Recurring Meeting of the Advisory Board

Date(s): November 20-21, 2014

Due to scheduling conflicts, the group meeting with the Advisory Board members were scheduled on an individual basis with each member. Please refer to Meeting Minutes for more details.

TableOfContents

Progress Report

Project Specific Aims

• To provide an open, freely available, and collaborative development, testing, simulation and dissemination platform for in silico exploration of the biomechanics of healthy and diseased knees.
• To develop in silico biomechanical models of healthy and diseased knee joints of different genders and ages, supported by specimen-specific joint and tissue level experimental mechanics.

Project Infrastructure

• https://simtk.org/home/openknee (project website)

• http://wiki.simtk.org/openknee (project wiki)

Project Contact

• Ahmet Erdemir, PhD, erdemira@ccf.org, https://simtk.org/users/aerdemir

Advisory Board

• Clinical. Jack Andrish, MD; Carl Winalski, MD; Morgan Jones, MD, MPH; Paul Saluan, MD (Cleveland Clinic)

• Engineering. Yasin Dhaher, PhD (Northwestern University); Trent Guess, PhD (University of Missouri), Rami Korhonen, PhD (University of Eastern Finland)

Progress Period

• May 19, 2014 - November 20, 2014

Development Team during Progress Period

• Cleveland Clinic Core Team. Craig Bennetts, Tara Bonner, Snehal Chokhandre, Robb Colbrunn, Ahmet Erdemir, Jason Halloran

• Stanford University. Scott Delp, Joy Ku, Henry Kwong

• University of Utah. Ben Ellis, Jeff Weiss, Steve Maas

• Community. Shannon Donnola, Chris Flask, Katie Stemmer

See https://simtk.org/project/xml/team.xml?group_id=485 for full details on the project team.

Goals of Progress Period

• Enhance prototype of web based computation infrastructure (Stanford University)
• Implement additional features in simulation software (University of Utah)
• Complete experimentation for Specimen 001 (Cleveland Clinic)
• Complete experimentation for Specimen 002 (Cleveland Clinic)
• Launch model for Specimen 001 (Cleveland Clinic)

• Complete development and review of modeling specifications (Cleveland Clinic & Community)

• Complete development and review of simulations specifications (Cleveland Clinic & Community)

• Start plans for 2015 summer internship program as part of community projects (reviews, internships, and collaborations) (Cleveland Clinic & Community)

• Publish previous work on Open Knee - Generation 1 (Cleveland Clinic)

Please also refer to previous meeting minutes of the Advisory Board at ["RecurringMeetings/2014-05-19"]. It should be noted that the timeline of activities has deviated from the original proposal, i.e., see the ["Roadmap"] and the proposed timeline of the proposal in attachment:GrantInformation/proposal.pdf.

Activities of Progress Period

• Cloud computing prototype

  • Cleveland Clinic and Stanford University teams continued to have monthly (and recently bi-monthly) conference calls to discuss web based computation interface. Please refer to meeting minutes in Cleveland Clinic - Stanford University section of ["RecurringMeetings"].

  • Detailed specifications on a prototype for web-based computing infrastructure can be found at the wiki page [http://wiki.simtk.org/openknee/Specifications/CloudComputingPrototype?action=recall&rev=19 Revision as of November 19, 2014] or [:Specifications/CloudComputingPrototype: current version].

  • SimTk.org site is currently under the process of migration to upgrade the infrastructure.

  • Web-based interfaces for submissions of simulations and for results retrieval were implemented and tested on a staging server. The team is waiting for SimTk.org upgrade to launch the cloud computing interface.

  • Upcoming steps include development of a model administration interface, implementation of quota management features, and public release of the cloud computing infrastructure.
• Simulation software features

  • Cleveland Clinic and University of Utah teams continued to have monthly conference calls to discuss enhancements in FEBio, the simulation software used in Open Knee(s). Please refer to meeting minutes in Cleveland Clinic - University of Utah section of ["RecurringMeetings"].

  • Detailed specifications for desired features can be found at the wiki page [http://wiki.simtk.org/openknee/Specifications/FebioFeatures?action=recall&rev=38 Revision as of November 19, 2014] or [:Specifications/FebioFeatures: current version].

  • In situ ligament strain feature was implemented in a generalized form. This work was presented by Steve Maas (University of Utah) at CMBBE 2014, 12th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering.
  • Feature on set definitions (nodes, elements, surfaces) was implemented. Testing needs to be conducted to evaluate the use of these features, both for pre-processing (input files) and post-processing (of output files).
  • Upcoming activities for simulation software enhancements include work on rigid body movement related features, e.g. kinematic joints, local coordinate systems.
• Experimentation
  • Experimentation scheduling changed significantly to accommodate routine testing of specimens and delivery of data for all specimens in an earlier fashion. The team decided to conduct joint imaging and joint mechanical testing (~3 full days of work for each knee) during the first week of each month until adequate number of specimens are tested. The tissue mechanical testing (~2 weeks of work for each knee) will be conducted in parallel. This scheduling helps the team to focus on experimentation and allow them to practice testing protocols in a regular fashion.
  • Two new knee specimens were acquired:

    • ["oks004"] (specimen to practice testing protocols), see [http://wiki.simtk.org/openknee/oks004?action=recall&rev=60 Revision as of November 20, 2014], and

    • ["oks005"] (Open Knee(s) - Generation 2 specimen), see [http://wiki.simtk.org/openknee/oks005?action=recall&rev=2 Revision as of November 20, 2014].

