Recurring Meeting of Cleveland Clinic - Stanford University teams

Date: October 7, 2013

Time: 5:00 PM EST

Means: Conference Call

Attendees:

1. Ahmet Erdemir (Cleveland Clinic)
2. Snehal Chokhandre (Cleveland Clinic)
3. Craig Bennetts (Cleveland Clinic)
4. Joy Ku (Stanford University)
5. Henry Kwong (Stanford University)

Agenda:

1. Project description
2. Expectations from Stanford University team
3. Scheduling of monthly conference calls
4. Action items for following month
5. Other

Immediate Action Items:

See notes for details.

• Cleveland Clinic (Ahmet & Craig)

  • Develop specifications and a test problem for implementation of a prototype compute gateway to Simtk.

• Stanford University (Joy & Henry)

  • Familiarize with web based gateways to high performance computing, e.g. those enabled by [https://www.xsede.org XSEDE].

Notes:

1. Project description
   • Ahmet gave a general overview of the project.

development, testing, simulation and dissemination platform for in silico exploration of the biomechanics of healthy and diseased knees.'

1. Expectations from Stanford University team
   • Stanford University team will be involved in achieving the Specific Aim 1 which is 'To provide an open, freely available, and collaborative * In the existing Simtk infrastructure have a link to provide a gateway to high performance computing platforms.

   • Users can submit jobs through the web based interface to the high performance computing systems, similar to [http://robetta.bakerlab.org/ Robetta].

   • Integration between such a gateway and Simtk will be accomplished as part of Open Knee(s) project, e.g.
     • Users can click on a 'Compute' link at the project website. This will open a web page (gateway) where users can select a model, specify simulation settings or upload a workflow file and run the job essentially on the cloud.
     • The gateway should eventually be able pull models from the source code repository or utilize release versions.
     • Authentication and keeping track of users will be required, with the gateway inherent to Simtk infrastructure, Simtk user access and authentication can be used.

     • Potential computing resources include high performance computation allocation from [https://www.xsede.org/ XSEDE] (allocation is easy to gain and gateway development is supported), a compute server at Stanford University, Google Compute Engine, or Amazon Elastic Computing. Selection of computing resources may need to accommodate commercial use. Computing power requirements will be based on how much the gateway is used.

     • Tools to run simulations include FEBio, finite element analysis for biomechanics. FEBio will need to be installed on the compute server.
     • All scripting to prepare models, conduct simulations and post-process results will be in Python.
     • Results can be kept in an abridged version on the cloud and provided publicly for crowd-sourced sensitivity analysis.
   • Immediate goal of the collaboration is to prototype a basic version of a gateway that can be extended for computing using Open Knee(s)
     • The prototype can initially utilize a mainstream compute server and then deployed to a high performance facility.
     • The prototype can also be developed utilizing XSEDE.
     • Open Knee Generation 1 can be used in prototyping.
2. Scheduling of monthly conference calls
   • The Cleveland Clinic and Stanford University teams will meet on every third Wednesday of the month at 4:00 PM EST.
   • Next meeting: November 20, 2013 at 4:00 PM EST.
3. Action items for following month
   • Ahmet and Craig will write specifications for a prototype workflow to implement the gateway.
   • Stanford group will get familiar with XSEDE framework.