shpp bioinformatics introduction. 1 st chr-16 workshop
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
SHPP Bioinformatics introduction.1st CHr-16 Workshop. Miraflores de la SierraAugust, 28th-29th 2012 Alberto Medina
Summary
1. Why? Scope and main aims.2. Participants3. Objectives4. Where are we?5. Activities and meetings6. Contact and support7. Sample information8. Future….
Summary
1. Why? Scope and main aims.2. Participants3. Objectives4. Where are we?5. Activities and meetings6. Contact and support7. Sample information8. Future….
Why? Scope and main aims
Scope: SHPP a) Bioinformatics support to SHPP members.
• Discussion forums and/or mail list.• Face 2 face support.
b) Common IT maintenance.• Common sequence databases.• Parsing rules
c) Data submission guidelines.• From MS/MSI data to data standards and public repositories
d) Software development.• Solve regular duties and laboratory’s needs.
Why? Scope and main aims
Scope: CHPP
Constructive Suggestion on the activities of the C-HPP’s Chromosome Informatics Subcommittee By Andrey Lisitsa: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.
Why? Scope and main aims
Chr 1. Ping Xu [email protected]; [email protected]; [email protected] 2. Amos Bairoch [email protected]; Pierre-Alain Binz [email protected] Chr 7. Robert Goode [email protected] 11.Kyung-Hoon Kwon [email protected] 12.Terrence C. Poon [email protected], Wen-Lian Hsu (email?), Ting-Yi Sung (email? )Chr 13.Seul-Ki Jeong [email protected] 14. Christophe BRULEY (CEA/Grenoble, Laboratoire de Biologie à Grande Echelle)
email: [email protected] BOUYSSIE (IPBS, Toulouse)email :[email protected]
Chr 16. Alberto Medina-Aunon, National Center for Biotechnology-CSIC, Madrid, Spain. email: [email protected] Fernando J. Corrales, CIMA, Navarra University, Pamplona, Spain. email: [email protected]
Chr 17.Ron Beavis ; William S. Hancock wi.hancock@neu/eduChr 18. Lisitsa Andrey; Ponomarenko ElenaChr 19. [email protected] Y: Babak Arefnezhad email: [email protected]
Ghasem Hosseini Salekdeh ([email protected]; [email protected])
Scope: CHPP
Summary
1. Why? Scope and main aims.2. Participants3. Objectives4. Where are we?5. Activities and meetings6. Contact and support7. Sample information8. Future….
Participants• Multisite initiative – horizontal layer• Well-known bioinformaticians
• CNB: Salvador Martínez de Bartolomé, Juan P. Albar and Alberto Medina.• CIMA: Victor Segura and F. Corrales.• UCM: Vital Vialas.• UV: Javier Ortíz.• IIBB/CSIC: Oscar Gallardo.• UPV: Gorka Prieto.
Summary
1. Why? Scope and main aims.2. Participants3. Objectives4. Where are we?5. Activities and meetings6. Contact and support7. Sample information8. Future….
Objectives (1)
Objectives (2)
Summary
1. Why? Scope and main aims.2. Participants3. Objectives4. Where are we?5. Activities and meetings6. Contact and support7. Sample information8. Future….
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 [email protected].• DropBox folder 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/
Where are we?
Where are we?
Where are we?
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
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
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)
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.
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.
Summary
1. Why? Scope and main aims.2. Participants3. Objectives4. Where are we?5. Activities and meetings6. Contact and support7. Sample information8. Future….
Activities and meetings
15th May 1st June 15th June 1st July 15th July 1st August 15th August Cristalera
Group set up Tasks draft
Teleconf04/06
Mail list, and wiki
MRM guidelines
Kick off Teleconf
22/05
Redundancy guidelines document
Web 1.0, Sequence DBs
Direct support
dist.
BioInfo introduction
SHPP meeting
MRM app 1.0
MRM DB 1.0
Definitive Sequence
DBs
HPP Data Analysis. Initial Phase.
Teleconf18/06
Teleconf3/07
Teleconf7/08
Lab. Teleconf.
4/7
MRM DB 1.1
MIAPE Extractor 1.0
Summary
1. Why? Scope and main aims.2. Participants3. Objectives4. Where are we?5. Activities and meetings6. Contact and support7. Sample information8. Future….
Direct support• Unattended support by email.• [email protected]
• 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.
Summary
1. Why? Scope and main aims.2. Participants3. Objectives4. Where are we?5. Activities and meetings6. Contact and support7. Sample information8. Future….
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
2
34
BRENDA tissue / enzyme source (BTO) ontology
Human Disease (DOID) ontology
Summary
1. Why? Scope and main aims.2. Participants3. Objectives4. Where are we?5. Activities and meetings6. Contact and support7. Sample information8. Future….
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 Miraflores working plan (to define tomorrow morning).
• Assume CHPP bioinformatics group guidelines (Boston meeting).
Questions
Acknowledges • CIMA:• Victor Segura• Fernando Corrales
• UCM:• Vital Vialas
• IIBB/CSIC:• Óscar Gallardo
• UPV:• Gorka Prieto
• UV:• Javi Órtiz
• CNB/CSIC:• Salvador Martínez
de Bartolomé.• Juan Pablo Albar