Proteomics Services Team

The Proteomics Services Team is the part of the PANDA Group that provides databases and tools for the deposition, distribution and analysis of proteomics and proteomics-related data. We contribute to the development of community standards for proteomics data in the context of the HUPO Proteomics Standards Initiative (PSI), and develop reference implementations for these standards.

The Proteomics Services team is headed by Henning Hermjakob.

Databases and Services

IntAct protein interaction resource(production)
PRIDE protein identification database(production)
UniProt DAS servers(production)
Protein DAS client (beta)
Activities Overview (4.7 MB ppt)

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Collaborations

Collaborations beyond formal collaborations in funded grants

International Molecular Exchange (IMEX) Consortium (DIP, MINT, MIPS)
HUPO
HUPO Proteomics Standards Initiative (PSI)
Shanghai Institutes for Biological Sciences

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Student Projects

The Proteomics Services Team offers a range of student projects, at undergraduate level, e.g. for an MSc thesis.

Computational projects will usually implement new features for our existing database systems, in particular the IntAct (http://www.ebi.ac.uk/intact/) and PRIDE (http://www.ebi.ac.uk/pride/) databases. The available projects range across a broad spectrum, from data analysis, evaluation, and statistics, to web interfaces and data visualisation. Projects will always be based on our open source, production quality database applications, and will contribute to the publicly accessible systems if successful. Examples of recent publications resulting from Marie Curie >> tranineeships/student projects are pmids 18508856, 18047271. All students are supervised by experienced staff members and have access to a broad array of local experts for the technologies used. All applicants should have solid knowledge of Java and relational databases, with domain-specific knowledge in molecular biology a definite plus.

Currently available project: quality control and visualization of proteomics data in the PRIDE database

PRIDE (http://www.ebi.ac.uk) is EBI's database holding proteomics data, acquired by mass spectrometry. The database is maintained by the Proteomics Services team. There is now the opportunity to join for a master student project, where the goal is to visualize summary and metadata, so that users get a quick idea of the quality of their data and can compare their data with other PRIDE experiments. Prior knowledge of proteomics is not essential, experience in R and/or Java graphics and web services is needed. Daily supervision will be by Matthieu Visser and Juan Antonio Vizcaino.

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Funding

Current funding for the Proteomics Services team is generously provided by:

EMBL Core funding
EU grants: SLING, ProteomeBinders, ENFIN, APO-SYS, LipidomicNet, PSIMEx
Wellcome Trust "PRIDE" grant

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Organisation

Proteomic Services team organisation

The Proteomics Services team is led by Henning Hermjakob. It is part of the The Protein and Nucleotide Database Group (PANDA). This is jointly headed by Dr. Rolf Apweiler and Dr. Ewan Birney, with Dr. Apweiler taking responsibility for Proteins.

Contact

The Proteomics Services Team can be contacted using the following:

Contact Details

Henning Hermjakob
Tel: +44 (0)1223 494 671
Fax: +44 (0)1223 494 468
Email: hhe@ebi.ac.uk

EMBL Outstation - Hinxton
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
United Kingdom

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