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SHPP Bioinformatics introduction. 1 st CHr-16 Workshop .

SHPP Bioinformatics introduction. 1 st CHr-16 Workshop . . Miraflores de la Sierra August, 28 th -29 th 2012 Alberto Medina. Summary. Why? Scope and main aims. Participants Objectives Where are we? Activities and meetings Contact and support Sample information Future…. . Summary.

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SHPP Bioinformatics introduction. 1 st CHr-16 Workshop .

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  1. SHPP Bioinformatics introduction.1st CHr-16 Workshop. Miraflores de la Sierra August, 28th-29th 2012 Alberto Medina

  2. Summary • Why? Scope and main aims. • Participants • Objectives • Where are we? • Activities and meetings • Contact and support • Sample information • Future….

  3. Summary • Why? Scope and main aims. • Participants • Objectives • Where are we? • Activities and meetings • Contact and support • Sample information • Future….

  4. Why? Scope and main aims Scope: SHPP • Bioinformatics support to SHPP members. • Discussion forums and/or mail list. • Face 2 face support. • Common IT maintenance. • Common sequence databases. • Parsing rules • Data submission guidelines. • From MS/MSI data to data standards and public repositories • Software development. • Solve regular duties and laboratory’s needs.

  5. Why? Scope and main aims Scope: CHPP Constructive Suggestion on the activities of the C-HPP’s Chromosome Informatics Subcommittee By AndreyLisitsa: Dear Young-Ki, in discussing the different ideas how heat-map can be represented on the Web it became intrinsically clear that this issue has to be ruled by C-HPP and Ed Nice, Rob Goode, Fernando Corrales and myself will appreciate in participation for the respective subgroup to coordinate the efforts. The following ideas were viewed ahead: (a) to allocate a "Chromosome Informatics"slot in Boston for discussing the avenues for knowing the adjacent genes along the chromosome; (b) to consolidate the "heat-map" data browsers (and also the requirements for such browsers) into an article in dedicated JPRissue. In my own modest experience, it is hard to deduce the intriguing ideas just by looking at the heat-map. I expect that Chr-informatics should develop and provide the means for implementing the scientific work on the chromosome. Mapping a series of genes, looking at their properties,comparing to the other gene sets, and so on -- towards the cognition if the observation is chr-specific or not.

  6. Why? Scope and main aims Chr 1. Ping Xuxupinggly@gmail.com; Lidong.bprc@foxmail.com; leedoong@gmail.com Chr 2. Amos Bairochab@isb-sib.ch; Pierre-Alain Binzpierre-alain.binz@isb-sib.ch Chr 7. Robert Goode Robert.goode@monash.edu Chr 11.Kyung-Hoon Kwon khoon@kbsi.re.kr Chr 12.Terrence C. Poon tcwpoon@cuhk.edu.hk, Wen-Lian Hsu (email?), Ting-Yi Sung (email? ) Chr 13.Seul-Ki Jeongjeongsk@proteomix.org Chr 14. Christophe BRULEY (CEA/Grenoble, Laboratoire de Biologieà Grande Echelle) email: christophe.bruley@cea.fr David BOUYSSIE (IPBS, Toulouse) email :david.bouyssie@ipbs.fr Chr 16. Alberto Medina-Aunon, National Center for Biotechnology-CSIC, Madrid, Spain. email: jamedina@cnb.csic.es Fernando J. Corrales, CIMA, Navarra University, Pamplona, Spain. email: fjcorrales@unav.es Chr 17.Ron Beavis ; William S. Hancock wi.hancock@neu/edu Chr 18. LisitsaAndrey; Ponomarenko Elena Chr 19. gyorgy.marko-varga@elmat.lth.se Chr Y: BabakArefnezhad email: babaref@yahoo.com GhasemHosseiniSalekdeh (Salekdeh@royaninstitute.org; hsalekdeh@yahoo.com) Scope: CHPP

  7. Summary • Why? Scope and main aims. • Participants • Objectives • Where are we? • Activities and meetings • Contact and support • Sample information • Future….

  8. Participants • Multisite initiative – horizontal layer • Well-known bioinformaticians • CNB: Salvador Martínezde Bartolomé, Juan P. Albar and Alberto Medina. • CIMA: Victor Segura and F. Corrales. • UCM: Vital Vialas. • UV: Javier Ortíz. • IIBB/CSIC: Oscar Gallardo. • UPV:GorkaPrieto.

  9. Summary • Why? Scope and main aims. • Participants • Objectives • Where are we? • Activities and meetings • Contact and support • Sample information • Future….

