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.
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.
First Call for Papers:
Computational Aspects of Metabolomics
239th ACS National Meeting
San Francisco, March 21-25, 2010
CINF Division
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 puttygen ssh , 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.
Our new Journal of Cheminformatics has as of today, 22/07/09, published 11 papers since its launch in March of this year. One of those 11 papers has now reached the “highly accessed” status after it has recently been downloaded more than 1000 times. This is time for a celebration since it again demonstrates the superior model of Open Access publications.
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 and the BBSRC. We have a long-standing history of promoting open access to scientific publications and data, and of publishing our software as open source projects [e.g. 4,5] and we are therefore delighted that our funding agencies now promote these principles and support us in our goal to make all of our tax-payer funded research and development openly available. In all of our recent grants we have promised to deliver the software infrastructure of our databases as open source software to the scientific community.
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.
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.
In a heroic act, our collaborator Dan Gezelter, University of Notre Dame, has unearthed an historical document about our Chemistry Development Kit (CDK) from a SCSI DDS-4 tape he found somewhere on his attic. This morning, I found an email from Dan in my Inbox saying:
I finally located a working SCSI DDS-4
tape drive and found a tape of the
appropriate age which had copies of those pictures.
I'll spare you the details of the hardware hacking
required, but we do have the original images attached below.
I hope they are useful at the next CDK meet-up, and I'm sorry
it took so long to line up the tape drive.
All the best!
--Dan
Thanks, Dan – I appreciate what you went through.
Now, why that hype from my side? Well, first of all because it is a piece of CDK history, in fact the earliest possible piece of documentation for the CDK. Second, because it is a piece of personal history. And third because is nicely shows how fragile our modern way of handling digital documents is.
So here is the background story: After I had written and published my first Java cheminformatics toolkit, the so-called CompChem classes, which formed the basis for my first version of JChemPaint and also for my structure elucidation package SENECA, it quickly became clear that there were some design flaws, including the whole thing not really being object-oriented, and that the package needed a re-write. By that time friend Egon had come on board, contributed a lot to JChemPaint development, and we also had joined the development of Jmol, now the worlds premier open source applet for 3D vizualization of molecular structure, started by Dan Gezelter.
In August 2000, Dan had just moved to his first assistant professorship at the University of Notre Dame in Chicago and it happend that Egon and I were going to a conference in Washinton, so we decided to stop over at ND and spend some time with Dan to discuss how a new cheminformatics toolkit should look like. During the brainstorming sessions in Dan’s office, the attached snapshot was taken from Dan’s whiteboard. On the flight back to Europe, I wrote the first version of the base classes and released them. The CDK grew rapidly and the rest is history. The photo was available on Dan’s Open Science website for a while but fell victim of some re-arrangment or upgrade of the site.
This year, we had held the fourth CDK workshop, for the first time at the European Bioinformatics Institute (EBI), and it occurred to me that that picture should be part of any introductory talk about the CDK. Having realized that I could not find the picture anywhere, and neither could Egon, I contacted Dan literally five minutes before the workshop, he immediately recognized the pressing nature of my request 🙂 and promised to look at the old backup tapes he knew where lying around somewhere on his attic. And so he did. Understandably, he didn’t make it in time for the workshop, but too be honest I did not think that he would find anything and so I’m extremely happy now.
The Journal of Cheminformatics, of which I have the pleasure to be editor-in-chief together with David Wild in Indiana, has now published its first few articles. We’ve been busy selecting and reviewing papers which we feel suitably demonstrate the scope of knowledge and quality we are looking to cover in the new journal. I think this is a good time to say ‘Thank you’ to the guys at Chemistry Central who keep the things running and do the real work, especially to Jan Kuras without whom this would not be possible.
Let me point that the article-processing charge has been waived for all papers published in Journal of Cheminformatics until end-August. We encourage you to support our new journal by submitting your papers to Journal of Cheminformatics, and also encouraging your colleagues to submit their papers too. This will help build a critical mass of high quality papers to attract further interest, submissions and citations, and help establish the journal amongst the research community.
Goslar’s old town is a UNESCO world heritage site.
We are inviting the submission of abstracts for talks and posters in the following plenary sessions:
Chemoinformatics and Drug Discovcery
Chemical Information, Patents, and Databases
Molecular Modelling
Computational Material Science and Nanotechnology In addition other highlights in the field of Computational Chemistry are also welcome.
Invited Speakers this year are:
Karl-Heinz Baringhaus, Sanofi-Aventis, Frankfurt am Main/D
Knut Baumann, University Braunschweig, Braunschweig/D
Günter von Kiedrowski, University of Bochum, Bochum/D
Ekaterina Ryjkina, Henkel, Düsseldorf/D
Christoph Sotriffer, University of Würzburg, Würzburg/D
Eberhard Voit, Georgia Institute of Technology, Atlanta/USA
Antony Williams, ChemSpider, Wake Forest/USA
Visit the conference website at www.gdch.de/gcc2009 for more information or access directly the Call-for-Paper (PDF)
The deadline for the submission of abstracts is 30 July 2009! Again we limit the number of participants to max 200. So please register early.
In addition we will introduce a limit of 60 posters.
I’m glad to announce that the recent round of recruitment for the ChEBIteam has been completed. We have two new colleagues, Steve Turner, our new Chemistry Curator, and Adriano Dekker, our new Software Engineer. Both will work with us to make ChEBI fit for the inclusion of more then 500.000 new ChEBI entries. Those chemical structure were brought to EBI by my esteemed colleague John Overington as part of the ChEMBL database, formerly known as Starlite, Candistore and Drugstore. ChEMBL obviously contains much more than chemical structure, namely their activities against around 4000 biological targets and other properties, and the ChEMBL resource will be manage by John and his team. ChEBI will provide the chemical structure, substructure and similarity searching for the ChEMBL structures and we will soon report on our recent advancements in this field.
For now, I wish Steve and Adriano a good start in my team. I’m sure we are going to have a good time together.
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