First Call for Papers:
Computational Aspects of Metabolomics
239th ACS National Meeting
San Francisco, March 21-25, 2010
CINF Division
We now invite papers for our symposium on computational aspects of Metabolomics at the 239th National Meeting
of the American Chemical Society (ACS) in San Francisco next spring.
Metabolomics studies the occurrence and change of concentrations of small molecular weight chemical compounds (metabolites) [...]
Entries Tagged as 'Chemoinformatics'
1st Call for Papers: Computational Aspects of Metabolomics (CINF Symposium, ACS Spring 2010)
September 7th, 2009 · No Comments · Chemoinformatics, Conferences and Meetings, Hot Science, Life of Chris, Open Science, Scientific Culture
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First paper in Journal of Cheminformatics reaches “highly accessed” status
July 23rd, 2009 · No Comments · Chemoinformatics, Open Science, Publishing, Scientific Culture
Our new Journal of Cheminformatics has as of today, 22/07/09, published 11 papers since its launch in March of this year. One of those 11 papers has now reached the “highly accessed” status after it has recently been downloaded more than 1000 times. This is time for a celebration since it again demonstrates the superior [...]
Tags: highly accessed·Journal of Cheminformatics·Open Access
What do we expect from a chemical structure editor applet?
July 11th, 2009 · 4 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 · 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 [...]
Tags: cheminformatics research·EBI·PhD
ChEBI chemistry ontology development funded by BBSRC
May 19th, 2009 · No Comments · ChEBI, Chemoinformatics, Open Data, Open Science, Open Standards
We received our official award letter from BBSRC Tools and Resources Fund today for the ChEBI ontology development grant. Needless to say, we are thrilled. We are now going to work together with Michael Ashburner’s group at the University of Cambridge to align ChEBI with other OBO Foundry ontologies by adoption of the Basic Formal [...]
Tags: ChEBI·Ontologies
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 [...]
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 Oracle-based [...]
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 [...]
Tags: CDK·Cheminformatics·Open Source