Database Curator@EBI for InterPro database

(EMBL-EBI seeking to recruit an enthusiastic Scientific Database Curator to join the InterPro team at the The European Bioinformatics Institute (EMBL-EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK.

The post-holder will work as part of a small team maintaining and curating the InterPro database. Their responsibilities will include updating existing InterPro entries, integrating new predictive signatures and adding annotation such as concise, literature-referenced abstracts. Data in InterPro needs to be of a consistently high quality and so potential candidates should have a good attention to detail and a thorough attitude to their work. We believe that understanding our users' needs and providing for them is critically important, and so the curator may be required to attend conferences, workshops or training events in order to meet with users, hear their ideas and expectations, and teach them about InterPro.

The EBI, part of the European Molecular Biology Laboratory (EMBL), provides cutting-edge research, services and training in the field of bioinformatics and is home to world-class resources such as UniProtKB and InterPro. InterPro generates and houses data predicting the functional classification of protein sequences and the presence of protein domains and sites. This information is widely used by genome sequencing projects and is disseminated to a large, global biological research community through web-based databases and software tools.

Requirements: 

The ideal applicant should hold at minimum a BSc. in a Biological Science, preferably with a strong background (e.g. 3 years post-graduate experience) in proteomics, molecular biology, biochemistry, cell biology and/or a related field.

Past work must either include work in a laboratory or in a biological database environment. A good understanding of proteomics and protein evolution would be advantageous, as would a high standard of scientific writing, with experience writing specifically for the web. Familiarity with the use of software tools for nucleotide/amino acid sequence analysis would be an advantage. The role is part of a tightly-knit team, so an ability to communicate ideas and openly discuss potential approaches will be very important. However, applicants should also be able to take their own initiative and work autonomously.

The candidate may be required to describe their work to a wider audience, including end-users of the database, so good presentation skills and an ability to write training materials and teach are a necessity; some of their work may also be published in scientific journals.

No computer programming skills are necessary but a proficiency at using Microsoft Office and a willingness to learn how to use new software tools are a must.

Contact Information: 

http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=48329&aid=15470

About Our Organization: 

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 for the Highly Skilled Migrants Programme.

GSK and Online Communities Create Unique Alliance to Stimulate Open Source Drug Discovery for Malaria

- GSK becomes first company to freely share chemical structures on 13,500 molecules from its compound library
- Alliances formed with leading scientific research communities from private industry and public-domain data provider

courtesy CDD Blog

GlaxoSmithKline (GSK) had teamed up with leading public-domain data providers European Bioinformatics Institute (EMBL-EBI), the U.S. National Library of Medicine (NLM) and the US-based informatics service provider Collaborative Drug Discovery (CDD) to make freely available key scientific information on more than 13,500 compounds that could ultimately lead to new treatments for malaria.

The release of this data marks the first time that a pharmaceutical company has made available the structures of so many compounds and is made possible through the collaboration of the web hosts and their specialist research tools, which will be available at no cost to researchers. The information, which is hosted on websites regularly used by researchers, includes high quality scientific data about the molecules from GSK’s own compound library which have demonstrated potency against the most deadly malaria parasite, P. falciparum.

“We are delighted that EMBL-EBI, NLM and CDD have joined us in this worthwhile endeavour to apply the principles of open source to drug discovery for malaria,” said Patrick Vallance, head of drug discovery at GSK. “Defeating this disease will require many scientific minds working together. We hope researchers from across the world will now use this information to drive further studies, and that other groups from pharmaceutical industry to academia will add their information to this on-line resource.”

This type of data is the first step on the road to developing new medicines. With the structure of the compounds and information about where they affect the malaria parasite, scientists could then carry out further research on these compounds for drug discovery or to understand how these might be used to inhibit the parasite’s life cycle and ultimately lead to new medicines. Opening up this information widely is essentially an example of ‘open source’ tactic being applied to drug discovery.

“Making life-science information openly available to the research community is at the heart of the EMBL-EBI’s mission,” added John Overington, leader of the EMBL-EBI’s ChEMBL team, which will act as the primary repository for the data through its ChEMBL resource. “We’re proud to be able to add value to the GSK data by incorporating it into ChEMBL and linking it with a vast array of information that could help researchers to find new treatments for malaria. This is the beginning of a new era of public–private collaboration in drug research.”

