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:
Recently, I have been blogging about Git:
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.