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. less than 1 minute read

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. 6 minute read

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 ). Let me present this bit of JavaScript I just ran in Bioclipse2: 2 minute read

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: less than 1 minute read

Next generation asynchronous webservices

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. This makes it rather unsuited for long running jobs. Workarounds are easy to come up with, and polling is a common solution. 2 minute read

Embedding Gists in blogs

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 . less than 1 minute read

Bioclipse2 Scripting #1: from SMILES to a UFF optimized structure in Jmol

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: 1 minute read