Bioclipse2 Scripting #3: XLogP calculatation using a XMPP CDK cloud service

In preparation of the CDK workshop next week, here is a small Bioclipse2 script to calculate the XLogP value for a given SMILES, using the a CDK-based XMPP service: less than 1 minute read

Multiple inheritence for content types?

Bioclipse is an environment for handling and processing life sciences data. This data is present in files with a wide variety of formats, each of which can contain a particular data type. For example, a we can have a single molecule in MDL molfile and in CML. less than 1 minute read

Rednael, CDK Git for Rajarshi's patches, PubChem SDF

Short blog item about some CDK Git updates. Could not get sleep, so might as well spend that time on CDK hacking, not? Reason why I actually could not catch sleep was the news that PubChem SD files are not regular MDL SD files, but use custom extensions, for example, for dative bonds (see this PDF). This surely explains the weird things I have seen, but, unfortunately, the big SDF button on PubChem does not warn about that. Anyway, thanx for Wolfgang for informing about that customization! 1 minute read

Groovy CDK and the Keyword List

Today I have been hacking a bit more on the CDK material for the CDK workshop (see CDK - The Documentation). Below are two previews, one with a LaTeX-ified keyword list (here as HTML): less than 1 minute read

"Open Knowledge: Reproducibility in Cheminformatics with Open Data, Open Source and Open Standards"

I have submitted today the abstract of my talk at the GDCh-Wissenschaftsforum Chemie 2009 in Frankfurt in August as part of the Open Notebook Science/Open Drug Discovery session: 1 minute read

Nature Jobs - Google Map mashup

Nothing much I need to say about the NatureJobs Interactive World Map, I think. Thanx to Partial Immortalization for the link on FriendFeed! less than 1 minute read

CDK - The Documentation

In preparation for the CDK workshop later this month, I am writing up my material for my kick-off presentation of the workshop. So, I better make it good. Using LaTeX at least overcomes my laziness which always made Word documents look stupid. Even default LaTeX looks good: 1 minute read