Recurring Meeting of the Advisory Board
Date(s): May 26-27, 2016
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.
Contents
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/projects/openknee (project website)
https://simtk.org/plugins/moinmoin/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
- November 20, 2015 - May 25, 2016
Development Team during Progress Period
Cleveland Clinic Core Team. Craig Bennetts, Tara Bonner, Snehal Chokhandre, Robb Colbrunn, Ahmet Erdemir
Stanford University. Scott Delp, Joy Ku, Henry Kwong
University of Utah. Ben Ellis, Jeff Weiss, Steve Maas
Community. Jason Halloran, Will Zaylor
See https://simtk.org/project/memberlist.php?group_id=485 for full details on the project team.
Goals of Progress Period
- Launch and test usability of web based computation infrastructure (Stanford University)
- Explore the possibility to implement additional convenience related features in simulation software (University of Utah)
- Complete joint imaging and joint mechanics experimentation on oks009, oks010, oks011 (Cleveland Clinic)
- Start tissue mechanics testing of all specimens (Cleveland Clinic)
Continue development and review of modeling & simulation specifications (Cleveland Clinic & Community)
- Continue developing models for all specimens (Cleveland Clinic)
Plan 2016 summer internship program as part of community projects (Cleveland Clinic & Community)
Follow up with case studies on modeling & simulation (Cleveland Clinic & Community)
- Follow up publications for Open Knee(s) - Generation 2 data sets (Cleveland Clinic)
Please also refer to previous meeting minutes of the Advisory Board at RecurringMeetings/2015-11-19. 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 GrantInformation/proposal.pdf.
Activities of Progress Period
- Cloud computing prototype
Upgraded SimTk.org site was launched during early May 2016. Cloud computing interface is ready to launch, i.e. available as a hidden feature. Cleveland Clinic team will provide Open Knee(s) - Generation 1 model with pre- and post-processing scripts for usability testing. The development of a model administration interface and the implementation of quota management features will likely shape after the usability testing.
Cleveland Clinic and Stanford University recently started the conference calls, following the upgrade of SimTk.org. 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 Revision as of May 25, 2016 or current version.
- 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 Revision as of May 25, 2016 or current version.
- All critical features related to joint mechanics simulations, e.g. representation of kinematic joint constrains, in situ strain feature, have been implemented along with convenience features to assist model development, e.g. sets. Work on in situ ligament strain feature was published in the Journal of the Mechanical Behaviour of Biomedical Materials for publication.
- Future efforts will likely add convenience features to define parts/components for assembly of models and strategies for surrogate mechanical representations, e.g. with shells, wrapping springs, etc.
- Prospective updates on the Open Knee(s) - Generation 1 model to incorporate in situ strains are expected.
- Experimentation
- Joint level testing continued during the progress period:
Joint imaging and joint mechanics testing were completed on oks009, see Revision as of May 25, 2016.
- Additional specimens were ordered to increase the diversity of Open Knee(s) (by adding specimens from mid-age donors) and augment data from young knees (by additional specimens). Yet, it is likely that testing of these specimens will not be prioritized to focus on tissue testing and model development.
Tissue testing has not started as the team decided to conduct more analysis on reproducibility of the outcome of the tests and resolve noise issues in the signal from mechanical testing system. Please refer to protocol evaluation plan; see the wiki page, Revision as of May 25, 2016 or current version.
- Joint level testing continued during the progress period:
Modeling & simulation
- Further developments in Open Knee(s) - Generation 1 are expected.
Since the SimTk.org upgrade was finalized, the current version of Open Knee(s) - Generation 1 can be ported to cloud computing.
Incorporation of meniscal constraints to the model has been stalled. Simulations reported in relevant wiki page Revision as of May 25, 2016 or current version will be helpful for enhancement of the Open Knee(s) - Generation 1 model.
- Given the implementation of in situ strain feature in FEBio and relevant work done with Open Knee(s) - Generation 1 model as a case study, upgrade of Open Knee(s) - Generation 1 model to incorporate in situ ligament strains is anticipated.
- Open Knee(s) - Generation 2 development has continued.
Development of pre-processing scripts to analyze mechanics testing data continued, e.g. for contact pressure analysis, see Revision as of May 25, 2016 or current version
- Various specifications for model development were documented in detail:
Image segmentation , see Revision as of May 25, 2016 or current version
Geometry generation, see Revision as of May 25, 2016 or current version
- First round of segmentation and geometry generation for oks001 has been completed. The segmented volumes and geometries are available in the source code repository.
- Further developments in Open Knee(s) - Generation 1 are expected.
