Berlin Proteomics Forum 2013 CHPP
07:30-09:00 Principal Investigator Council (PIC) Meeting
Chair: Young-Ki Paik & William S. Hancock
- Matters related to the Leadership & Membership of the Consortium
- Team organization (policy on the replacement of the consortium members)
- Annual Report and Evaluation System
- Designation of Global Resources Centers
- Data sharing between teams (format, credits, deposit),
- Channeling with ENCODE: guidelines, cell lines, and other resources,
- RNAseq services through the major providers (e.g., BGI etc.)
- C-HPP scientific workshop plans during the Yokohama HUPO meeting (9/14-18)
- New directions for the Genome-wide multidisciplinary platform for the C-HPP
- Coordination with B/D-HPP teams to make synergistic outputs and more.
- JPR Special Issue in Jan 2014 (Deadline: August 1, 2013)
9:30-11:00 Plenary Session I (10 minutes each)
Chair: William S. Hancock
- Mike Snyder (Stanford Univ., Stanford, CA, USA): Transcriptome and Proteome: RNA-seq and proteomic evidence for ENCODE project (non-coding RNA and ASVs-amino acid polymorphisms)
- Ian Wilson (Imperial College of London, London, UK): Large Scale Metabolic Phenotyping in a Systems Medicine World
- Emma Lundberg (KTH Royal Institute of Technology, Stockholm, Sweden): Update on the Human Protein Atlas
- Ruedi Aebersold (Institute of Molecular Systems Biology, ETH Zurich, Switzerland): Networking Proteomics
Plenary Session II (10 minutes each)
Chair: György Marko-Varga
- Juan Antonio Vizcaino (EBI, Honxton, UK) ProteomeXchange: globally co-ordinated proteomics data submission and dissemination
- Siqi Liu (Beijing, China): BGI and support of C-HPP transcriptomic works
- William S. Hancock (Boston, USA): An approach to define the missing parts list for a chromosome and PTM characterization in an alternative spliced variant (sEGFR)
11:00-11:20 Discussion
11:35-12:30 Part 1: Working Group Session 1: C-HPP Bioinformatics
Chair: William S. Hancock
- C-HPP Web Browsers Update.
- Peter Horvatovich: C-HPP Wiki. Presentation can be download here.
- Ping Xu: Caper, Chr 1,
- Ed Nice (on behalf of Rob Goode): The Proteome Browser, TPB, Chr 7 Seul-Ki Jeong: GenomewidePDB, Chr 13
- Andrey Lisitsa: Chromosome-Centric KB
13:30-15:00 Part 2: General Data Management
- Implementation of the standard metrics for the HPP and C-HPP
- Integrated DB for all teams; Data submission;
- Informatics tools and resources for the C-HPP
- Integration of PeptideAtlas and GPM protein identifications
- Uploading individual lab data sets and compare with what is known
- Integration of RNAseq data
- Collaboration between ENCODE and C-HPP: How ENCODE datasets can be integrated into our C-HPP work to produce more insightful meaning of biological readouts?
- SRM peptides
15:50-16:30 Working Group Session 2: Brief Progress Updates (7 min each)
Chair: Young-Ki Paik
- Chr 5: Rainer Bischoff (The Netherlands)
- Chr 6: Leonard Foster (on behalf of Paul Keown) (Canada)
- Chr 9: Je-Yoel Cho (Korea)
- Chr14: Jerome Garin (France)
- Chr15: Gilberto B Domont (Brazil)
- Chr18: Alexander Archakov (Russia)
- Chr 19: Transcriptomic study. Carol Nilson (USA)
- Mitochondria: Andrea Urbani (Italy)
16:30-17:20 Working Group Session 3: Resources & Bio-banks (10 minutes each)
Chair: György Marko-Varga
- Bio-banks and its utilization, Cell Lines: Gyorgy Marko-Varga
- Rare tissues (nasal epithelia): William S. Hancock
- Antibody: Ed Nice, Emma Lundburg and Tadashi Yamamoto (Antibody Ranker)
17:20-17:30 Wrapping Up and Announcement
Young-Ki Paik, William S. Hancock and György Marko-Varga
Other presentations
- Power Point presentation of William Hancock can be download here.