Courtesy of Andres Rueda, Flickr

There are still places available at the 2012 conference on Therapeutic Applications of Computational Biology and Chemistry (TACBAC), 12-14 March 2012, at the Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

This conference will bring together leading researchers investigating computational chemistry and biology techniques as applied to advancing our ability to predict, diagnose and modulate human disease. This broad and multidisciplinary meeting will explore the major challenges in drug discovery and development where innovation in computational approaches and tools can really make a significant and tangible contribution towards novel treatments.  You should attend this conference if you are a researcher interested in drug discovery, or developing or using computational approaches to the development of therapeutics, or if you are a key decision maker in a pharmaceutical or biotechnology company.

Each of the sessions, which progress from identifying disease mechanisms to implementing new therapeutic and diagnostic approaches in the clinic, will bring together experts in both the biomedical and the computational aspects of the topic under discussion. Sessions chairs will encourage discussion and contribution from the attendees.

Session topics
• Clinical implications of individual genomes
• Metabolism and biomarkers
• Computational systems biology
• Discovery of chemical probes
• Modelling xenobiotic metabolism

Registration and submission of abstracts is open now.

Courtesy of GreenNeticen

What does it mean to live a good life? Philosophers have written about this questions for thousands of years, and very often we find surprisingly up-to-date answers and suggestions in texts as old as 2000 years. Sadly, most of the people in our hectic western societies (and the more and more hectic eastern societies and ….) feel that their life is getting out of hand and they grave for answers but ironically feel that they have no time to retreat and read those timeless pieces of advice. On the other hand, there is a rich corpus of new literature and online media dealing with these questions.

I have spent countless hours in the past 15 years thinking and reading and acting about this problem of what it means to live a good life. I’m certainly influenced by humanist ideas and some eastern philosophical streams. I feel that “Mens sana in corpora sana” is a good starting point for thinking about good life. Then, everybody has to define for him or herself, what that exactly translates into.
In this and a couple of following blog items I will try to report on my portfolio of thoughts, sources and solutions

As scientist, we can’t help but being a scientist 24/7. Simply by definition. We are driven by curiosity and encapsulated in an incredibly dynamically moving field. The scientific endeavour doesn’t start at 9 am and ends at 5pm. No way we could stop thinking and working after and before the end or start of a regular work day.  That makes is even more important to create islands of leisure and to indulge in good reading, arts, music, physical practice, being with loved ones and friends.
And the good news is: All of this will make us better at our core profession. We all know that many of our best ideas come at unexpected times and at unexpected places. My wife, a psychiatrist, likes to say: “Don’t disturb your brain while it is doing its job”.

In the September 1st issue of NATURE, you can find two articles that very nicely layout the problem: On page 20, Heidi Ledford  writes about “The 24/7 Lab”, subtitle “Working weekends, leaving at midnight, Friday evening meetings, does science come out the winner?”. She describes one of those restless 24/7 labs led by a scientist who demands late night hours and working over christmas from his staff and who sometimes regrets a bit that he sees his children so rarely. But he drives them to swimming lessons (while he does that, he is efficient by having phone calls with lab members). I have met a number of colleagues over the years who work like this and who were quite intolerant against other scientific lifestyles. An obvious thing to observe is that at least in earlier days, these people lived those demanding lifes on the back of others, such as their partners who stay at home, look after the children and do the household.  Now, don’t get me wrong: I firmly believe that everybody should live the life of their choice, as long as it is concious and doesn’t hurt anyone.

Then again, on page 27, Julie Overbaugh, a team leader in the Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, thinks that ’24/7 isn’t the only way: A healthy work–life balance can enhance research’, and I couldn’t agree more. She delivers an extremely well-balanced opinion, including a paragraph where she says: “To be a successful scientist there are times when it is important to pull out all the stops — when a big grant deadline is looming or a high-impact paper is wrapping up. Sometimes, when we are competing with other labs on an exciting story, I briefly imagine locking everyone in the lab to try to push for results more quickly.” And this is actually very fulfilling, if you know that times of retreat and re-energizing will follow. The most enlightening exercise here is indeed to look back at the life of many successful scientists in the past (just think ‘pre-internet times’), who where not constantly connected, burdened by administration, applying for research money and frantically jetting around the world. There it turns out that more time to think, less communication and long stretches of isolation are very beneficial for fostering intellectual achievements. As a starting point you might watch David Levy’s talk entitled ‘No time to think’ at Google. It is worth-it just for Meng’s introduction

I’m going to stop here. This post was mainly to alert you of these two articles. I had it sitting on my hard disks and now my phd student John May put the article on the table again.

But let me say one last thing: Do not let others dictate how you live your life. Very often they are completely disqualified to do that. An old bon mot says that, on their death bed, very few people regret that they didn’t spend enough time in the office.

Courtesy of Andres Rueda, Flickr

I’m co-organizing the 2012 conference on Therapeutic Applications of Computational Biology and Chemistry (TACBAC), 12-14 March 2012, at the Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

This conference will bring together leading researchers investigating computational chemistry and biology techniques as applied to advancing our ability to predict, diagnose and modulate human disease. This broad and multidisciplinary meeting will explore the major challenges in drug discovery and development where innovation in computational approaches and tools can really make a significant and tangible contribution towards novel treatments.  You should attend this conference if you are a researcher interested in drug discovery, or developing or using computational approaches to the development of therapeutics, or if you are a key decision maker in a pharmaceutical or biotechnology company.

Each of the sessions, which progress from identifying disease mechanisms to implementing new therapeutic and diagnostic approaches in the clinic, will bring together experts in both the biomedical and the computational aspects of the topic under discussion. Sessions chairs will encourage discussion and contribution from the attendees.

Session topics
• Clinical implications of individual genomes
• Metabolism and biomarkers
• Computational systems biology
• Discovery of chemical probes
• Modelling xenobiotic metabolism

Registration and submission of abstracts is open now.

More here.

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.

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.