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)

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.

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.

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;

CDK 1.1.x releases are well in progress, but a recent commit broke a number of unit tests. Here comes git-bisect.

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.

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 ). Let me present this bit of JavaScript I just ran in Bioclipse2:

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.

Mark pointed me to the embed functionality of Gist, product on GitHub where I host some todo software and a git mirror of CDK 1.2.x .

Johannes joined a Bioclipse Workshop a long time ago, and introduced the participants to the idea of using XMPP (aka Jabber) for asynchronous web services. SOAP is commonly user to run webservices over HTTP, but via (SMTP) email and XMPP is possible too (see SOAP over XMPP). Using HTTP as transport layer has problems. The biggest problem, is possibly that HTTP connections are timed out, e.g. by intermediate router.

After some difficulties this week with making an export of CDK plugins in the Bioclipse2 Cheminformatics feature of with the cdk-eclipse software, I got the following cute Bioclipse2 script up and running: