Recurring Meeting of Cleveland Clinic Core Team

Date: September 30, 2013

Time: 10:30 AM EST

Means: In person meeting

Attendees:

1. Ahmet Erdemir
2. Jason Halloran
3. Craig Bennetts
4. Snehal Chokhandre
5. Robb Colbrunn
6. Tara Bonner

Agenda:

1. Description of the project
2. Organization and infrastructure
3. Logistics of work @ Cleveland Clinic
4. Meeting schedules for Cleveland Clinic team
5. Action items for following week

Immediate Action Items

See notes for details.

• Ahmet

  • Move older open knee related information in source code repository to a folder named G1.

• Snehal

  • Send a meeting request every thurday for upcoming meetings scheduled for Tuesdays 10:30 AM EST.
  • Assign tasks to all attendees by Thursday Oct 3,which will be discussed in the upcoming meeting.
  • Write meeting minutes.

• All

  • Subscribe to the relevant wiki pages to stay up to date with changes.
  • Deliberate on assigned tasks to discuss at the next meeting.
  • Start updating wiki pages.

Notes:

-- ["aerdemir"] DateTime(2013-10-02T20:46:15Z) Please help to organize these notes in relation to agenda items.

Description of the project

• Ahmet commenced the meeting by giving a general overview and motivation behind the grant.
• The grant is for 4 years starting September 16th, 2013.
• First year's funding will be for 8 months. There was an overall budget cut of 25%. To accommodate that organization, infrastructure and effort levels were discussed later in the meeting.
• Specific aims were discussed in detail and roles of all members were defined.
  • To achieve the first specific aim, the goal will be to allow anybody to use the models built by the team and run their own simulations on the cloud through a high performance computing interface. Stanford University and University of Utah teams will support this effort.
  • To achieve the second specific aim, modelers and experimenters will take the lead and focus on regularly bringing the community (collaborators, researchers, students etc) to monitor and to contribute to the project development. All relevant information will be periodically disseminated (data, models, scripts, computing platform). At the beginning of the project once the testing protocols are decided, community members can review them and modification will be made if deemed necessary.

Organization and infrastructure

• Overall organization map was discussed.
• The advisory board consists of 4 clinicians (Drs. Andrish, Jones, Saluan and Winalski) and 3 modeling experts (Drs. Dhaher, Guess, Korhonen). The team will meet them twice a year and update them on progress. Dr. Morgan Jones will be involved in the testing by providing his help with dissections, assessment of specimens etc.
• Ahmet and Snehal will have monthly conference calls with the collaborating teams, others can join if necessary.
• Stanford meeting; a request will be made for a gateway to high performance computing systems, e.g. to XSEDE, a national resource for high performance computing. An application to XSEDE will be necessary to provide a web based gateway where all users including community members can run simulations.
• FEBio will be used as simulation software. Models can be converted to Abaqus versions if users wish to do so. Features to facilitate joint level analysis, can be implemented in FEBio in the future.

Logistics of work @ Cleveland Clinic

• Effort levels were also discussed. For the first year of the grant efforts will be as follows:
  1. Robb: 2 months
  2. Tara: 3 months
  3. Snehal: 11 months
  4. Craig: 1 month
  5. Jason: 3 months The goal is to test 6 specimens, but more can be accommodated if time and funding permits.
• Initial work was defined for all Clinic members.
  1. Snehal will take care of overall experimentation organization.
  2. Robb, Snehal and Jason will create the robotics testing specifications.
  3. Tara and Snehal will take care of the tissue testing specifications.
  4. Craig, Jason and Snehal will work on the imaging specifications.
  5. Snehal will update the task list on SimTK.
  6. Jason will develop the simulation specifications.
  7. Ahmet will develop the simulation software specifications.

  • With all these specifications a standard operating pipeline will be generated.

• Members will subscribe to the relevant wiki pages to stay up to date with changes.
• Simtk and wiki organization was also discussed. Wiki site will be updated by members regularly.
• Task manager will be used to assign specific tasks to members with time frame and hour requirements. This will establish accountability.

Meeting schedules for Cleveland Clinic team

• The team decided to meet every Tuesday at 10.30 am EST to stay on track with goals and action items.

Other

• Ahmet proposed an internship program where 2-3 students can work with the Cleveland Clinic team on simulations. Other incentives for community involvement will be planned as time progresses.
• Robb suggested promoting the project at ISTE 2013 conference in San Antonio.
• The old open knee information will be archived.
• Utility tools will be developed as general purpose tools.
• Naming convention was discussed. Previous open knee : archive, name as generation 1
  • Everything done for this project will be generation 2. Naming convention : generation 2, specimen 1 First model generated : version 1 0.1, 0.2, etc for each data component. eg: MRI can be version 0.1, robotics : version 0.2 etc Any simulation/ validation will be version 2 (built model : version 1, ran and evaluate model: version 2) {Examples: generation2.specimen1,version1 (first model)/ generation2.specimen2.version0.1 (data)}
• Utility codes will be disseminated separately. At each version relevant utility code snapshot can be included.
• Publications/ abstract will be linked to Simtk page for visibility (Grant number has to be on every published document).
• Decision was made to disseminate the grant for public viewing.
• Public forums will be constantly monitored to identify and address user problems.
• User feedback will be requested from users through surveys. anybody who downloads Open knee automatically gets added to the mailing list and can be reached and updated periodically.
• Feature and bug tracking will be assigned to members.
• All monthly conference meetings will be attended by Snehal and Ahmet.
• XSEDE : Craig will start looking for the requirements to submit a proposal.
• Community will be involved when the pipeline and procedures are in place.
• Ahmet proposed a developers workshop at the Clinic in the future.
• A small Open Knee meeting was also proposed by Ahmet.
• Videos and pictures will be taken to chronicle the experimentation and model development process for each specimen. Videos may be incorporated to a Youtube channel.
• Robb emphasized the need to have a clear roadmap for interactions between specifications.
• Old open knee related information in source code repository will be moved to folder a folder named G1.
• Ahmet informed the team to not include any proprietary and patient related information on Wiki.
• Snehal will send a meeting request every thurday for upcoming meeting on tuesday.
• Action items for next meeting were decided.
• Members will deliberate on assigned tasks to discuss at the next meeting and will start updating Wiki pages.