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.
Entries Tagged as 'Scientific Culture'
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
Tags: NMR·NMRShiftDB·Open Access
ChemSpider aquired by the Royal Society of Chemistry
May 11th, 2009 · 3 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 [...]
Tags: ChemSpider·RSC
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
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 [...]
Tags: CDK·Cheminformatics·Open Source
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 [...]
Tags: CDK·Cheminformatics·Open Source
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 still [...]
Tags: CDK·Cheminformatics·Open Source
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 [...]
Tags: CDK·Cheminformatics·Open Source
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 [...]
Tags: CDK·Cheminformatics·Open Source
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 [...]
Tags: CDK·Cheminformatics·Open Source