Open position for Junior Researcher
Progetto Cluster (WP4): "Database and Data management for Proteomics"
| What | ClusterEvent |
|---|---|
| When |
2007-06-12 from 10:00 to 17:00 |
| Where | Parco Tecnologico - Pula |
Workshop
12 Giugno 2007 Workshop: "Database and Data management for Proteomics"
Parco Tecnologico Sardegna Ricerche, Edificio 1
PROGRAMMA:
10,00 - “Present your data with PRIDE” – Henning Hermjakob (European Bioinformatics Institute)
11,00 - “Managing and analysing proteomic data using the Proteios database application” - Fredrik Levander (Lund University)
14,00 - “The Proteomics Platform of Porto Conte Ricerche: facilities, activities, and applications” - Maria Filippa Addis (Porto Conte Ricerche)
15,00 - “Proteomics Databases: managing data for large scale studies” - Patricia Rodriguez-Tomé (CRS4)
I seminari sono aperti a tutti.
Per gli utenti del Progetto cluster di Bioinformatica è richiesta una
conferma della presenza all'indirizzo brunetti@crs4.it
Seminars are open to all - everybody welcome
For the users part of Progetto cluster Bioinformatica, please send a
confirmation of your presence to brunetti@crs4.it
Seminars and speakers:
"Present your data with PRIDE" – Henning Hermjakob (European Bioinformatics Institute)
Abstract:As of today, valuable proteomics data is produced at a high rate, and lost at a high rate. Experimental data supporting proteomics manuscripts is provided in text files, pdf tables, authors' web sites, or not at all. As a result, simple questions like "show me all experiments in which protein X has been identified" currently cannot be answered with realistic effort. We will discribe current status and future developments of the EBI's Protein Identification Database (PRIDE), which aims to improve this situation through the systematic capture of published proteomics data and long-term data exchange with other proteomics repositories. As of May 2007, PRIDE contains 304.000 protein identifications, supported by 1.400.000 peptide identifications from more than 2.000 experiments, among them the HUPO Plasma and Brain Proteome projects. PRIDE can be queried by protein identifiers, and experimental parameters like species or tissue. It allows download of entire experimental datasets, as well as their interactive comparision using Venn and bar diagrams. Deposition of proteomics data in PRIDE is supported by user-friendly tools and is now strongly recommended by the PROTEOMICS and Nature Biotechnology journals.
Henning Hermjakob (http://www.ebi.ac.uk/~hhe) is Team Leader for Proteomics Services at the European Bioinformatics Institute. He is chair of the HUPO Proteomics Standards Initiative, member of the BSPR executive committee, and a senior editor of the Proteomics journal. In the context of the HUPO Proteomics Standards Initiative, he contributes to the development and implementation of data representation and annotation standards in Proteomics. Major resources provided by his team are the IntAct database for molecular interactions, the PRIDE database for protein identifications, and the ChEBI database for biochemical nomenclature. In the context of the BioSapiens and Enfin projects as well as the IMEx consortium, he contributes to the integration of molecular biology data across data types and their efficient exchange. Current research interests include the comparative analysis of large scale proteomics datasets, and user-friendly approaches to data capture in systems biology.
"Managing and analysing proteomic data using the Proteios database application" - Fredrik Levander (Lund University)
Abstract: Workflows for proteomics generate data in different formats that need to be integrated. In this seminar usage of the Proteios database
application for management of proteomic data will be described. Furthermore, combination and analysis of protein identification search
results from different search engines, as well as other analysis possibilities using Proteios will be discussed.
Fredrik Levander is working on method and software development for high-throughput proteomics in the group of Peter James, Lund
University. Accurate protein identification and protein quantification using LC-MS are his main areas of interest.
“The Proteomics Platform of Porto Conte Ricerche: facilities, activities, and applications” - Maria Filippa Addis (Porto Conte Ricerche)
Abstract: Dr. Addis will introduce the facility and its investigative potential, illustrating some of its past and current applications for research and development.
Maria Filippa Addis is one of the researchers operating in the proteomics platform of Porto Conte Ricerche. She has a background in biology, biochemistry, and microbiology.
“Proteomics Databases: managing data for large scale studies” - Patricia Rodriguez-Tomé (CRS4)
Abstract: In today's large scale proteomics studies it is essential to have a well thought pipeline and databases to manage the large amounts of heterogeneous data to produce reliable and comparable results. In this talk will be presented the current methodologies and the different systems that can be used.
Patricia Rodriguez-Tomé has worked at CEPH and Généthon managing databases for the sequencing projects, the biobank and the genetic map project, before joining the European Bioinformatics Institute from 1994 to 2000, as a Team Leader in R&D for databases and data integration research. At the end of 2000, she joined GeneProt Inc., in Geneva, to head the databases group, developing databases to manage proteomics data. She joined the CRS4 in september 2005, to head the service and development team of the new Bioinformatics Laboratory.