• RecurringMeetings
• 2016-03-01-1300

Recurring Meeting of Cleveland Clinic - Stanford University

Date: March 1, 2016

Time: 1:00 PM EST

Means: Conference Call

Attendees:

1. Ahmet Erdemir (Cleveland Clinic)
2. Joy Ku (Stanford University)

Agenda:

1. Update on documentation of preliminary work on data management system (Galaxy).
2. Progress on installation and testing of Girder for data management.
3. Allocation of human resources for work on data management systems.
4. Planning for Interim Progress Review at May 16, 2015.
5. Other.

Immediate Action Items:

• Ahmet (Cleveland Clinic)
  • Invite other members of the Cleveland Clinic team to the next conference call.
  • Provide raw data as a sample for data management system prototyping.
• Joy (Stanford University)
  • Provide screenshots and evaluation criteria on the wiki for prototype data management systems.
  • Setup a conference call with Mike Wong, the new consultant on the project, and Ahmet.

Notes:

1. Update on documentation of preliminary work on data management system (Galaxy).
   • Joy will update the documentation on the use of Galaxy for data management. Mike Wong, the new consultant, has sent some information to Joy in this regard.
2. Progress on installation and testing of Girder for data management.
   • Joy will let Mike Wong, the new consultant to play with Girder.
3. Allocation of human resources for work on data management systems.
   • Mike Wong joined the team as a consultant to implement data management and database features. Mike is mostly working on the front-end. He has already dome work using data from Open Knee(s) - sister project. He can pull data into a sample system. He can also populate metadata straight out of wiki pages. It is possible to conduct queries on the metadata.
   • Ahmet asked about the possibility to organize raw data. He differentiated between storage/organization of raw data and databases for derivative data. He wondered how data can be manipulated on the cloud to generate new derivative data, which can fill in databases automatically including associating of metadata and query. He also noted that a manual upload and data association would be necessary to allow any user provide their derivative data, which they may generate offline.
   • Joy and Ahmet discussed a sample workflow for Mike to utilize. Open Knee(s) data may be a good starting point and will be directly relevant to the workflow of Operation Multis. This workflow includes DICOM files for a joint specimen as raw image data; NIfTI files for a joint specimen as derivative data that result in the organization of these; segmentation information as image volumes (NIfTI files) and as geometries (STL surfaces), for each tissue within the joint specimen, as further derivative data. The derivative data sets are available publicly. Ahmet will need to provide the raw DICOM files.
4. Planning for Interim Progress Review at May 16, 2015.
   • Ahmet is hoping to have a working prototype before the review, i.e. something that he can pull up in the meeting and browse/upload data. This does not need to be the final product but it should illustrate progress.
5. Other.
   • Joy will have a call with Mike on upcoming Thursday. She requested that we have a conference call all together, earlier than one month. Ahmet asked her to set up a time for it.
   • Ahmet mentioned Osteoarthritis Initiative as a challenging data set that may be used for prototyping.
   • Ahmet also recommended Joy to check I-DASH, to see how they tackle data management issues.