Bioclipse beta 5 was just released by Ola, and the team had some bad days over an problem that happened after a merge of an important branch regarding the managers we are using to allow scripting of Bioclipse.

In the end, Jonathan found a workaround for the problem, even though we still have no clue what was the exact cause. Additionally, Arvid implemented one of the last missing features of the JChemPaint editor, being the ability to draw bonds in any arbitrary direction, and the ability to create a new bond to an already existing atom. This really seems to be the last beta before the 2.0 release candidate. So, head over to SourceForge as it is now time to report this smaller things you like to see improved.

A recent post by Cameron on his visit last week with Nico, Peter and Jim, discussed Open Data licensing. This lead to an interesting discussion on these matters, and questions by me on why people care so much about only public domain data (or licensed with PDDL or CC0).

Open licensing for data has not as much matured as for software, and international law seems to be more confusing about the issues. I guess that is because data aggregation has been around for way before the computer era.
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Last Monday the CHMINF-L brought the news to me that ChemSpider was acquired by the RSC (not the press release). Twitter (my Twitter post) and FriendFeed (see this series).

Reading blogs used to be to get the news, but this has changed. Still, blogging gives more freedom, more space. Blogs did soon follow. Chris was the first to blog about it: This is great news and I’m confident that it will be a move to even more openess in chemistry and cheminformatics.
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Dear lazyweb!

I have been trying to figure out which Eclipse 3.4 feature I must install from the update site to get the org.eclipse.zest plugin in my environment.

I installed the Zest feature (which I am going to use to visualize an RDF network), but my workspace still complained that I did not have the plugin.

PubChem-CDK is a project that runs CDK code on the PubChem data. As we speak. a groovy script reads about 100 PubChem Compounds XML entries per second into the database. Mind you, not the SDF they distribute which uses a custom extension to overcome the limits of the real MDL SDF format.

Right now, it has run the atom type perception algorithm on about 1M compounds, and has a pretty good coverage of the organic chemistry domain.
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Just hit the below icon, and use 140 characters why you think the CDK should be nominated.
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Johannes asked me what the Lipinski Rule of Five for farnesol is, in reply to the matching XMPP cloud service.

My thesis was released slightly over a year ago in print form. The electronic form has not yet, which has social and legal barriers. Like many before me, I made the mistake to publish in journals that require me to reassign copyright. Combine that with the custom to publish papers in your thesis as is, which means reduction of work for the manuscript committee, as they can know which chapters have undergone peer-review in the form they are present in the thesis too.
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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
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