Ciencias QuímicasInglésJekyll

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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OpenscienceBlue-obeliskOpendataOpensourceCiencias QuímicasInglés
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I value ODOSOS very high: they are a key component of science, and scientific research, though not every scientist sees these importance yet. I strongly believe that scientific progress is held back because of scientific results not being open; it’s putting us back into the days of alchemy, where experiments were like black boxes and procedures kept secretly.

TavernaEbiCdkBioclipseMyexperimentCiencias QuímicasInglés
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The second part of the morning session featured a presentation by Sirisha Gollapudi which spoke about mining biological graphs, such as protein-protein interaction networks and metabolic pathways. Patterns detection for nodes with only one edge, and cycles etc, using Taverna.

TavernaJavaCiencias QuímicasInglés
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I arrived at the EBI last night for the Taverna workshop, during which the design of Taverna2 is presented and workflow examples are discussed. Several ‘colleagues’ from Wageningen and the SARA computing center in Amsterdam are present, along with many other interesting people. This afternoon is my presentation.

SmilesBlue-obeliskCiencias QuímicasInglés
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Craig James wants to make SMILES an open standard, and this has been received with much enthusiasm. SMILES (Simplified molecular input line entry specification) is a de facto standard in chemoinformatics, but the specification is not overly clear, which Craig wants to address. The draft is CC-licensed and will be discussed on the new Blue Obelisk blueobelisk-smiles mailing list.

AcsRssCiencias QuímicasInglés
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A couple of people now confirmed the problem with the ACS journal RSS feeds. Being back behind my desktop machine, I can post the obligatory screenshot: The feed for Chemical Biology shows 79 feed items and the first one was a Environ. Sci. Technol. paper.

GoogleBioclipseCiencias QuímicasInglés
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I was just about to install Subclipse (for the millionth time), and googled for the update site details: Does anyone know how you can get Google pick up or how it detects the Download/UpdateSite/etc pages, shown as direct links below the primary hit? Are HTML <link> elements used for that? Or does it use certain meta data, microformats, …?

BioclipseJchempaintCiencias QuímicasInglés
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The second Programmeerzomer and the second summer of code for me, will end tomorrow with a presentation of Niels on his new JChemPaint code. The summer is over before you know it. One of the goals was making the JChemPaint editor Swing independent and more easy to integrate with SWT widgets. So, I hacked up the last bits of Bioclipse code.

RdfConnoteaInchiCiencias QuímicasInglés
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Using the InChI and the new rdf.openmolecules.net website, it is now possible to tag molecules. And if you use Connotea for that, your tags will even show up on the rdf.openmolecules.net website. For example, at the time of writing, methane was tagged with alkanes and gas . The trick I use, is that the rdf.openmolecules.net gives every molecule a unique HTTP URL.