chem-bla-ics
A new environment means new tools. Bioclipse is Eclipse RCP-based, so colleagues work with Eclipse and are much more into Eclipse too. For example, into Mylyn. Mylyn is a tool to track tasks and assign context to them. The tasks I am interested in (for this blog item), is fixing bug reports. Mylyn is rather suited for this, as it allows linking Java source files to bug reports.
Five days ago, my chem-bla-ics blog turned 3. Here’s the first post . It defined:
As you might have seen, we, Uppala and the EBI, are working on the next generation JChemPaint. JChemPaint is an editor, and therefore, consists of a model (IChemModel), a view (IRenderer) and a controller (IController). See the many posts in Gilleain’s blog.
About a week ago, I hooked up my GitToDo software with Freemind. This allows me to organize the projects I am working on, without having to code this in GitToDo directly.
Some time ago Noel ran a poll on chemoinformatics and cheminformatics , so I set up a poll too in part #1 of this series . The outcome is clear: The Obernai meeting strongly suggested chemoinformatics [1], but the start of the open access Journal of Cheminformatics is the killer.
Just updated Bioclipse2 with Jmol 11.6 RC 18:
Lee et al. published last week a paper on pKa prediction (doi:10.1021/ci8001815). As the paper says, the pKa, and in particular the ionic state of a molecule at physiological pH, affects pharmacokinetics and pharmacodynamics. The paper describes a (binary) decision tree using presence or absence of SMARTS substructures to traverse the tree, allowing prediction of monoprotic molecules.
Felix has a small tool on his website to show me (or anyone else) who likes what I post on my FriendFeed account:
There was some talk about the history of chemoinformatics toolkits by Noel and Andrew, which made me wonder on the exact history of Jmol and JChemPaint.
Some of you heard me complain about commit messages resulting from git cherry-pick which allows me to apply patches from CDK trunk to a branch, without needing to do a full merge of what happens in trunk. The commit messages would be identical, which made it seem that those original messages were mine.