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SpHPP Bioinformatics. 3 rd CHr-16 Workshop. . Miraflores de la Sierra December, 10 th -11 th 2012 Alberto Medina. Summary. Logistics Activities and meetings Data Analysis pipeline Shotgun MRM Sharing data Viewing data Conclusions. Summary. Logistics Activities and meetings

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Sphpp bioinformatics 3 rd chr 16 workshop

SpHPP Bioinformatics.3rd CHr-16 Workshop.

Miraflores de la Sierra

December, 10th-11th 2012

Alberto Medina


Summary
Summary

  • Logistics

  • Activities and meetings

  • Data Analysis pipeline

    • Shotgun

    • MRM

  • Sharing data

  • Viewing data

  • Conclusions


Summary1
Summary

  • Logistics

  • Activities and meetings

  • Data Analysis pipeline

    • Shotgun

    • MRM

  • Sharing data

  • Viewing data

  • Conclusions


Logistics
Logistics

  • Logistics:

    • FTP. Public FTP for exchanging “regular” files. A new system should be developed for high throughput instruments.

    • Mailing list. Different lists grouping by working groups

    • Wiki space: http://community.uv.es/mediawiki/

    • Web site: http://hpp-sp.com

    • Google code site:

      https://code.google.com/p/s-chpp/

      Webex teleconference


Website http hpp sp com
Website(http://hpp-sp.com)


Website consortium introduction
Website. Consortiumintroduction


Website wg introduction
Website.WG introduction


Website bd page
Website. BD page


Website chpp
Website CHPP



Summary2
Summary

  • Logistics

  • Activities and meetings

  • Data Analysis pipeline

    • Shotgun

    • MRM

  • Sharing data

  • Viewing data

  • Conclusions


Activities and metings
Activities and metings

9/3rd: Follow-up teleconference.

9/19th: Follow-up teleconference.

10/3rd: Follow-up teleconference.

10/17th: Follow-up teleconference.

10/31st: Follow-up teleconference.

11/21st: Follow-up teleconference.


Summary3
Summary

  • Logistics

  • Activities and meetings

  • Data Analysis pipeline

    • Shotgun

    • MRM

  • Sharing data

  • Viewing data

  • Conclusions


Summary4
Summary

  • Logistics

  • Activities and meetings

  • Data Analysis pipeline

    • Shotgun

    • MRM

  • Sharing data

  • Viewing data

  • Conclusions


Data analysis pipeline shotgun
Data Analysis Pipeline. Shotgun


Data analysis pipeline shotgun1
Data Analysis Pipeline. Shotgun



Main improvements
Mainimprovements

  • Somebugshavebeenfixed

  • Data Analysiscouldbedirectly done byend-users

  • Sequest has beenincluded.

  • ProteinInference – ProteinGrouping.


Data analysis protein grouping
Data Analysis. ProteinGrouping


Main improvements1
Mainimprovements

  • Somebugshavebeenfixed

  • Data Analysiscouldbedirectly done byend-users

  • Sequest has beenincluded.

  • ProteinInference – ProteinGrouping.

  • Mascot Server

  • Curatedexperiments


Curated experiments
Curatedexperiments


Summary5
Summary

  • Logistics

  • Activities and meetings

  • Data Analysis pipeline

    • Shotgun

    • MRM

  • Sharing data

  • Viewing data

  • Conclusions


Data analysis mrm
Data Analysis. MRM


Data analysis mrm1
Data Analysis. MRM


Data analysis proteotipic
Data Analysis. Proteotipic?


Summary6
Summary

  • Logistics

  • Activities and meetings

  • Data Analysis pipeline

    • Shotgun

    • MRM

  • Sharing data

  • Viewing data

  • Conclusions


Sharing data
Sharing Data


Sharing data1
Sharing Data


Sharing data2
Sharing Data


Summary7
Summary

  • Logistics

  • Activities and meetings

  • Data Analysis pipeline

    • Shotgun

    • MRM

  • Sharing data

  • Viewing data

  • Conclusions


Public data
Public Data


Viewing data
Viewing Data


Viewing data1
Viewing Data


Viewing data2
Viewing Data


Viewing other data
Viewingother “data”


Summary8
Summary

  • Logistics

  • Activities and meetings

  • Data Analysis pipeline

    • Shotgun

    • MRM

  • Sharing data

  • Viewing data

  • Conclusions


Conclusions
Conclusions

  • Website should be filled. WG description ASAP.

  • Continuous activities and meetings.

  • Data Analysis.

    • Shotgun analysis is great!

  • MRM DB

  • Data submission pipeline. Sequest is “active”.

  • Interaction with C-HPP and other chromosomes (TPB).


Acknowledges
Acknowledges

  • CIMA:

    • Victor Segura

    • Fernando Corrales

  • UCM:

    • Vital Vialas

  • IIBB/CSIC:

    • Óscar Gallardo

  • Ibermática

    • Aitor Moreno

  • UPV:

    • GorkaPrieto

    • Kerman Aloria.

    • Jesús M. Arizmendi.

  • UV:

    • Manuel S. Pino

    • JaviÓrtiz

  • CNB/CSIC:

    • Salvador Martínez de Bartolomé.

    • Juan Pablo Albar


Discussion
Discussion

  • Submission pipeline.

  • Protein Inference. Resubmit the data.

  • Sequence BDs.

  • MRM queries.

  • Logo and name.


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