“NLM is excited to be involved in this groundbreaking release of information to the public,” said Steve Bryant, head of NLM’s PubChem database, which is housing the data. “By making these data available through public resources such as PubChem, GSK is greatly facilitating the research process, as the information is linked to related compounds, bioactivity results, published literature, and other resources that will assist researchers in making new discoveries to combat malaria.”

“CDD is delighted to be playing a role in this truly historic event,” commented Barry A. Bunin, CEO of Collaborative Drug Discovery. “In decades of medical breakthroughs from Big Pharmas, this is the first time a group is openly sharing all the chemical and biological data – not just the few hits. Furthermore, for phenotypic screens, the CDD tools allow researchers to begin to hypothesize and validate the targets from the whole cell screens.”

EMBL-EBI will act as the primary repository for the data on this compound set, and will index and format further information that is contributed. GSK will add more information as it is generated and external scientists researching these compounds and the data will be asked do the same.

About the data

The data contains the ‘hits’ or results from a screening of the 2 million compounds in GSK’s compound library to determine the effect of these compounds on the malaria parasite. The screening project identified ~13,500 compounds that showed strong inhibition on the parasite.

Kinase inhibitors constituted a large proportion of the molecules with previously known activity and now identified as antimalarial hits. The data includes the chemical families that GSK is currently researching for this indication and the ‘mechanisms of action’ for those compounds which the company has previously tested for other indications.

Most of the compound structures identified have been classified as capable of being converted into medicine.

The current microbiological information for the compounds and the structures have been put on online resources that are easily accessed by researchers. The EMBL-EBI site has been constructed so that scientists globally can add their data to the information there, with access free to all. The value of the release of information is enhanced by the collaboration of the web hosts and the specialist research tools on the site, that are being made available to researchers at no cost to them.

GSK gratefully recognises the support of Medicines for Malaria Venture, which contributed funding for this project.

Full information can be viewed online at:

www.ebi.ac.uk/chembl/

http://pubchem.ncbi.nlm.nih.gov/

www.collaborativedrug.com/

Do you want to know more?

EMBL Launches Genomics Data Resource

The European Molecular Biology Laboratory (EMBL) has launched a genomics resource called the European Nucleotide Archive (ENA) that consolidates three DNA and RNA sequence databases.

EMBL's European Bioinformatics Institute (EMBL-EBI) will host the ENA resource, which is made up of the EMBL Nucleotide Sequence Database, the European Trace Archive, and the Sequence Read Archive (SRA).

The European Trace Archive, formerly maintained at the Wellcome Trust Sanger Institute, contains raw data from electrophoresis-based sequencing machines, while the SRA is a new repository for raw data from next-generation, array-based sequencing platforms.

The ENA research team plans to launch new features for the resource over the coming year, including enhancements for the browser, improved interactive submissions tools and organism and project-centered portals into ENA data.

"ENA has been designed to provide our users with improved access both to annotated and to raw sequence data through the same user-friendly interface," Guy Cochrane, ENA's team leader, said in a statement.

"It provides graphical browsing, web services, text search, and a new rapid sequence similarity search. ENA also provides access to related information, with over 190 million cross references to external records, many of which are in other EMBL-EBI data resources," Cochrane added.

"As major generators of DNA sequence data, it is important to us that the research community has ready access not only to annotated sequence information, but also to raw data," Tim Hubbard, head of informatics at the Wellcome Trust Sanger Institute, added in the statement.

Funding for the ENA is provided by EMBL, the Wellcome Trust, and the European Commission's Framework Programme 7.

Transfer of pharmaceutical data resources, private to public domain has greatest impact

While this is very encouraging what's going to be it's impact on the industry on proprietary database vendors? More & more of open database consortia and open curation models are on the offing, with high level of participation from both the academia and the Industry.

The European Molecular Biology Laboratory's European Bioinformatics Institute has launched a "vast online database" of genomic-based drug and small molecule information available in an open access format for researchers seeking new therapeutics, according to EMBL-EBI.

The ChEMBLdb holds translational information on more than 520,000 small molecules, including data on target binding, the affect these compounds have on cells and organisms, and information about the molecules' absorption, distribution, metabolism, excretion, and toxicity.

