So, while Steinblog was about my scientific life and event or news related to it, my travel blog reported about two other aspects, the need to travel a lot and the better and less good places that I encounter as well as my passion for good food (liquid and solid) and the places where you get it. I called this travel blog “Reports from a quest for quality and silence” because that’s what it is. And quality and silence is hard to find.

A short while ago I stayed at the Marriott Metro Center in Washington during the 2009 ACS Fall National Meeting. The first night was good, the room is nice and reasonably quiet, as requested. My satisfaction received a first hit when I tried to have breakfast the morning after and, after being seated, found myself  between two competing sources of loud music, one from the lobby and one from the bar in the breakfast restaurant. So much for my quest for silence The local starbucks did a much better job, so I had breakfast there. Overall, the Marriott Metro Center gets a good rating:

Location: 8/10, two blocks away from the conference center, $50 by taxi from the airport.

Room: 7/10 Could be bigger but well fitted with everything you need. Nice wide LCD TV. Internet for $12 a day.

Lobby and Chill-out areas: 5/10. Lobby area is too small, as is the seating area with too few sofas and chairs.

Breakfast: 3/10 See above. Couldn’t really test it but even without the music the place feels a bit like eating in the middle of a highway.

Room Service and Laundry: 8/10, Fast, reliable.

Concierge: 8/10 Very friendly and professional.

Gym: 9/10, well equipped, spacey, every machine you need, yoga mats available.

Overall, my impression was more like 7/10.

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.

We now invite papers for our symposium on computational aspects of Metabolomics at the 239th National Meeting
of the American Chemical Society (ACS) in San Francisco next spring.

Metabolomics studies the occurrence and change of concentrations of small molecular weight chemical compounds (metabolites) in organisms, organs, tissues, cells and ultimately cell compartments in the context of environmental changes, disease or other boundary conditions. It does this by means of spectroscopic and chromatographic techniques and by observing at once not only a few but all compounds visible to the particular technique used. As such, it is a field at the boundary between chemistry and biology, helping to answer biological questions using analytical chemistry and cheminformatics techniques.

The metabolomics symposium at the 239th ACS national meeting in San Francisco invites submissions of talks about computing, informatics as well as chemical information aspects of metabolomics. Topics could include the analysis of metabolomics experiments, metabolomics databases, computer-assisted structure elucidation of metabolites and more. Abstracts may be submitted via http://abstracts.acs.org. You’ll find the metabolomics session as part of the CINF division symposiums. Deadline is October 19, 2009. In case of questions, please email Christoph Steinbeck at steinbeck@ebi.ac.uk.

ChEBI Release 57 now contains links to NMRShiftDB. Search ChEBI for “caffeine”, for example, and you find the link to the carbon NMR spectrum of caffeine on the “automatic XREFs” page of ChEBI, in the “Small Molecules” section.

ChEBI now contains just under 17,963 manually annotated entries of which 108 entries have been submitted via the ChEBI Submission tool  (www.ebi.ac.uk/chebi/submissions). The next ChEBI Release will be on the 24 June 2009.

See our entity of the month, Oseltamivir.

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.

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

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.

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

• 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.