Using the model deployment and prediction service, I put up the two linear regression models I had built so far (described in more detail here) While REST is nice, a simple web page that allows you to paste a set of SMILES and get back predictions is handy. So I whipped together a simple interface [...]
Posts Tagged ‘REST’
ONS Solubility Predictions
Posted in software, tagged ons, prediction, qsar, REST, solubility on January 14, 2009 | Leave a Comment »
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 [...]
Playing with REST Descriptor Services
Posted in cheminformatics, software, tagged cdk, descriptor, google, javascript, REST, web service on January 7, 2009 | 4 Comments »
As part of my work at IU I have been implementing a number of cheminformatics web services. Initially these were SOAP, but I realized that REST interfaces make life much easier. (also see here) As a result, a number of these services have simple REST interfaces. One such service provides molecular descriptor calculations, using the [...]
Quick Comments on an Analysis of Antithrombotics
Posted in cheminformatics, tagged performance, database, pubchem, python, REST, factor Xa, inchikey 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 [...]
Chemistry in Google Docs
Posted in software, tagged cheminformatics, density, google, pubchem, REST, service on December 10, 2008 | 4 Comments »
I met with Jean-Claude Bradley yesterday and we had a pretty useful hack session, allowing him to easily incorporate chemical and cheminformatics functionality into a GoogleDocs spreadsheet.
A common task that Jean-Claude wanted to automate was the calculation of milligrams (or milliliters) of a chemical required for a certain molarity. So what we need for this [...]
