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What is man but that lofty spirit – that sense of enterprise.

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Open PhD position in Steinbeck group (Cheminformatics and Metabolism)

May 29th, 2013 · Open Science

Where we live: EBI Main Building on Genome Campus

Where we live: EBI Main Building on Genome Campus

We have an opening for a Ph.D. position in Chris Steinbeck’s cheminformatics and metabolism team at the European Bioinformatics Institute (EBI) in Cambridge, UK.

Ph.D. topics are available in a wide range of areas such as analysis of metabolomics experiments, metabolism, computational natural product biochemistry, elucidation of natural products, text mining and image processing, and more. Applications should be submitted through the EMBL International Ph.D. programme.  Ph.D. students successfully pursuing and completing their projects will retrieve their Ph.D. from the University of Cambridge, UK.

The group leaders at the EBI recruiting in this round are Sarah Teichman, Alex Bateman, John Overington and Chris Steinbeck. Candidates invited to the final assessment have the opportunity to consider all of the recruiting groups. The registration and submission deadlines are approaching quickly.

 

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More personal

January 9th, 2013 · Fun, Leisure, Life of Chris, People

Courtesy of http://www.flickr.com/photos/saverello/

This blog has been mostly about my work so far and was labelled “A molecular-informatics weblog”. For a while, however, my group has also been running its own blog at http://metabolights.blogspot.com/ and I will use this group blog from now on for postings about bioinformatics, cheminformatics, metabolism, etc.

So from now on, this blog will be about person stuff and will be more diverse. I will make sure that the blog is not listed in, e.g. the chemical blog space anymore.

Hope that some of you will still be interested in the posts :-)

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Two new thematic series in the Journal of Cheminformatics

August 10th, 2012 · Open Science

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

ImageGuest 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

ImageGuest 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:

To find out more and to stay up-to-date

Register for updates  /  Read our Blog  /  Follow us on Twitter

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Journal of Cheminformatics receives Impact Factor of 3.42

July 4th, 2012 · Chemoinformatics, Hot Science, Life of Chris, Open Access, Open Science, Publishing, Scientific Culture

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

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MetaboLights official launch at Washington Metabolomics Society Meeting

July 3rd, 2012 · Open Science

The MetaboLights repository for metabolomics data has officially been launched at the Metabolomics Society Meeting in Washington, June 25-28, 2012.

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.

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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.

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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.

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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)

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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.

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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.

 

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