  • Joint imaging and joint mechanics testing were conducted on the following specimens:

    • ["oks001"], see [http://wiki.simtk.org/openknee/oks001?action=recall&rev=40 Revision as of November 20, 2014],

    • ["oks002"], see [http://wiki.simtk.org/openknee/oks002?action=recall&rev=41 Revision as of November 20, 2014],

    • ["oks004"], see [http://wiki.simtk.org/openknee/oks004?action=recall&rev=60 Revision as of November 20, 2014],

  • A few experimentation specifications, detailed description of protocols, were brought to a mature state (completely documented or close finalization):

    • For specimen preparation, see [http://wiki.simtk.org/openknee/Specifications/SpecimenPreparation?action=recall&rev=139 Revision as of November 20, 2014] or [:Specifications/SpecimenPreparation: current version].

    • For tissue mechanical testing, see [http://wiki.simtk.org/openknee/Specifications/ExperimentationTissueMechanics?action=recall&rev=76 Revision as of November 20, 2014] or [:Specifications/ExperimentationTissueMechanics: current version].

• Modeling & simulation

  • TBD
• Dissemination

  • As of November 19, 2014, Open Knee(s) provided 1 release package, Open Knee - Generation 1 version g1-s1-v1.0.1.202, which was downloaded 683 times (502 unique downloads), see [https://simtk.org/project/xml/downloads.xml?group_id=485 Open Knee(s) download page].

  • As of November 19, 2014, Open Knee(s) provided 5 developer, 2 user documentation in release form, see [https://simtk.org/docman/?group_id=485 Open Knee(s) documents page].

  • With a few exceptions (as requested by a collaborating team), all of the project website; wiki site, e.g. specifications, meeting minutes; and source code repository are publicly accessible.

  • As of November 19, 2014, Open Knee(s) website received 149,146 page hits in the past 180 days with 30,678 unique visitors, see [https://simtk.org/project/stats/usagemap.php?group_id=485 Open Knee(s) project activity].

  • As of November 19, 2014, Open Knee(s) enabled 8 studies by external research teams, see [https://simtk.org/project/xml/publications.xml/?group_id=485 Open Knee(s) publications page].

  • At this moment joint imaging and mechanical testing data are available for three knees, oks001, oks002, oks004. Dissemination of these data sets is pending, following organization of the information.
• Community projects

  • There were no feedback from the community on specifications disseminated through documents for developers in [https://simtk.org/docman/?group_id=485 Open Knee(s) documents page]. These specifications are still open for feedback through [https://simtk.org/forums/viewforum.php?f=485 Open Knee(s) public forums] and public write discussion pages at the wiki. Additional specifications disseminated through documents for developers in [https://simtk.org/docman/?group_id=485 Open Knee(s) documents page] are:

    • Anatomical imaging of knees, see [http://wiki.simtk.org/openknee/Specifications/ExperimentationAnatomicalImaging?action=recall&rev=120 Revision as of November 20, 2014] or [:Specifications/ExperimentationAnatomicalImaging: current version].

  • Ahmet has been exploring the logistical details of implementing Community Internship Program. It seems like the initial implementation may require hosting intern at the Cleveland Clinic site during summer periods.
  • Few synergistic short duration side projects that was started in previous progress report duration has been completed:

    • Cara Sullivan worked on a project through curation media and development of a promotional video. She developed a short movie script that can be used to create an Open Knee(s) video, see [http://wiki.simtk.org/openknee/Visibility?action=recall&rev=8 Revision as of November 20, 2014] or [:Visibility: current version].

    • Elvis Danso, a PhD student from Rami Korhonen's laboratory, along with Open Knee(s) Cleveland Clinic team, worked on testing tissue properties within the knee. The project informed fine-tuning of Open Knee(s) tissue testing protocols on the mechanical testing system acquired specifically for the project.
  • A synergistic short duration side project was started and has been completed:

    • Katie Stemmer, an undergraduate student from Ohio State University, joined the laboratory during Summer 2014 as part of the NSF Research Experience for Undergraduates program. Katie worked on a project for development of a cruciate ligament complex model, see [https://simtk.org/home/cruciate_model project site]. She wrote specifications for segmentation, geometry generation, and meshing for her project. These information will be ported to Open Knee(s) wiki to populate modeling related specifications pages.

  • Ahmet Erdemir had discussions with external investigators on philosophy of the Open Knee(s) and potential collaborations based on the Open Knee(s):

    • Peter Laz and Kevin Shelburne, Department of Mechanical & Materials Engineering, University of Denver, have significant expertise in knee joint modeling. Their insight can facilitate robust development of Open Knee(s) and its widespread adaptation. The team at the University of Denver also has significant knowledgebase and data on population related variations of knee anatomy and mechanics.

