Modification of HID for AIDB

The Mouse BIRN group works with many types of images and deals with multiple data sources. Many of the groups work with 3D volumes (mostly MR volumes). These may be raw or processed data, including atlases (which contain several types of information associated with anatomy). Our goal with this work is for the AIDB to be one of the primary Mouse BIRN publicly accessible data sources for users to upload and expose their data using tools created by the FBIRN group that are modified to fit our needs.

This resource would be available for:

• Mouse BIRN source databases (clone relevant parts of their DB)
• Any external users to access through simple user interfaces

How to upload data to AIDB?

• How to use Upload Scripts?

Information on HID

• Access the AIDB development site
• Manuals on the FBIRN Wiki
• FBIRN tutorials
• FBIRN Upload scripts tutorial
• FBIRN upload scripts on SRB at /home/dwei.uci-bic/fBIRNupload.tgz

• Site IDS can be found on the BIRN portal at https://portal.nbirn.net/gridsphere/gridsphere?cid=srbresources.

Relevant Mouse Work

• Mouse BIRN work on XCEDE
• Outcomes from working with the FBIRN group
  • HIDUserWorkflow.doc: General Workflow used by FBIRN and specifics of EAE example from Allan
  • EAE_ProjectSetup.xml: Project Setup Example from EAE experiment
  • EAE_Visit.xml: Visit/Subject Example XML from EAE experiment

Progress tracking

• Renewed work began summer 2007 to upload MR data into the HID
• Mouse BIRN working group was formed including Jeff B, Edriss, Diana, Allan, Queenie, and Jyl tasked with getting data into AIDB
• In person meeting 9/25/07 at Irvine with Dave Keator, Dingying Wei, and Jeff Grethe to run through test data: Documentation
  • HIDmeeting9_25_07.doc: Minutes from the joint meeting 9/25/07
  • HIDUserWorkflow.doc: General Workflow used by FBIRN and specifics of EAE example from Allan
  • EAE_ProjectSetup.xml: Project Setup Example XML from EAE experiment
  • EAE_Visit.xml: Visit/Subject Example XML from EAE experiment
  • What's next:
    • Allan and Deepthi will take the XML scripts modified by Dingying and Dave today and try to make them work at UCLA.
    • Dingying will try to get their local upload script working and look at it to make sure it’s what we want.
    • Meet again before and at the AHM

• 11/07: Mouse_XML_Upload.zip: simple JAVA gui for creating project and subject XML files
  • Due to meetings and other deadlines, no progress on uploading to AIDB yet, meet again this month

• 11/19/07: met with Jeff B, Dingying, Allan, and Jyl: meeting minutes. All groups will try to upload a single dataset and meet next Tuesday 27th 10 AM to discuss any problems.
  • AIDBmeeting11_19_07.doc: meeting minutes

• 12/11/07: Allan has been able to set up a project on the AIDB, but he's having problems uploading data. Jeff B has set up a project on the portal and is working on modifying the project XML file.
  • AIDBmeeting12_11_07.doc: Minutes from the joint meeting 12/11/07

• 1/29/07: Allan is still having problems with the Path and hasn't been able to upload data yet. Jeff B ran into several issues while trying to run the installation and has started working on the Subject XML (he will look at Allan's examples on this wiki to see if those help). Queenie will put together some documentation that's specific for Mouse BIRN to help us through this process.
  • AIDBmeeting1_29_08.doc: Minutes from the joint meeting 1/29/08