SteinBlog » Cheminformatics

Web chemistry components in JavaScript

Christoph Steinbeck — Thu, 08 Oct 2009 12:33:36 +0000

non-chem doodle by Dan Paluska

Colleague Noel O’Boyle has already reported it: There is now an open collection of javascript-based chemistry components for the web, called ChemDoodle, released under GPL license by iChemLabs, inc. The stuff looks really neat.

The collection comprises viewers, an editor, a look-up component (try entering accession numbers such as “1″, “2″ or “3″ (you get the point?)) and more. The interesting part is that no java applet needs to be loaded and things are supported by the browser directly. This does not mean that they didn’t have to go through a hell of compatibility testing.

Some seats left at German Conference on Cheminformatics 2009

Christoph Steinbeck — Thu, 08 Oct 2009 11:53:38 +0000

In Goslar's old town ((c) Philipp Andre)

There are a few seats left for the 5th German Conference on Cheminformatics in Goslar and we’ll extend the deadline a bit to give you the chance to register if you haven’t done so.

The GCC is a great chance to meet with around 200 other participants from all areas of life science informatics and listen to talks about the latest research in the field. This year we have an exciting collection of keynote speakers with topics ranging from modelling of biological systems and systems chemistry via computer-aided material design to the latest developments in ChemSpider.

The program is complemented by 60 posters and again prices will be awarded for the three best posters.

Goslar itself is a wonderful place to visit, with its two UNESCO world heritage sites, the old town centre and the ore mine.

We are looking forward to meeting you in Goslar. Registration is still open.

CDK Workshop 2009 Wrap-up

Christoph Steinbeck — Thu, 23 Apr 2009 09:14:38 +0000

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 chemical search engine, scripting of CDK from within Bioclipse and CDK-based workflows in KNIME. The second day brought talks about science and applications based on CDK by John van Drie, Asad Rahman und Oliver Karch. I reported earlier on those talks.

This official part was followed by a developers workshop in the format of an unconference. Participants suggested topics on the fly and then voted with their feet. The topics that then made it where:

all of which reported their results on the CDK wiki.

Another important outcome was a movement to join forces in creating and maintaining joint CDK-based plugins for KNIME and Bioclipse. There is a lot of synergy to be harvested. Licensing problems will need to be overcome but that seems doable.

Oliver Karch about Molwind – Using CDK to Visualize Molecule Spaces in a Geospatial Context

Christoph Steinbeck — Tue, 21 Apr 2009 09:57:56 +0000

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 is then used for display. The map-like structure of the spaces visualized by projecting structures on a globe in this way depends of course on some kind of relationship leading to geographical neighborhood, such as similarity, common fragments, etc. They have come up with a sophisticated scheme of layers for visualization and providing a good zooming experience.

A nice thing about molwind is that is they have open-sourced it. It lives at molwind.org

Asad Rahman on Small molecules and reaction mechanism – Rewiring the enzyme space

Christoph Steinbeck — Tue, 21 Apr 2009 09:23:20 +0000

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 with finding shortest pathes in a metabolic network. The problem here lies in finding maximum common substructures or calculating similarities which allow to judge which molecule in a multi-component reaction was formed out of which product. He show a number of application cases, talks about performance problems of CDK MCSS and then introduces his new tool called “Small Molecule Subgraph Detector (SMSD)”.

John van Drie’s talk on CDK in Virtual Drug Discovery

Christoph Steinbeck — Tue, 21 Apr 2009 09:05:08 +0000

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 costs a hundred thousand bucks. In 2015, John envisions drug discovery to be largely outsourced and distributed in a FIPnet, a network of alliances. He also believes that the limited access licensed comp chem software will be displaced by ubiquitous open source software. He encourage us to think about what single pieces of software are actually missing to get this distributed scenario.

In a second part, he jumps to explaning a typical use case, a pharmacophore-based virtual screening setup. After a historical view back, he showed his work with Rajarhi Guha on CDKPsearch. John and Rajarshi have created an XML pharmacophore description, which allows to define a pharmacophore, walk through an SDF and find fitting compounds. John has used the package in three different application scenarios with three different companies.

To finish, John brings up the question what we would need to use a pharmacophore setup to mine the data in ChEMBL, the new Chemgenomics Resource at EBI.

Thorsten Meinl and Bernd Wiswedel talking about CDK workflows in KNIME

Christoph Steinbeck — Mon, 20 Apr 2009 16:52:06 +0000

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 CDK 1.2, the combination of KNIME and CDK will really rock.

For all of you out there, I’ll urge you to download KNIME from http://www.knime.org/ and try it out.

Ola Spjuth talks about “Accessing and scripting CDK from Bioclipse”

Christoph Steinbeck — Mon, 20 Apr 2009 16:42:20 +0000

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 extended set fo phantastic cheet sheats, which the user can simply run and which translate into Bioclipse scripts which are downloaded via a GIST repository. These cheat sheets can be downloaded via Bioclipse’s software update feature and I urge you to try them out.

Mark Rijnbeek’s talk about CDK and databases

Christoph Steinbeck — Mon, 20 Apr 2009 15:17:07 +0000

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 machine (called “Aurora”).

Mark points out a few performance issues (finding all rings in a Bucky Ball ).

He then goes into how (and why) to use a combination of the CDK fingerprinter and the CDK subgraph ismorphism to achieve a good performance in chemical database searching. Mark has put up an exercise on http://www.ebi.ac.uk/~markr.

Feel free to go ahead and fill the gaps.

Egon’s introductory talk about getting started with CDK

Christoph Steinbeck — Mon, 20 Apr 2009 14:08:52 +0000

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 really nice environment for writing CDK code. You can say things like

import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.*;
import org.openscience.cdk.atomtype.*;
import org.openscience.cdk.config.*;
import org.openscience.cdk.tools.manipulator.*;
import javax.vecmath.Point3d;

molecule = new Molecule();
atom = new Atom(Elements.CARBON);
molecule.addAtom(atom);
matcher = CDKAtomTypeMatcher.getInstance(
DefaultChemObjectBuilder.getInstance()
);
type = matcher.findMatchingAtomType(molecule, atom);
AtomTypeManipulator.configure(atom, type);
println “Atom type: $type.atomTypeName”

As you can see, you do not need to handle things like Exceptions or Data Types. Groovy, like most other scripting environments will handle that for you.

If CDK.jar is in your CLASSPATH, you can run this code inside GroovyConsole and you’ll get “C.sp3″ as an output.

Egon’s course material have many more examples.