    • Jason Halloran, Department of Mechanical Engineering, Cleveland State University, has recently accepted a position to launch his research program. Jason has been an active member of Open Knee(s) development team during his tenure at the Cleveland Clinic. There are opportunities to incorporate Open Knee(s) in his research program and the training he provides as part of the mechanical engineering curriculum.
• Publications
  • There were no progress on Open Knee - Generation 1 publication. At this moment, no estimate is available for a potential timeline to return back working on such a manuscript.
  • There is an opportunity to publish an Open Knee(s) related article in Journal for Knee Surgery. Trent Guess is organizing a special issue and the Open Knee(s) team may submit a use case to illustrate the scientific and clinic utility of finite element analysis of the knee.
  • Open Knee(s) team presented work in various national and international conferences:
    • Maas, S. A., Erdemir, A., Halloran, J. P. and Weiss, J. A. Computational framework for application of residual stress when the stress-free configuration is unknown, 12th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering, October 13-15, 2014, Amsterdam, The Netherlands. (podium presentation by Steve Maas)
    • Erdemir, A. Bringing finite element analysis of biological structures to the masses by extending simulation software with open access models, 7th World Congress of Biomechanics, July 6-11, 2014, Boston, MA. (podium presentation by Ahmet Erdemir)
    • Bonner, T. F., Halloran, J. P., Erdemir, A. and Colbrunn, R. W. Pathway to quantify the effects of peripheral soft-tissue and capsule on knee joint response, 7th World Congress of Biomechanics, July 6-11, 2014, Boston, MA. (poster presentation by Tara Bonner)
• Other
  • Ahmet Erdemir and Morgan Jones wrote a lay article about Open Knee(s) for Orthopaedic Insights, the newsletter of the Department of Orthopaedic Surgery, Cleveland Clinic. The article will appear in the Fall 2015 issue of the newsletter.

  • Wiki pages on case studies ([http://wiki.simtk.org/openknee/Cases?action=recall&rev=6 Revision as of November 19, 2014] or [:Cases: current version]) and on related knee projects ([http://wiki.simtk.org/openknee/KneeProjects?action=recall&rev=2 Revision as of November 19, 2014] or [:KneeProjects: current version]) were created. The former page is intended to list clinical and scientific uses of Open Knee(s). The latter is aimed towards collating a list of publicly available knee biomechanics data and models that may be of use for Open Knee(s) users and developers.

Details of activities can be found in past meeting minutes of various teams at ["RecurringMeetings"].

Plans for Next Progress Period (November 20, 2014 - May 2014)

• Launch and enhance web based computation infrastructure (Stanford University)
• Implement additional features in simulation software (University of Utah)
• Disseminate joint imaging and joint mechanics data for oks001, oks002, oks004 (Cleveland Clinic)
• Complete joint imaging and joint mechanics experimentation on oks003, oks005, oks006, oks007 (Cleveland Clinic)
• Complete tissue mechanics testing of oks001, oks002, oks004 (Cleveland Clinic)

• Continue development and review of modeling and simulation specifications (Cleveland Clinic & Community)

• Start developing models for oks001, oks002, oks004 (Cleveland Clinic)
• Upgrade and disseminate Open Knee(s) - Generation 1 (Cleveland Clinic)

• Implement 2015 summer internship program as part of community projects (Cleveland Clinic & Community)

• Publish previous work on Open Knee - Generation 1 (Cleveland Clinic)

It should be noted that the timeline of activities has deviated from the original proposal, i.e., see the ["Roadmap"] and the proposed timeline of the proposal in attachment:GrantInformation/proposal.pdf.

Meeting Minutes

Date, Time, Means:

• November 20, 2014, 9:00 AM EST, in person meeting (JA)
• November 20, 2014, 12:30 PM EST, in person meeting (PS)
• November 20, 2014, 2:00 PM EST, conference call (TG)
• November 21, 2014, 9:00 AM EST, conference call (RK)
• November 21, 2014, 12:00 PM EST, conference call (YD)

Attendees:

1. Ahmet Erdemir (Cleveland Clinic)
2. TBD

Agenda:

1. Progress update, see progress report at:

   • http://wiki.simtk.org/openknee/RecurringMeetings/2014-11-20

2. Recap of previous meeting minutes, see meeting minutes at:

   • http://wiki.simtk.org/openknee/RecurringMeetings/2014-05-19

3. Action items for following meeting.
4. Other.

Immediate Action Items:

See notes for details.

• All Advisory Board Members

  • TBD

• Ahmet Erdemir

  • TBD

Notes:

1. Due to scheduling conflicts, a series of meetings were conducted to inform the Advisory Board about Open Knee(s) activities and get feedback.
2. Progress update.
   • TBD
3. Recap of previous meeting minutes.
   • TBD
4. Action items for following meeting.
   • TBD
5. Other.
   • TBD