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Entries Tagged as 'People'

Do a cheminformatics PhD thesis at a world-class institution

June 16th, 2009 · 1 Comment · Chemoinformatics, Hot Science, Open Access, Open Data, Open Science, Open Source, People, Scientific Culture, Teaching

If the pompous title caught your attention, and you are ashamed of that: Don’t worry. It is all true. My cheminformatics and metabolism group at the European Bioinformatics Institute (EBI) is looking for a phd student this year and all you need to do is apply through the regular route.  The range of possible topics [...]

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ChemSpider aquired by the Royal Society of Chemistry

May 11th, 2009 · 4 Comments · Databases, Open Science, People, Scientific Culture

It’s going to be all over the place soon anyway, so I’ll make it short: The Royal Society of Chemistry has announced that it has aquired ChemSpider. This is great news and I’m confident that it will be a move to even more openess in chemistry and cheminformatics. It will also allow the RSC to [...]

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ChEBI release 56, now with SD file

April 30th, 2009 · 6 Comments · ChEBI, Chemoinformatics, Databases, Open Access, Open Science, Open Source, People, Scientific Culture

We are pleased to announce release 56 of our database of Chemical Entities of Biological Interest (ChEBI).
SDF files are now available with ChEBI Release 56. They can be exported via the Downloads section or the search results page. We also have automatically generated links from IntEnz (www.ebi.ac.uk/intenz) and Rhea (www.ebi.ac.uk/rhea). This release contains 17842 annotated [...]

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CDK Workshop 2009 Wrap-up

April 23rd, 2009 · No Comments · Bioclipse, Blue Obelisk, Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Databases, Fun, Life of Chris, Open Science, Open Source, People, Scientific Culture, Teaching

The CDK workshop 2009 is over and what is left is a bad cold. But I’ll get over it.
The workshop itself was phantastic – we had 40 participants with well balanced contributions from industry and academia. The first half day was dedicated to tutorials on various aspects of CDK, basic installation, our CDK and Oracle-based [...]

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Oliver Karch about Molwind – Using CDK to Visualize Molecule Spaces in a Geospatial Context

April 21st, 2009 · 3 Comments · Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Life of Chris, Open Science, People, Scientific Culture

Oliver Karch from Merck-Serono gave the last talk on Tuesday morning, showing how to visualize CDK to visualize molecular spaces in a way “as easy as Google Earth”. They us a workflow with Pipeline Pilot, a MolWind Server, which is Java and Apache based and then render 2D structures with CDK. The NASA Molwind client [...]

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Asad Rahman on Small molecules and reaction mechanism – Rewiring the enzyme space

April 21st, 2009 · No Comments · Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Life of Chris, Open Science, People, Scientific Culture

In the second research talk on Tuesday morning Asad from EBI talks about his research on finding pathes in metabolic networks. Asad and I have been working together CUBIC in Cologne and are now again colleagues at EBI. Goal of his work has been to find patterns in biological reaction networks. His first examples deals [...]

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John van Drie’s talk on CDK in Virtual Drug Discovery

April 21st, 2009 · No Comments · Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Life of Chris, Open Science, People, Scientific Culture

John has started his talk this morning by giving a manifesto for open source in drug discovery. He gives an introduction to the history of virtual drug discovery, starting in 1985 (showing some dinosaur computers ) and then quickly jumps to y2k. While the hardware has dramatically fallen in price, the drug discovery software [...]

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Thorsten Meinl and Bernd Wiswedel talking about CDK workflows in KNIME

April 20th, 2009 · No Comments · Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Life of Chris, Open Science, People, Scientific Culture

Our friends from Konstanz present their KNIME workflow solution which contains the CDK for achieving cheminformatics functionality.We have a long-standing collaboration with them to help them to get CDK working in KNIME. Unfortunately, we are still at cdk 1.1 in KNIME where a number of issues prevent CDK/KNIME to perform really well.With an integration of [...]

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Ola Spjuth talks about “Accessing and scripting CDK from Bioclipse”

April 20th, 2009 · No Comments · Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Life of Chris, Open Science, People, Scientific Culture

Our friend Ola Spjuth from Uppsala talks about how to access CDK from within Bioclipse using Bioclipse’s built-in scripting capabilities. Ola will cover

Bioclipse
The Use of CDK in Bioclipse
Scripting in Bioclipse
Calculating CDK properties

First we’ll download Bioclipse 2.0Beta4 from http://www.bioclipse.net.
Ola continues by explaining Bioclipse’s component architecture. For the tutorial part of his talk, he has prepared an [...]

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Mark Rijnbeek’s talk about CDK and databases

April 20th, 2009 · No Comments · Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Life of Chris, Open Science, People, Scientific Culture

Mark is working in my group on a CDK-based plugin for Oracle to enable chemistry searching: Similarity and Substructure. In his talk at the CDK workshop, he points out in the beginning that this is not a cartridge as defined by Oracle. It is a set of java classes loaded by the Oracle Java virtual [...]

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