CDK-Taverna workflow

We are glad to announce that our article about CDK-Taverna, an open workflow solution for cheminformatics, is now online on BMC Bioinformatics. CDK-Taverna, which lives at http://www.cdk-taverna.de/, features more than 160 workers for various tasks in molecular informatics.

The workflow paradigm allows scientists to flexibly create generic workflows using different kinds of data sources, filters and algorithms, which can later be adapted to changing needs. In order to achieve this, library methods are encapsulated in Lego(TM)-like building blocks which can be manipulated with a mouse or any pointing device in a graphical environment, relieving the scientist from the need to learn a programming language. Building blocks, so-called workers, are connected by data pipelines to enable data flow between them, which is why pipelining is often used interchangeably for workflow.

Now, this does of course include the chemical structure editor mentioned above. As a pure coincidence , I had started a chemical structure editor in the late 1990s, called JChemPaint, which was later influenced a lot contribution from Egon Willighagen and others. JChemPaint experienced several rounds of re-architecture but for some reason it was never really considered to be production-ready.

We are now taking another go at it, at its applet version to be precise. And this time my charming profession team will give it a try and I’m confident that this time we’ll get it right. The fact that we are not alone in developing JChemPaint is both boon and bane. Everyone in an open source project is happy about harvesting the man-power of others but on the other hand you loose some control. While we, for example, are looking at the applet from a usability and GUI perspective, Egon and Arvid at Uppsala do a re-architecturing of the controler (the piece of software dealing with the user input) in order to make it maintainable through modularization.

So, in order to get an idea of what we actually need, we decided to do an analysis of a) existing structure editor applets and what they to well and not so well and b) how our curators do their work. For the latter, we did a screen recording of our curators’ work and looked at the type of functionality they used and how they did this (keyboard shortcuts, mouse, buttons, menus). The preliminary results are available on the JChemPaint wiki and we are more than happy to receive input from the community about this.

The European Bioinformatics Institute (EBI)

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 is wide open, going from metabolomics via automated structure elucidation of metabolites to mining chemical information from the printed literature, and more. Your own suggestions are of course welcome.

The EBI is the world’s largest open provider of biological and chemical information.We are located, together with the Sanger Institute for Genome Research, on the beautiful campus of Hinxton Hall, a few miles south of Cambridge.

One of the small lakes on the Wellcome Trust Campus in Hinxton

Our PhD students are enrolled with the University of Cambridge.

The important part for now: The application deadline for the Fall PhD selection is July 15, 2009. And: Please drop me a note if you applied.

Assigned proton spectrum in NMRShiftDB

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.

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 chemical entities (and not compounds, as I wrote earlier – we also have classes of compounds and abstract concepts) with 74 of them new submissions entered via the ChEBI submission tool. The next ChEBI Release will be on the 27 May 2009.

See our entity of the month, Ethyl formate.

All data are also available on the public FTP site:

ftp://ftp.ebi.ac.uk/pub/databases/chebi/

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:

• Clojure
• Mining ChEMBL with CDK pharmacophore stuff
• Threading group
• Top 10 improvements (CDK WS 2009 unconference)
• JChemPaint/Rendering

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.

As anyone can read on our CDK homepage, the CDK was started because my old compchem java classes that I had written for the first version of my structure elucidator SENECA and which where also the basis for the first JChemPaint releases needed a re-write (they where actually not bad and pretty fast, but not really object-oriented). By that time, friend Egon had come on board and so we took advantage of a joint visit to Jmol creator Dan Gezelter at Universtiy of Notre Dame to start the redesign. Unfortunately, we lost the two screenshots from Dan Gezelter’s whiteboard at nd.edu where we sketched the object hierarchy which is still largely in place today.

So, here is the current status of CDK in numbers:

• In September 2009, CDK will turn 9 years old and we already start planning for the 10th anniversary workshop.
• Its code base is more than 90,000 lines of code in more than 900 classes and over 9000 methods.
• As of today, 20/04/2009, CDK on Sourceforge has 67 registered developers and
• 86 (111) people are subscribed to the cdk-devel (cdk-users) mailing lists.
• According to Ohloh, CDK is now worth $ 4.6M and took an effort of 84 person years to create.
• The CDK article published in 2003 has been cited 68 times according to Google Scholar (I could not get my VPN to work so I do not know what WebOfScience says about our current citation count)
• According to SourceForge, CDK has been downloaded 90,000 times since 2001.

On the first workshop day, we’ll have tutorials on

• How to get started with CDK, given by Egon Willighagen
• CDK and databases, by Mark Rijnbeek
• CDK and Bioclipse, by Ola Spjuth
• CDK Workflows in KNIME, by Thorsten Meinl and Bernd Wiswedel

followed by the workshop dinner and a second day with scientific talks John van Drie, Asad Rahman and Oliver Karch.

The final discussion will include a presentation by Mark Forster, Syngenta, on his observations on the usability issues of CDK in industry. We also owe Mark a lot for creating the freely distributable linux image with the CDK and all the CDK related software used at the workshop.

On Tuesday afternoon we’ll have a developers workshop, which, traditionally, has the format of an unconference. The ideas for this format are taken from a concept called “Open Space Technology“, which we only discovered after having practised them for more than 5 years . To be fair, OST conceptualizes things nicely and relieves one from figuring out how to run meetings as openly as possible. Citing from the Wikipedia articles linked above, the idea is to have a facilitated, participant-driven conference centered around a theme or purpose, in a self-organising process; participants construct the agenda and schedule during the meeting itself.

A facilitator (me in this case) introduces the principles of OST to the participants. Participants then write the title of a session they would be interested in on a piece of paper, walk to the front of the auditorium and announce the title. If a participant proposes a topic, he or she should be passionate enough about the topic to lead the respective session.

OST philosophy is based on four rules and a law:

1. Whoever comes is the right people: this alerts the participants that attendees of a session class as “right” simply because they care to attend
2. Whatever happens is the only thing that could have: this tells the attendees to pay attention to events of the moment, instead of worrying about what could possibly happen
3. Whenever it starts is the right time: clarifies the lack of any given schedule or structure and emphasises creativity and innovation
4. When it’s over, it’s over: encourages the participants not to waste time, but to move on to something else when the fruitful discussion ends

There also exists another tentative “law”, usually referred to as the “Law of Two Feet“ (or “The Law of Mobility”), which reads as follows: If at any time during our time together you find yourself in any situation where you are neither learning nor contributing, use your two feet. Go to some other place where you may learn and contribute.

Having said all this, I hope that this largest CDK workshop ever will be asuccess and most importantly fun for everyone. We’ll keep you informed at the CDK 2009 Workshop wiki page.

At least, the article informs us about lots of money being pumped into another collaborative effort to exploit systems biology to make better drugs, which might be a good thing. I’m having a hard time to understand the fundamental difference between this and existing open approaches, but I’m happy to learn. Part of this lack of understanding comes from a lack of meat in this article. Maybe one of my readers can comment.

We are glad that the EBI Industry Program as well as the EBI outreach and training department are sponsoring the event. This means that things will be much more organized as they used to be . We are going to have one day (lunch time to lunch time the next day) of tutorials on how to use CDK and talks on research using the CDK. Afterwards, we’ll have our usual free-form developers workshop for the rest of the second day with all the usual fun. Both the evening of the 20th and the 21st will be opportunities for enjoying refreshments. We also have a small nominal registration fee of 50 Pounds to cover the costs for the workshop dinner and other food and drinks.