Milestones...

While I am still looking around for a assisting/associate professor position, there are two milestones around my scientific work I want to briefly mention here. This blog is the 500th blog on chem-bla-ics, and the two CDK papers have combined reached 100+ citations as counted by Web-of-Science, as can be seen on my ResearcherID profile. less than 1 minute read

Bioclipse Manager for MyExperiment.org

Some time ago I wrote about using Bioclipse to query to MyExperiment.org SPARQL end point . I think I had not mentioned that I have also written a manager to download MyExperiment Bioclipse Scripting Language scripts (though there are no GUI elements yet): less than 1 minute read

Maintaining patches is fixing patches

Today I had a question about having to fix patches against upstream changes because those patches were not included upstream yet is not very productive. 2 minute read

CrossRef writes up RSS usage recommendations

CrossTech announced that a CrossRef working group has written a best practices for the use of RSS feeds by publishers. Nice introduction for anyone who is creating RSS feeds. Only comment I could make, is the lack of other modules. For example, a Chemistry module has been proposed by us 5 years ago already (DOI:10.1021/ci034244p) and about which I blogged on several occasions. less than 1 minute read

Work in Progress: an Open DocCheck replacement

While it is still very much in progress, I have already made more progress than I had hoped for. The JavaDoc Doclet API is actually not too difficult to use, though my use will very likely improve more later. The CDK has been using Sun’s DocCheck utility for testing the library’s JavaDoc quality, but the reports never really satisfied me. Moreover, the most recent version is ancient and because it is closed source, no one can continue on those efforts. DocCheck is MIA. 1 minute read

PMD 2.4.5 installed in the CDK 1.2.x branch

Today I installed PMD 4.2.5 in the CDK 1.2.x branch which contains mostly bug fixes compared to the 4.2.2 version we had earlier. Several of these include false positives: warnings which were not really problems, but tests going bad. less than 1 minute read

SPARQL end points, Jena and bif:contains

I have been having fun with SPARQL in Bioclipse for a while now, and blogged at several occasions: less than 1 minute read