As reported in a previous post, the Journal of Cheminformatics has received its first Impact Factor of 3.42. JEditors-in-Chief David Wild (Indiana University, US) and Christoph Steinbeck (European Bioinformatics Institute, UK) commented: “Our aim when we started Journal of Cheminformatics in 2009, was to impact a wide audience with high quality, interesting and relevant cheminformatics research. Three years on, we are delighted at our progress, and we believe our Impact Factor of 3.42 (very high for a first Impact Factor for a new journal) demonstrates the difference our journal is making in the field of cheminformatics and beyond, into other related disciplines of science. Being Open Access, our papers can be read by a wide range of researchers, scientists in industry and independent practitioners.” We also believe that the papers in the following two new thematic series will have a considerable amount of attention from our readers and will contribute to the growing success of the journal in the future.
Announcing Two New Themed Series of Papers, to Be Published in 2012
Semantic Physical Sciences –Fall 2012
Guest Editors: Peter Murray-Rust, University of Cambridge Henry Rzepa, Imperial College London
2012 Herman Skolnik Award winners
A series of papers arising from an invited workshop and symposium to investigate and formalize the use of semantics in physical sciences
Applying primary technologies based on chemical mark-up language (CML) and MathML to create fully semantic declarative scientific objects
Represents output from groups such as CSIRO, PNNL, STFC, Kitware, IUCr, the Blue Obelisk, and the Unilever Centre for Molecular Informatics
The InChI Project –Winter 2012
Guest Editor: Antony Williams, Royal Society of Chemistry
A series of papers describing the applications and utility of the IUPAC International Chemical Identifier (InChI)
Reviews the need for a standard identifier in chemistry, the development of InChI, and its applications, limitations and future developments
Publications will report on the perspectives and research of academia, government labs, publishers, pharmaceutical companies and others
Journal of Cheminformatics has previously published themed series of papers covering:
We just wanted to update you with some good news from the Journal of Cheminformatics. The Thomson / ISI 2011 Journal Impact Factors were just released, and the Journal of Cheminformatics received an Impact Factor of 3.42 – the first year we have been given an impact factor. This is very high for a new journal, and reflects our commitment to publishing interesting, important and high quality research with a wide scope of application in cheminformatics and related fields, with maximum accessibility. The impact factor compares very favourably with other much more established journals, both open access and subscription (e.g. BMC Bioinformatics = 2.75; PLoS ONE = 4.092).
Of course Impact Factors are not everything, and there has been much discussion recently about article-level metrics being more informative than proprietary journal-level metrics. We’re thus pleased that the Journal of Cheminformatics is now supplying a variety of article-level statistics in the “about this article” section, including the increasingly discussed altmetric score (http://altmetric.com/help.php)
So thanks to all of you who made the Journal of Cheminformatics such a success, and we look forward to a bright future for the journal!
David Wild & Chris Steinbeck
Editors-in-Chief, Journal of Cheminformatics
The MetaboLights repository aims to become the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. The European Bioinformatics Institute (EMBL-EBI) ensures long-term stability and maintenance of the resource. Deposited datasets are assigned a stable identifier of the form MTBLS1 (the first dataset ever deposited in MetaboLights). These identifiers, like other stable identifiers in Bioinformatics, can be used to mark datasets in publications or merge data in systems biology applications.
Like all other EBI resources, the MetaboLights database is completely open to the public, including open access to the data. Data are made available in publicly accepted open standards compliant with community standards (BioSharing), including Minimum Information for Biological and Biomedical Investigations (MIBBI) checklists. The software is open source and adheres to the promotion of open source file formats, such as mzML and nmrML. One of the main submission channels for MetaboLights use is the ISA Tools Suite.
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.
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.
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 Find phone , 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.
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.
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)
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.
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
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 Find phone , 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.
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