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 [...]
Entries Tagged as 'Conferences and Meetings'
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
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
Egon’s introductory talk about getting started with CDK
April 20th, 2009 · No Comments · Chemistry Development Kit, Chemoinformatics, Conferences and Meetings, Life of Chris, Open Science, People, Scientific Culture
After my opening talk at the CDK workshop, Egon Willighagen gave an introduction on how to get started with the CDK. He uses the scripting environment Groovy to demonstrate things. Egon has prepared a LaTeX document with his teaching material as well as the code examples on at http://pele.farmbio.uu.se/groovy. Turns out that Groovy scripting is [...]
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
3rd International Biocuration Conference in Berlin
April 17th, 2009 · No Comments · Conferences and Meetings, Life of Chris, Open Data, Open Science, Open Standards, People, Publishing, Scientific Culture
I’m attending the 3rd International Biocuration Conference in Berlin, which looks like a pretty successful meeting in terms of numbers of participants. Seems like somewhere between 100 and 200 participants. It looks like the time for recognition for biocuration and curated biological resource has come. The International Society for Biocuration has been inaugurated yesterday. People [...]
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ChEBI at the Fall 2009 ACS meeting in Washington
March 27th, 2009 · No Comments · Conferences and Meetings, Databases, Life of Chris, Open Data, Open Science, Open Standards, Publishing, Scientific Culture
I’ve been invited to present our ChEBI ontology at the 2009 Fall Meeting of the American Chemical Society. Here is our abstract: ChEBI – An open ontology for Chemical Entities of Biological Interest Paula de Matos (1), Kirill Degtyarenko (2), Marcus Ennis (1), Janna Hastings (1), Inma Spiteri (1) and Christoph Steinbeck (1) (1) European [...]
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ACS Meeting Salt Lake City
March 23rd, 2009 · No Comments · Chemoinformatics, Conferences and Meetings, Life of Chris, Publishing, Scientific Culture
I’ve just arrived at the ACS meeting in Salt Lake City. The trip was a real nuisance, 19 hours or so, and I always ask myself why I do this stuff.Still, after a fantastic breakfast in my even more fantastic hotel, the Grand America Hotel (review pending), and now being at the meeting, is is [...]
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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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