SteinBlog

A molecular informatics weblog

SteinBlog header image 1

Open Position for a Scientific Database Curator/Annotator in ChEBI team

April 11th, 2012 · ChEBI, Chemoinformatics, Databases, Open Data, Open Standards, Publishing, Scientific Culture

An early chemistry lab

An early chemistry lab

We are looking for a Scientific Database Curator/Annotator to work on the ChEBI (Chemical Entities of Biological Interest) project within the Cheminformatics and Metabolism Team. The position is based at the European Bioinformatics Institute (EMBL-EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK.

The successful applicant will work on the existing ChEBI database, in particular on extending it towards better coverage of natural products and metabolites. (S)He will also annotate entities as requested by our users.

The Chemoinformatics and Metabolism Teams conduct research and create community resources for Chemoinformatic and Metabolism research. We are a friendly, multi-national team with collaborations all around the world. The aim of the ChEBI project is to provide a high-quality, hand-curated chemistry database to the biomedical community, to standardise chemical and biochemical terminology across biological databases and to develop a chemical ontology.

Qualifications and Experience

Applicants should have a degree in Biochemistry/Chemistry and ideally some years professional experience. Knowledge of natural products and metabolites would be a definitive plus. Self-motivated candidates with good communication skills and ambition to work in an international field are invited to apply.

Application Instructions

Please apply online through www.embl.org/jobs

Additional Information

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation.

Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

Note that special visa requirements apply to employees from non-EU countries working at EMBL-EBI in the UK. The period of work does not qualify them for the Highly Skilled Migrants Programme.

→ No CommentsTags:

Call for abstracts for Washington Metabolomics Society Meeting, June 25-28, 2012

March 19th, 2012 · Open Science

 

Thanks to Epicadam for providing this

Registration and submission of abstracts is now open for the 2012 Metabolomics Society Meeting in Washington, June 25-28.

We put together an exciting programme with sessions and workshops in a number of areas. Allow me to draw your attention to the two sessions I’m helping to organize, the Databases & Data Analysis session and Funding Opportunities and International Initiatives.

The Databases & Data Analysis session will highlight the characteristics of existing and future metabolomics databases and their application to high through-put profiling, biomarker identification, and the development of advanced algorithms for data processing and analysis.

This Funding Opportunities and International Initiatives session provides information on funding opportunities around the world for metabolomics research. Scientific advances can be accelerated by working across international borders. Likewise, major funding opportunities available in various continents including North America, Europe, and Asia will promote global research on metabolomics. Specific examples include Funding Opportunities in the USA (NIH Common Funds, NSF, and EPA), Metabolomics in Australia or Europe, and Lipid and Mass Spectrometry Consortium in Singapore.

We are very much looking forward to receiving your abstract and to see you in Washington.

→ No CommentsTags:

Philadelphia Symposium on Cheminformatics Opportunities in Personalized Medicine and Chemogenomics.

March 19th, 2012 · Chemoinformatics, Conferences and Meetings, Hot Science, Life of Chris, People, Scientific Culture

We are accepting submissions of abstracts for consideration for an ACS Division of Chemical Information (CINF) Symposium on Cheminformatics Opportunities in Personalized Medicine and Chemogenomics.
This session will bring together researchers investigating computational chemistry and cheminformatics to study the development of drugs based on our knowledge of genomes and to develop better methods to personalize medicine.  This broad and multidisciplinary session 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 and personalized treatments.

You should contribute to and attend this session if you are a researcher interested in drug discovery, metabolism and personalized medicine, 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.
Contributions could include but are not limited to the areas of:

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

Presentations will be 40 minutes, including time for questions. The deadline for submitting an abstract for consideration is March 30, 2012.

Abstracts may be submitted via: http://abstracts.acs.org.

Please contact the co-organizers if you have any questions and to discuss a paper.