"The data lie at the heart of translating information from the human genome into successful new drugs in the clinic," EMBL-EBI said this week.

EMBL-EBI is hosting the database, which was transferred from the biotech company Galapagos through a £4.7 million ($7.7 million) Strategic Award from the Wellcome Trust.

"This unprecedented transfer of pharmaceutical data resources from the private sector to the public domain should have the greatest impact on researchers in academia and in small companies on limited budgets," Alan Schafer, director of science funding at the Wellcome Trust, said in a statement.

"ChEMBLdb will be a major resource of information for driving forward medicinal chemistry and drug development in the UK and internationally," Schafer said.

EMBL-EBI also said that, along with partner Wellcome Trust, it has released an integrated resource of sequence, compound, and screening data from a range of sources for protein kinases, called Kinase SARfari.

Position open Group Leader - Bioinformatics/Systems Biology

The Computational Biology Unit (CBU) has been established to conduct top-level European research in bioinformatics, and to serve functional genomics research in Norway with relevant training and services.

CBU is searching for an additional group leader. The group leader will carry out research in the field of computational biology/bioinformatics and contribute to the overall objectives of CBU. The group leader should have a PhD and post-doctoral experience including a solid publication record in a relevant subject. Candidates will be evaluated with emphasis on their ability to raise external funding and to supervise and carry out research projects. The research profile of the candidate should be within a relevant area for CBU. Candidates with profiles in direction of systems biology will be preferred. The group leader will direct a research group consisting of Ph.D. and post-doctoral scientists.

The CBU and its partners currently have bioinformatics research activities in the fields of protein biophysics, molecular modeling and protein dynamics, transcriptional regulation microarray and proteomics bioinformatics, and genome assembly and annotation. Activity has been initiated towards integrative bioinformatics and systems biology. There are excellent opportunities for collaboration with the molecular biological and biomedical as well as mathematical and informatics research groups in Bergen.

CBU is part of Bergen Center for Computational Science (BCCS) and located together with the Department for Informatics, the Molecular Biology Department and the SARS Centre for Marine Molecular Biology, a partner of EMBL. BCCS owns and operates large scale computing facilities that provide an excellent computational environment. CBU is partner in the Molecular and Computational Biology research school (http://www.mcb.uib.no). CBU is coordinating the bioinformatics technology platform for the national functional genomics programme (FUGE) in Norway.

Salary and professional resources are internationally competitive. Please send your CV, your ten most relevant publications, and a detailed statement of research interests to Professor Inge Jonassen (Inge.Jonassen@bccs.uib.no), head of the CBU. Evaluation of applications will commence January 4th 2009 and continue until a suitable candidate has been identified. For more information about CBU, please refer to http://www.cbu.uib.no/, or contact Inge Jonassen.

Courtesy:

Inge Jonassen, PhD

Department of Informatics and

Computational Biology Unit, BCCS

University of Bergen

HiB

No5020 Bergen

Norway

email: inge.jonassen@ii.uib.no

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"Viruses are masters of cunning" - Imaging Of Influenza Virus Protein Opens Way To Design New Anti-viral Drugs

Already blogging about vital information that can be obtained form publications and scientific literature Smart tools to track, analyze and visualize research and the importance of Protein structure information in Protein structure databases with new web services for structural biology and biomedical research.

Now one of the tactics used by influenza virus to take over the machinery of infected cells has been laid bare by structural biologists at the European Molecular Biology Laboratory (EMBL) and the joint Unit of Virus Host-Cell Interaction of EMBL, the University Joseph Fourier and National Centre for Scientific Research (CNRS), in Grenoble, France.

The high-resolution image of the influenza virus' PB2 protein shows how the virus steals a 'cap' molecule from its host to take over the protein production machinery and multiply. PB2 binds the cap by sandwiching it between aromatic amino acids.

"Viruses are masters of cunning when it comes to hijacking the normal functioning of the host cell. The influenza virus steals a password from host messenger RNAs, molecules that carry the instructions for protein production, and uses it to gain access to the cell's protein-making machinery for its own purposes," says Cusack.

In the current issue of Nature Structural and Molecular Biology they publish a high-resolution image of a key protein domain whose function is to allow the virus to multiply by hijacking the host cell protein production machinery. The findings open the way for the design of new drugs to combat future influenza pandemics.