We are glad to announce that our article about CDK-Taverna, an open workflow solution for cheminformatics, is now online on BMC Bioinformatics. CDK-Taverna, which lives at http://www.cdk-taverna.de/, features more than 160 workers for various tasks in molecular informatics. The workflow paradigm allows scientists to flexibly create generic workflows using different kinds of data sources, filters [...]
Entries Tagged as 'Open Source'
CDK-Taverna paper published
March 29th, 2010 · No Comments · Chemistry Development Kit, Chemoinformatics, Open Science, Open Source, Open Standards
Tags: CDK-Taverna
What do we expect from a chemical structure editor applet?
July 11th, 2009 · No Comments · ChEBI, Chemistry Development Kit, Chemoinformatics, JChemPaint, Open Science, Open Source, Scientific Culture
My team at the EBI maintains a couple of databases [1,2,3] dealing with various aspects of (bio-) organic chemistry. All of them need chemical structure editor applets where users can specify queries for substructure searches and which are used by our curators for data entry.The development of these databases is funded by the European Union [...]
Tags: JChemPaint·Open Source
Do a cheminformatics PhD thesis at a world-class institution
June 16th, 2009 · No Comments · 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 [...]
Tags: cheminformatics research·EBI·PhD
NMRShiftDB now with more than 12.000 proton spectra
May 14th, 2009 · 1 Comment · Databases, Open Access, Open Data, Open Science, Open Source, Publishing, Scientific Culture
The number of structures and spectra in NMRShiftDB now exceeds 31.000 and 35.000, respectively. The number of proton spectra alone is now 12.934. This is due to NMRShiftDB developer Stefan Kuhn in my group importing a recent donation from our collaborators Reinhard Dunkel and Heinz Kolshorn. Thanks to Heinz and Reinhard for their generosity.
Tags: NMR·NMRShiftDB·Open Access
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 [...]
Tags: ChEBI·Curation·Ontologies
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 [...]
Tags: CDK·Cheminformatics·Open Source
CDK Workshop 2009 kick-off talk
April 20th, 2009 · 2 Comments · Blue Obelisk, Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Databases, Fun, Life of Chris, Open Science, Open Source, People, Scientific Culture, Teaching
I’m collecting some thoughts for my CDK workshop kick-off talk on Monday and I guess I’ll go for the boring regular version, with an introduction to CDK history, followed by some statistical figures and ending with an explanation of the format for the developers workshop on Tuesday afternoon. As anyone can read on our CDK [...]
Tags: CDK·Cheminformatics·Open Source
Open Access Journal of Cheminformatics now live!
March 17th, 2009 · 1 Comment · Blue Obelisk, Chemoinformatics, Conferences and Meetings, Databases, Informatics, Life of Chris, Open Access, Open Science, Open Source, People, Publishing, Scientific Culture, Structure Elucidation, Teaching, Uncategorized
I’m delighted to announce that the first open access journal of our field, the Journal of Cheminformatics, is now live and has published its first articles. Journal of Cheminformatics is a new open access journal from Chemistry Central publishing peer-reviewed research in all aspects of cheminformatics and molecular modelling. It is run by Editors-in-Chief David [...]
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“new open source era … for better drugs”
March 3rd, 2009 · No Comments · Chemoinformatics, Conferences and Meetings, Open Access, Open Data, Open Science, Open Source, People, Publishing, Scientific Culture, Teaching
As we learn from a rather poorly written article over at xconomy, “Biology has never really had a social-networking movement like open-source computing, where thousands of loosely-affiliated people around the world pool brainpower to make better software”. If you translate that into what was needed for biology (or chemistry) according to the xconomy author, it [...]
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CDK Workshop at EBI on April 20/21
February 17th, 2009 · 1 Comment · Blue Obelisk, Chemistry Development Kit, Conferences and Meetings, Fun, Life of Chris, Open Science, Open Source, People, Teaching
The CDK team is glad to announce the Spring 2009 CDK workshop held at the European Bioinformatics Institute (EBI). More than two years have passed since the last CDK workshop in Cologne and we hope to have these great events more regularly again. We are glad that the EBI Industry Program as well as the [...]
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