Thank you,

Christoph Steinbeck, Head of Chemoinformatics and Metabolism, European
Bioinformatics Institute, UK (steinbeck@ebi.ac.uk)
David Wild, Assistant Professor of Informatics and Computing, Indiana
University School of Informatics, USA (djwild@indiana.edu)

→ No CommentsTags:

Open position in MetaboLights team (Software Engineer/Bioinformatician/Cheminformatician)

December 9th, 2011 · Open Science

Courtesy of JimmyWayne

We are looking for a Software Engineer/Bioinformatician/Cheminformatician to join the Cheminformatics and Metabolism team at the European Bioinformatics Institute (EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK.

The post-holder will join a project team of currently 4 people to build the new Metabolomics database at the EBI and be part of the larger cheminformatics and metabolism team with around 20 team members in total. This team will closely interact with other teams at the EBI and incorporate existing technology developed in our Institute as well as elsewhere. The responsibilities of the Software Engineer are the design, implementation, documentation, debugging, testing, and support of various software components.

More information as well as the electronic application system here.

→ No CommentsTags:

Upcoming conference: Therapeutic Applications of Computational Biology and Chemistry (TACBAC)

December 9th, 2011 · Chemoinformatics, Conferences and Meetings, Databases, Hot Science, Life of Chris, People, Scientific Culture

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.

 

→ No CommentsTags:

A more complete human, Part 1

November 22nd, 2011 · Leisure, Life of Chris, Open Science, People, Scientific Culture, Teaching

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.

→ 2 CommentsTags:

Postdoc position in my group: Deadline approaching.

September 13th, 2011 · Open Science

Just wanted to make you aware that the deadline on Sep 15 for the chemical information mining postdoc position in my group is approaching quickly. For more information on the position, please refer to http://www.steinbeck-molecular.de/steinblog/index.php/2011/07/10/opening-for-a-postdoc-in-my-group/.

→ No CommentsTags:

Opening for a postdoc in my group

July 10th, 2011 · Open Science

We now have an opening for a postdoc position in my group in collaboration with the group of Dietrich Rebholz-Schuhmann at the EBI. The position is funded for three years by the EIPOD scheme at EMBL.

The proposed work combines methods from image recognition (OSRA, Filippov2009), cheminformatics (CDK ,Steinbeck2003), chemometrics (Gkoutos2003) and text-mining (OSCAR3, Corbett2006, Tiago2009) to extract information relevant to small molecules from the primary literature. The project will deliver methods to discover information about chemical entities linked to their chemical structures and their assigned spectra. The research focus lies on the cross-validation of the extracted information against cheminformatics prediction methods to compensate error propagation and to benchmark prediction methods on published data.

You’ll find a one-page project description on the EIPOD page, together with information on how to apply. If you are interested and have questions, feel free to contact me at steinbeck [at] ebi.ac.uk.

References
Corbett and Murray-Rust. High-throughput identification of chemistry in life science texts. LCNS (2006), 1611-3349
Filippov and Nicklaus. Optical Structure Recognition Software (OSRA). J. Chem. Inf. Model (2009), 49(3), 740–743
Gkoutos GV et al. Chemical Machine Vision. (2003) 43:1342–1355.
Grego T et al. Identification of Chemical Entities in Patent Documents. In: LNCS (2009) 5518:942-949
Guha et al. The Blue Obelisk – Interoperability in Chemical Informatics. J Chem Inform Model (2005) 46(3):991-998
Steinbeck et al. The Chemistry Development Kit (CDK). J chem inform comp sci (2003) 43(2): 493-500

→ No CommentsTags:

ChEBI release 80

June 7th, 2011 · Open Science

ChEBI release 80 is now available, with 25,518 fully annotated at the highest 3* level.

We have an old friend as our entity of the month this time: The Electron.

 

 

→ No CommentsTags:

Therapeutic Applications of Computational Biology and Chemistry 2012 (TACBAC)

June 2nd, 2011 · Conferences and Meetings, Hot Science, Life of Chris, People, Scientific Culture

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.

→ No CommentsTags: