D contains about 17.3 million 3D structures for PubChem compounds, stored in a Postgres database. One of the things we wanted to do was 3D similarity searching and to achieve that we’ve been employing the Ballester and Graham-Richards method. In this post I’m going to talk about performance – how we went from a single [...]
