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chem-bla-ics

chem-bla-ics
Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
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CdkOpenscienceKimya Bilimleriİngilizce
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So, with all these people blogging about the Open Science Notebook (yes, each word is one distinct blog) it is worth looking back in time. To make clear what I put under the OSN: a notebook in which experimental details and outcome are written down. So, what did the OSN look like almost ten years ago?

CdkKimya Bilimleriİngilizce
Yayınlandı

Second in a series of articles summarizing articles that cite one of the main CDK articles for CDK News. The first CDK Literature was already half a year ago, so it was about time. Bioclipse Nothing much I have to say about that. Just browse my blog and you’ll see that it heavily uses CDK, JChemPaint and Jmol. See also the Bioclipse blog.

Kimya Bilimleriİngilizce
Yayınlandı

Everyone of use knows that big pile of paper on your desk that contains the things we want to read, scan or just browse. I even have an electronic equivalent. Another pile contains leaflets and glossy folders from conferences, like the ACS meeting in Chicago. OK, going to get rid of those last ones, and will shortly put the links here. The first leaflet is from Chemistry Central, one of the open access publishers.

CdkJunitKimya Bilimleriİngilizce
Yayınlandı

Atom typing is one of principal activities in chemoinformatics. Atom types provide additional information that cannot be derived from the connection table that is being used, or may define what force fields terms should be used. This makes perception of atom types very important. The CDK has a few places where atom types are perceived. The HydrogenAdder and ValencyChecker are two examples.

BioclipseQsarCdkAmbitKimya Bilimleriİngilizce
Yayınlandı

Over the last few weeks I continued the work on getting (descriptor-based) QSAR/QSPR implemented in Bioclipse. JOELib (GPL) and the CDK (LGPL) being two prominent opensource engines that can calculate molecular descriptors, and AMBIT a front-end. To be able to do QSAR/QSPR model building from start to end in Bioclipse, I worked in April on an architecture for selecting descriptors.

Blue-obeliskOpenscienceKimya Bilimleriİngilizce
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Last week I started the Blue Obelisk Chemical Test File Repository, a repository of OSI-approved-licenced test files (from various sources) to improve interoperability between chemoinformatics software. Following a discussion on the mailing list earlier, a directory hierarchy has been set up, and each files contains an index.xml to describe the content.

CmlInchiNmrKimya Bilimleriİngilizce
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Ryan blogged in Archive This about some advices from ACD on how to store spectra in your electronic lab notebook. Use InChI This reminded me of a discussion I had with with Colin when he was at the CUBIC, which was about experimental sections. I proposed that the InChI should have a prominent place in the experimental section.