chem-bla-ics
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  • Jul 6, 2007

    Standing on the shoulders of ... the Blue Obelisk

    The Seven stones wondered what to do with a petaflop in science, in response to Declan’s The petaflop challenge in Nature. Declan discusses in this commentary the increase in computing power and the necessity of parallel programming to make use of it. Now, I do have some ideas (e.g. enumerating metabolomic space, mining the RDF graph of our collective biological and chemical knowledge base for the one hundred most supported contradictions), but that is not what I want to talk about. It is this fragment from Declan’s piece:

    2 minute read
  • Jul 1, 2007

    Atom typing in the CDK

    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.

    2 minute read
  • Jun 27, 2007

    Chemical RDFa with Operator in the Firefox toolbar

    December last year I proposed the use of microformats and RDFa for simple semantic markup of molecular information. I linked that with the InChI extension for the Postgenomic.com software for Chemical blogspace and wrote these tools to work with the markup:

    2 minute read
  • Jun 27, 2007

    QSAR plugin for Bioclipse getting in shape

    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.

    1 minute read
  • Jun 25, 2007

    Test File Repository and RelaxNG

    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.

    1 minute read
  • Jun 25, 2007

    Nature should host our Electronic Lab Notebooks

    Pedro suggested in Nature Networks What’s Next forum that Nature should add a new service for scientists: hosting electronic lab notebooks. And I think this will be a killer application. I am rather excited about the idea, and feel ashamed not putting one-and-one together myself. We have our chemoinformatics tools and RDF is just around the corner, that combined with semantic wikis, and we have science of the 21st century. This is my reply posted on Nature Network:

    1 minute read
  • Jun 22, 2007

    Archiving spectra: use InChI and CML

    Ryan blogged in Archive This about some advices from ACD on how to store spectra in your electronic lab notebook.

    1 minute read
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  • Egon Willighagen
  • 0000-0001-7542-0286

Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.