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 [...]
Entries Tagged as 'Chemistry Development Kit'
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
Tags: JChemPaint·Open Source
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
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 his talk, he has prepared an [...]
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 a [...]
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 homepage, [...]
Tags: CDK·Cheminformatics·Open Source