- Dissemination
As of May 25, 2016, Open Knee(s) provided 9 packages (5,206 total downloads, 1215 unique downloads), see Open Knee(s) download page:
- oks001 version g2-s1-v0.2.0.20150825 (113 unique users as of May 25, 2016)
- oks002 version g2-s2-v0.2.0.20150916 (27 unique users as of May 25, 2016)
- oks003 version g2-s3-v0.2.0.20151013 (15 unique users as of May 25, 2016)
- oks004 version g2-s4-v0.2.0.20151029 (14 unique users as of May 25, 2016)
- oks006 version g2-s6-v0.2.0.20150915 (12 unique users as of May 25, 2016)
- oks007 version g2-s7-v0.2.0.20151021 (15 unique users as of May 25, 2016)
- oks008 version g2-s8-v0.2.0.20151021 (20 unique users as of May 25, 2016)
- oks009 version g2-s9-v0.2.0.20151208 (19 unique users as of May 25, 2016)
Open Knee - Generation 1 versions g1-s1-v1.1.0.391 & g1-s1-v1.0.1.202 (651 unique users as of May 25, 2016):
As of May 25, 2016, Open Knee(s) provided 11 developer, 5 user documentation in release form, see 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 May 25, 2016, Open Knee(s) website received 11,081 page hits in the past 180 days with 1,329 unique visitors, see Open Knee(s) project activity. It should be noted that theses statistics were likely reset at the time of Simtk.org update during early May 2016.
As of May 25, 2016, Open Knee(s) enabled 17 studies by external research teams, see Open Knee(s) publications page.
At this moment joint imaging and mechanical testing data are disseminated for eight knees: oks001, oks002, oks003, oks004, oks006, oks007, oks008 & oks009 (see Open Knee(s) download page).
- Community projects
There were no feedback from the community on specifications disseminated through documents for developers in Open Knee(s) documents page. These specifications are still open for feedback through Open Knee(s) public forums and public write discussion pages at the wiki.
- Participation to 2016 summer internships were decided upon:
- Connor Lough, from Saint Louis University, will return back to continue working on model development.
- Raghav Malik, from Mentor High School, will return back for his senior high school project to continue working on software development for automated measurement of tissue thickness using a camera-based system.
- Jason Halloran and Will Zaylor, from the Cleveland State University, has been attending recurring meetings of the Cleveland Clinic team. Will Zaylor contributed to analysis scripts to extract joint kinematics-kinetics from experimentation files.
- Publications
- First drafts of manuscripts on anatomical imaging and joint mechanics testing of the Open Knee(s) - Generation 2 specimens:
- Bennetts, C. J., Chokhandre, S., Donnola, S. B., Flask, C. A., Bonner, T. F., Colbrunn, R. W., Winalski, C., Erdemir, A. (in progress) Open Knee(s): magnetic resonance imaging data for specimen-specific next-generation knee models, to be submitted to Scientific Reports.
- Bonner, T. F., Colbrunn, R. W., Chokhandre, S., Bennetts, C. J., Erdemir, A. (in progress) Open Knee(s): comprehensive tibiofemoral joint testing for specimen-specific next generation knee models, to be submitted to Scientific Reports.
- Colbrunn, R. W., Halloran, J., Bonner, T. F., Chokhandre, S., Bennetts, C. J., Erdemir, A. (in progress) Open Knee(s): comprehensive patellofemoral joint testing for specimen-specific next generation knee models, to be submitted to Scientific Reports.
- Open Knee(s) team published articles in peer-reviewed journals:
- Maas, S. A., Erdemir, A., Halloran, J. P. and Weiss, J. A. (2016) A general framework for application of prestrain to computational models of biological material, Journal of the Mechanical Behavior of Biomedical Materials, 61, 499-510.
- First drafts of manuscripts on anatomical imaging and joint mechanics testing of the Open Knee(s) - Generation 2 specimens:
- Other
- Open Knee(s) mentioned in an article in Biomedical Computation Review:
SimTK ReLaunch by Miller, K. (2016) Simtk relaunch: back at the cutting edge, Biomedical Computation Review (Spring 2016), published by Simbios, the NIH National Center for Physics-Based Simulation of Biological Structures.
Jason Halloran (Cleveland State University) and Ahmet continued discussions with Kevin Shelburne and Peter Laz (University of Denver), Carl Imhauser (Hospital for Special Surgery), and Thor Besier (Auckland Bioengineering Institute) for potential collaborative work in modeling & simulation of the knee joint.
Ahmet submitted a grant application to Burroughs Wellcome Fund to expand upon Open Knee(s) through a structured verification & validation study - Community perspectives meet regulatory considerations: accreditation of Open Knee(s) as a medical device development tool for restoration of knee mechanics.
- Craig Bennetts, a significant contributor to Open Knee(s) project, has moved on to new adventures.
Details of activities can be found in past meeting minutes of various teams at RecurringMeetings.
Plans for Next Progress Period (November 20, 2015 - May 2016)
Port Open Knee(s) - Generation 1 model to cloud computing at SimTk.org (Cleveland Clinic & Stanford University)
- Upgrade Open Knee(s) - Generation 1 to reflect meniscal constraints and in situ ligament strains (Cleveland Clinic)
- Start implementing additional convenience features for simulation of joint mechanics using FEBio (University of Utah)
- Start tissue mechanics testing of all specimens (Cleveland Clinic)
Continue development and review of modeling & simulation specifications (Cleveland Clinic & Community)
- Continue developing models for all specimens (Cleveland Clinic)
Start 2016 summer internship program as part of community projects (Cleveland Clinic & Community)
- Submit publications for Open Knee(s) - Generation 2 data sets (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 GrantInformation/proposal.pdf.