  10. Objectives (1)

  11. Objectives (2)

  12. Summary • Why? Scope and main aims. • Participants • Objectives • Where are we? • Activities and meetings • Contact and support • Sample information • Future….

  13. Where are we? • Logistics: • FTP. Public FTP for exchanging “regular” files. A new system should be developed for high throughput instruments. • Mail list. For any bioinformatics question, please write to shpp@proteored.org. • DropBoxfolder or similar. • Wiki space: http://community.uv.es/mediawiki/ • Web site: http://hpp-sp.com • Google code site: https://code.google.com/p/s-chpp/

  14. Where are we?

  15. Where are we?

  16. Where are we?

  17. Where are we? • Lab tasks • Sequence databases. For protein and peptide identification, the defined sequence databases should be installed on our local search engines. • Databases and installation guidelines are available at: http://hpp-sp.com/bases-de-datos/ Databases will be updated by Bioinfo Team

  18. Where are we? • Protein annotations and additional information. • CIMA adds some columns from initial bioinformatics study (HPA, GPMDB, etc). • PIKE service is available for further functional and biological data • http://proteo.cnb.csic.es/pike

  19. Where are we? • SRMAtlas provides a “valuable” information regarding MRM/SRM transitions. • The interface is not so “friendly” for any of us. • A new MySQL database were built following SHPP approach: • Gene  Protein  Peptide  Transition. Feed web site to provide a “real” status of the project (f.i. % identified proteins)

  20. Where are we? • non-computational people are not quite comfortable typing SQL commands on OS console. • HPP-MRM prototype has been developed to: • Check the available information for a specific gene/protein/peptide. • Check the protein annotations. • Add/edit new transitions. • Validate the results. Get/retrieve user’s requirements to design a comprehensive project.

  21. Where are we? • Data standards guidelines…. Next • We should: • Get experimental data using PSI’s standards (mzML, mzIdentML, traML and mzQuantML). • Create MIAPE reports (MS, MSI and MS-QuantML). • PRIDE reports (ProteomeXchange). • Compare and analyse the data from a “global” point of view (MIAPE extractor). • Provide a standardized manner for the biological annotations.

  22. Summary • Why? Scope and main aims. • Participants • Objectives • Where are we? • Activities and meetings • Contact and support • Sample information • Future….

  23. Activities and meetings Kick off Teleconf 22/05 Teleconf 04/06 Teleconf 18/06 Teleconf 3/07 Teleconf 7/08 SHPP meeting Group set up Tasks draft Direct support dist. BioInfo introduction MRM guidelines Lab. Teleconf. 4/7 1st July 15thJuly 1st August 1st June 15th June 15th May 15th August Cristalera Definitive Sequence DBs Mail list, and wiki HPP Data Analysis. Initial Phase. Web 1.0, Sequence DBs MRM app 1.0 MRM DB 1.0 Redundancy guidelines document MRM DB 1.1 MIAPE Extractor 1.0

  24. Summary • Why? Scope and main aims. • Participants • Objectives • Where are we? • Activities and meetings • Contact and support • Sample information • Future….

  25. Direct support • Unattended support by email. • shpp@proteored.org • Direct (contact person): • Each laboratory will be assigned to any of us. • It will study the query/issue to solve. If it is not possible it will pass the problem to the group.

  26. Summary • Why? Scope and main aims. • Participants • Objectives • Where are we? • Activities and meetings • Contact and support • Sample information • Future….

  27. Sample information • OPEN CALL: MIAPE MS doesn’t include any information regarding the sample origin or preparation. So, a minimal description should be added for any experiment. MIAPE tools add a new feature to include it, but we need to know if it is enough! 1 BRENDA tissue / enzyme source (BTO) ontology 2 3 4 Human Disease (DOID) ontology

  28. Summary • Why? Scope and main aims. • Participants • Objectives • Where are we? • Activities and meetings • Contact and support • Sample information • Future….

  29. Future • Consolidate submission pipeline. • Get users’ feedback (developed applications) • Develop a central repository for MRM experiments. • Create/design a web portal. • Improve experimental reports using data standards (f.i. PRIDE multiexperiment). • Include Sample origin data (web form, app form). • Integrate Mirafloresworking plan (to define tomorrow morning). • Assume CHPP bioinformatics group guidelines (Boston meeting).

  30. Questions

  31. Acknowledges • CIMA: • Victor Segura • Fernando Corrales • UCM: • Vital Vialas • IIBB/CSIC: • Óscar Gallardo • UPV: • GorkaPrieto • UV: • JaviÓrtiz • CNB/CSIC: • Salvador Martínez de Bartolomé. • Juan Pablo Albar

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