chem-bla-ics: November 2008

Software is a Method (Meme)

it provides a recipe to approach (scientific) questions

let's you cook up a (scientific) answer

you can use it as a black box (like an orbitrap)

you can refine existing methods (well, some can, others don't)

it has an error (but I do not believe it is normally distributed)

Now, to me it's trivial to work put how Open Source supports this.

Nov

Scripting JChemPaint

Today and tomorrow, Stefan, Gilleain, Arvid and I are having a JChemPaint Developers Workshop in Uppsala, to sprint the development of JChemPaint3, for which Niels layed out the foundation already a long time ago.

Gilleain and Arvid are merging their branches into a single code base, while Stefan is working on the Swing application and applet. The Bioclipse SWT-based widget is being developed for Bioclipse2.

Nov

Solubility Data in Bioclipse #1

I am working on converting Jean-Claude's Solubility data to RDF (after Pierre's model, see here, here, and here, here for first data exploration), so that I can integrate it with data from DBPedia, Freebase, rdf.openmolecules.net, etc. Bioclipse will be the workbench in which this will be visualized, and just got graph depiction online using Zest.

Nov

Re: Open Source != peer review

Andrew has an interesting thread on the content of a slide of a recent presentation. In the comments you can read the back and forth on things; indeed, there are very many aspects to things and he did ask a very complex question, of which he assumed that I understood what he was asking, and I indeed assumed too that I understood what he was asking:Some argue that doing good computational-based science requires open source.

Nov

Finding the commit that causes the regressions...

CDK 1.1.x releases are well in progress, but a recent commit broke a number of unit tests. Here comes git-bisect.$ git checkout -b my-local-1.2 cdk1.2.x

$ git bisect start

$ git bisect bad

$ git bisect good 8219139e9236ab8036e9d08c13fcd0482d500c79

These lines indicate that the current version (HEAD) is broken, and that revision 8219139e9236ab8036e9d08c13fcd0482d500c79 was OK.

Nov

Open{Data|Source|Standards} is not enough: we need Open Projects

The Blue Obelisk mantra ODOSOS, Open Data, Open Source, Open Standards, is well known, and much cited too. Jean-Claude Bradley popularized the Open Notebook Science (ONS). This has always been nagging me a bit, because the CDK, Jmol, JChemPaint and other chemistry projects have done that for much longer, though we did not use notebooks as much, so called it just an open source project. It really is no different, IMO, though surely, there are differences.

Nov

Next generation asynchronous webservices #2

Getting back to some webservice stuff (see part #1 of this series)... actually, I'll use cloud service from now on, since web service is reserved for SOAP/WSDL (see my EMBRACE presentation).

Nov

EMBRACE workshop in Uppsala

This Monday and Tuesday I will attend the EMBRACE workshop Understanding, creating and deploying EMBRACE compliant WebServices. I will present there the ongoing work in Bioclipse to support services and web services in particular. The sheets of the presentation will look like:

Bioclipse and WebservicesView SlideShare presentation or Upload your own.