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.

Cognizant & Eagle Genomics with Pistoia Alliance to Develop a Cloud-based Platform

Cognizant, a leading provider of consulting, technology, and business process outsourcing services, and Eagle Genomics Ltd., a bioinformatics software company specializing in genomic data management and integration, has announced they are working with the Pistoia Alliance, Inc., a nonprofit, precompetitive alliance of life science companies and vendors, as one of the groups engaged to develop a conceptual cloud-based platform to facilitate access to public and proprietary sources of gene sequence data.

The Pistoia Alliance’s sequence services working group aims to define and document an externally hosted service for securely storing and mining both proprietary derived gene/sequence information and public domain gene databases. This conceptual platform developed by Cognizant and Eagle Genomics, as part of this piloting stage, will enable working group companies to securely share their bioinformatics resources among simultaneous, registered users in a secure, encrypted environment, while leveraging the flexibility, scalability, and cost-efficiencies of a cloud-based Software as a Service (SaaS) platform. The future of collaboration and externalization within the life sciences industry will increasingly utilize hosted information services, and the Pistoia Alliance expects to run future pilots to further explore this business model involving a range of participants.

“This engagement supports the Pistoia Alliance’s goal to inspire different ways of thinking in the life sciences industry and effect real change to benefit all our organizations,” said Nick Lynch, President at Pistoia Alliance. “With the combined strengths of Cognizant and Eagle Genomics and the broader Pistoia community, we will build a platform to define standards in sequence services, while overcoming the challenges of disparate data and tools.”

Cognizant and Eagle Genomics will combine the best of their consulting, domain, technology, and business process expertise to effectively deliver the business solution. While Eagle Genomics will contribute specialized bioinformatics knowledge, Cognizant will manage the development of the platform, oversee testing and security validation, and help strengthen the initiative by managing relationships with existing and potential member organizations. The platform will deploy a secure and scalable installation of Ensembl, a software system and supporting database developed jointly by the Wellcome Trust Sanger Institute and the European Bioinformatics Institute to produce and maintain automatic annotation on selected eukaryotic genomes. The platform will deliver a Plasmapper and a gene alias service as part of the initial functional services.

EBI–Sanger Postdoctoral (ESPOD) Programme

Two ESPOD fellowships available in 2010

The EBI and Wellcome Trust Sanger Institute share the Wellcome Trust Genome Campus. This proximity fosters close collaborations and contributes to an international and vibrant campus environment. Researchers are supported by easy access to scientific expertise, well-equipped facilities and an active seminar programme.

The EBI–Sanger Postdoctoral (ESPOD) Programme builds on the strong collaborative relationship between the two institutes, offering projects which combine experimental (wet lab) and computational approaches. Projects may be selected from the areas defined below or proposed by the applicant. In the case of self-defined projects, the area of work must have been agreed with both the EBI- and Sanger-based group leaders. Two postdoctoral fellowships will be awarded in 2010, to start as soon as possible after October 2010 but within 12 months of the fellowship being awarded.

Available projects

Birney/Semple: Integrated high resolution phenotyping and genetics in the zebrafish

Flicek/Hurles: Functional genomic analysis of structural variations in the human genome

Le Novere/Grant: Inference and representation of post-synaptic protein pathways using proteomic and phenotypic data

Luscombe/Bilker: Identification of regulatory networks that control development in a malaria parasite

Luscombe/Dougan: Genome-scale investigation of pathogenic regulatory networks in Salmonella

Overington/Rayner: Target discovery and validation for novel malaria drugs using an integrated chemical biology approach

The full directory of EBI group leaders can be found here and the Wellcome Trust Sanger Institute Faculty page lists the academic faculty members.

Application and selection dates:
Application deadline: 15 August 2010. 

Applications should consist of:
(a) cover letter specifying the project the candidate wished to apply for;
(b) CV with two references;
(c) project proposal if the candidate opts to propose a project themselves (please note that this is not required if a project is selected from the list of available projects). Self-proposed projects should be described in a maximum of 1000 words and must be pre-approved by the group and team leaders involved before the application is submitted.

Applications should be submitted via email to Tracey Andrew, by 15 August at the latest.

Interviews and selection process will take place from mid-September to mid-October 2010. Interviews will include one-to-one discussion with the group leaders associated with the project of interest and also a panelinterview.

Fellowships are expected to start from mid-October 2010. Fellowship start dates can be delayed in agreement with the project leaders but must be undertaken within 12 months of the fellowship being awarded.

Benefits of working at EMBL-EBI

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. In addition to a competitive salary, EMBL offers additional allowances dependent on family circumstances as well as an optional healthcare scheme for fellows and their families (spouse and children). Please see our leaflet about working at EMBL-EBI.

Contact:

For questions on ESPOD projects, please contact the group leader in question (for individual projects) orTracey Andrew for general enquiries on how to apply. 



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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/

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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.