Meeting Minutes
Date, Time, Means:
- May 26, 2016, 11:30 AM EST, face-to-face meeting (AE,PS)
- May 26, 2016, 1:30 PM EST, phone call (AE,YD)
- May 26, 2016, 2:30 PM EST, phone call (AE,MJ)
- May 27, 2016, 8:00 AM EST, skype (AE,RK)
- May 27, 2016, 11:30 AM EST, phone call (AE,TG)
- May 27, 2016, 2:30 PM EST, phone call (AE,JA)
Attendees:
- Ahmet Erdemir (Cleveland Clinic)
- Jack Andrish (Cleveland Clinic)
- Morgan Jones (Cleveland Clinic)
- Paul Saluan (Cleveland Clinic)
- Yasin Dhaher (Northwestern University)
- Trent Guess (University of Missouri)
- Rami Korhonen (University of Eastern Finland)
Agenda:
- Progress update, see progress report at:
- Recap of previous meeting minutes, see meeting minutes at:
- Action items for following meeting.
- Other.
Immediate Action Items:
See notes for details.
All Advisory Board Members
- Continue thinking potential projects for Open Knee(s) related grant applications.
Paul Saluan
Provide example case studies where modeling & simulation of the knee can support clinical decision making.
- Connect medical students with Ahmet for observation/contribution to Open Knee(s).
Rami Korhonen
- Inform Petri Tanska to communicate with Ahmet to prepare for his visit.
Ahmet Erdemir
- Identify the required steps in Cleveland Clinic for Petri Tanska's visit.
Notes:
- Due to scheduling conflicts, a series of meetings were conducted to inform the Advisory Board about Open Knee(s) activities and get feedback.
- Progress update.
- Ahmet had separate calls and meetings with individual members of the Advisory Board. In each of these, he provided a summary of progress and plans for the last year of funding period. He emphasized completion and dissemination of anatomical imaging and joint testing data on eight knees. He described the challenges to minimize uncertainties in tissue mechanical testing. He noted that the next year would be the last year of funding and the work will focus on tissue testing and development of models. He also mentioned future plans for expansion of Open Knee(s) work through different funding mechanisms, i.e. he recently applied to Burroughs Wellcome Fund for verification and validation, and regulation of Open Knee(s). He updated the participants about the status of data papers and asked for contributions from physicians. Other highlights from the individual meetings are noted below.
- Paul and Ahmet discussed case studies where modeling and simulation can help the mental analysis of the physician. Paul will send some case examples for promotion of modeling and simulation in the clinics. Paul and Ahmet discussed Open Knee(s) future, in the short term to have virtual specimens to let clinicians answer research problems and in the long term to have models and strategies for personalization and intervention to let clinicians explore the potential impact of their decision making and to support their mental models. Paul also mentioned about the possibility to send medical students this summer to observe and contribute to Open Knee(s) work.
- Yasin and Ahmet talked about MCL segmentation and the ligament's stabilizing effect on meniscus. Yasin was interested in a study to quantify uncertainty in segmentation process, i.e., a multi-center project supported by the undergraduate programs where randomized and blinded image can be sent to groups for segmentation. Ahmet mentioned the Knee Segmentation Challenge and also informed Yasin about the knee data disseminated by Kevin Shelburne.
- Ahmet asked Morgan how he would like to see the models help his clinical work. They discussed funding opportunities, e.g. Burroughs Wellcome Fund., and work done by Neil Segal and Don Anderson, which may be relevant to Morgan's research interests.
- Rami and Ahmet discussed Petri Tanska's visit to Cleveland Clinic. Petri will be finishing his doctoral work first. There is a possibility to host him as a post-doc or a visiting fellow. Ahmet recommended Rami to start the process soon. Ahmet will also check with his department about the necessary steps to accommodate Petri's visit. Rami asked about the in situ strains and ligament slack lengths, specifically about their influence on patellofemoral joint contact pressures. Ahmet noted that the patellofemoral joint contact pressures will likely influenced by the slack lengths of the joint's ligaments, e.g. MPFL. In addition, changing the tibiofemoral joint ligament slack lengths may affect the resultant equilibrium of that joint joint, which may also affect the patellofemoral joint kinematics. Rami also mentioned an upcoming EU funded program to recruit doctoral students from abroad. Ahmet will spread the word.
- Trent informed Ahmet about his involvement with an ORS group focused on meniscus. He is interested in building a meniscus library. Ahmet recommended that he may be able to consolidate data from different sources. Trent also wondered if contact pressures in the tibiofemoral joint contact were collected. Ahmet mentioned that that was not part of the testing protocol.
Jack asked about tracking of downloads by users. Ahmet responded that SimTk.org provides the infrastructure to collect this information.
- Recap of previous meeting minutes.
- The discussions mainly focused on progress and future plans (see item above).
- Action items for following meeting.
- See Immediate Action Items above.
- Other.
- Refer to notes above for the agenda item on progress update.