Meeting Notes 20101103 NEMO core meeting - NEMO toolkit updates

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  • Convened by: NEMO core
  • Presenter: Bob Frank
  • Notes by: Gwen Frishkoff
  • Where: WebEx
  • Attendees: Gwen, Paea, Dejing, Bob, Snezana, Allen, Haishan, Alex B.



The goal for this meeting was for Bob Frank to update NEMO core on progress with the NEMO analysis toolkit.


  • Bob noted that the NEMO ERP Analysis toolkit is now available through the Sourceforge repository:

svn co nemoontologies

  • He demonstrated that the repository can be accessed through a terminal or using an SVN GUI such as Versions or RapidSVN
  • He then demonstrated how to set the path to each of the three tool modules (Decomposition, Segmentation, and Metric Extraction) in matlab ("Add with subfolders" > select each module in turn and save)
  • He reviewed the structure and organization of his code:
    • Meta-structures
      • reader class (file I/O)
      • experiment info or "metadata" class (data provenance)
    • Specific structures
      • decomposition class
      • segmentation class
      • metric extraction class
  • Also noted that he segmented the I/O scripts out from Decomposition class (and Segmentation class). Allen also noted that EGI is working on new data file format ("MMF" for "meta file format") with API to translate MMF into different file formats.
  • Allen described use of ACSIS (sp?) cloud, which can be used to run these tools on the "back end" (using portal interface to set up & execute workflows).
  • Make sure that results of workflows are input to db and properly attributed (linked to data provenance).
  • Four types of files:
  **1. input files (data)
  **2. parameter files (meta-script)
  **3. output files (data)
  **4. program files (application itself)
  • List of query-able properties -- can be extracted from matlab files
  • Allen: What other applications can be used to query data within database?
  • Bob showed EP toolkit reader ('EPTreader')

Action items

  • Toolkit testers: Please set up SVN links to NEMO sourceforge repository:

svn co nemoontologies

For Mac users who like to use a GUI rather than command line interface, consider purchasing the shareware, Versions:

WebEx Recorded Archive

If you wish to review the recording of the web conference, click the link below:


NEMO core meeting-20101103 1830-1 Wednesday, November 3, 2010 4:29 PM New York Time 1 hour 45 minutes

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