Proteomics pipelines

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Workflows

Corra workflow

Corra workflow

NBIC IBM workflow

NBIC IBM workflow

DAF IBM workflow

DAF IBM workflow

Sharing the workflows

Shared creatly account (will be published in wiki as well):

  • user: proteomics-interest@lists.nbic.nl
  • pass: Njo27B

Use the following procedure for sharing the diagrams:

  1. Register your own account at creatly.
  2. Draw a diagram.
  3. Add "proteomics-interest@lists.nbic.nl" as a collaborator

If somebody want to contribute he has to:

  1. Login as "proteomics-interest@lists.nbic.nl" with password above.
  2. Make changes & save.



Deliverable 1 proposal

The proposal is a simplified version of the pipeline.

NBIC IBM workflow


Issues to discuss:

  1. Who are the responsible developers for each step?
  2. How far are we in adopting APML format in each of these steps?
  3. What kind of data is supported in the first two steps? MS^E, centroid peaks?
  4. How are the alignments reported in the "Feature Alignment" step?

Goals:

  • We want to compare the results and the performance of this workflow against a similar workflow running in the commercial Progenesis software.

Tasks:

  • We need test data: Twan (WUR/PRI) will work on this once the issues above are addressed
  • Validation of the workflow: Twan will run the comparison with Progenesis
  • more...

Planning:

  • Discuss integration tests dates and a delivery date.