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.

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.

At EBI, I will re-establish my research group and become leader of the chemoinformatics-related service teams, including the ChEBI and Reactome teams.

Future Directions at EBI

All of my ongoing research projects (SENECA, Bioclipse, CDK) will be continued at EBI and constitute a solid base for the rapid formation of a strong research group.

In addition, there is a plethora of fascinating modeling and data-analysis projects to be envisioned in Systems Biology in addition to the final grand goal of achieving a whole-cell or even whole-organism metabolic simulation. At EBI we will pursue the implementation of a metabolic simulation environment, with the goal of creating novel approaches to drug discovery. The “one-target, one-drug” paradigm still followed in many pharmaceutical chemoinformatics studies presented at conferences has clearly not lead to an increased number of drugs on the market and it is most importantly not capable of preventing failures of novel compounds in late clinical trials. Only a systems biology approach to drug discovery, taking into account transport phenomena, the interaction with all or as many targets as possible may allow us to make correct predictions.

To alleviate the abysmal lack of chemical data in some crucial areas of Systems Biology, we are interested in text, or better, publication mining techniques. In an ongoing collaboration with the Center for Molecular Informatics at Cambridge University, we will aim at creating an automated workflow for the extraction of molecular structures and data from the printed literature – past and present.

The Steinbeck Group offers PhD student positions via the EBI’s PhD program in 2008. Applications need to be submitted by Dec. 17 2007.

As leader of the chemoinformatics-related service teams at EBI (ChEBI, Reactome, etc.), my emphasis will be to enhance the existing resources with complete chemical semantics and raise funding for a substantial growth of the resources while securing their quality. The chemistry-related databases at EBI have the chance to become a valuable resource in pharmaceutical and medicinal chemoinformatics and serve as an integration point between chemo- and bioinformatics.

I wonder how it would translate into modern day terms and if there are any people out there below the age of 40 who know that the author means by “Trash-80s”.

I’m sure a lot of you were dead jealous when you saw the wonderful Blue Obelisks given by PMR to Bob, Geoff and me. Well, don’t despair. Here’s what to do:

First, get two A4 sheets of thick, stable paper, one in a nice blue, the other one in a color of your choice. Also, get some paper glue and a pair of scissors.

[[image:bao-01.png:Paper, Glue and Scissors:center:0]]

Next, download the following PDF documents to your hard disk. They contain printable paper models of an obelisk and a foundation.

[[download:obelisk-small.pdf:icon::]]

[[download:foundation.pdf:icon::]]

Now, print the obelisk model on the blue paper and the foundation model on the other piece. Use your scissors to cut out the models. Use a moderatly sharp item to score the models along the printed lines. Here is what you get:

[[image:bao-02.png::center:0]]

Glue things together:

[[image:bao-03.png::center:0]]

[[image:bao-04.png::center:0]]

Finally, glue the Blue Obelisk on top of its foundation and ready you are:

[[image:bao-05.png::center:0]]

Your colleagues will envy you for this beautiful piece.