Recurring Meeting of the Advisory Board
Date(s): December 22, 2016 - January 5, 2017
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
- May 26, 2016 - December 21, 2016
Development Team during Progress Period
Cleveland Clinic Core Team. Tara Bonner, Snehal Chokhandre, Robb Colbrunn, Ahmet Erdemir, Benjamin Landis, Erica Morrill, Tyler Schimmoeller
Stanford University. Scott Delp, Joy Ku, Henry Kwong
University of Utah. Ben Ellis,Steve Maas, Jeff Weiss
Community. Jason Halloran, Connor Lough, Raghav Malik, Will Zaylor
See https://simtk.org/project/memberlist.php?group_id=485 for full details on the project team.
Goals of Progress Period
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)
Please also refer to previous meeting minutes of the Advisory Board at RecurringMeetings/2016-05-26. 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
Cloud computing interface has need been launched to resolve logistics, e.g. authorization/authentication, user tracking, software licensing etc. These issues were resolved in recent meetings between Cleveland Clinic, Stanford University, and University of Utah. Please refer to meeting minutes in Cleveland Clinic - Stanford University section of RecurringMeetings.
Ahmet has developed a simplified model from Open Knee(s) - Generation 1. This model is a kinematics driven femur, anterior cruciate ligament, tibia complex providing ligament force as output. For more details, please refer to the relevant wiki page, Revision as of December 21, 2016 or current version.
Detailed specifications on a prototype for web-based computing infrastructure can be found at the relevant wiki page, Revision as of December 21, 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.
- Efforts during the reporting period primarily focused on convenience features. In situ strain plug in has been disseminated at FEBio site. Parts feature was implemented. Work on wrapping springs (to model ligaments) continued. Next release of FEBio will include a new shell element formulation, which may be useful to model cartilage.
- Experimentation
- Joint level testing was completed. There will not be any additional specimen testing during the current funding period, keeping total number of Open Knee(s) specimens to 8.
Tissue testing has not started. Repeatability and reproducibility of tissue testing protocols have continued with successes and failures. Tissue testing specifications provide a dashboard to summarize protocol evaluation and repeatability assessment; see the wiki page, Revision as of December 21, 2016 or current version.
Modeling & simulation
- Further developments in Open Knee(s) - Generation 1 have not progressed. Model improvements to incorporate meniscal constraints and to implement in situ ligament strains are still planned but they are not a priority.
A simplified femur-anterior cruicate ligament-tibia model was developed based on Open Knee(s) - Generation 1. This will be used as a sample problem for cloud computing. For more details, please refer to the relevant wiki page, Revision as of December 21, 2016 or current version.
Segmentation work on Open Knee(s) - Generation 2 specimens is ongoing in a collaborative fashion. The segmented volumes and geometries are available in the source code repository. For current state of work, please refer to dashboards in the segmentation and geometry progress sections in the Roadmap (Revision as of December 21, 2016)
- Benjamin Landis developed Python scripts to utilize with Salome to automate mesh generation, mesh assembly, and model generation. Documentation of these processes has started in specifications related to:
Mesh generation (Revision as of December 21, 2016 or current version),
mesh assembly (Revision as of December 21, 2016 or current version), and
model assembly (Revision as of December 21, 2016 or current version).
- Dissemination
As of December 21, 2016, Open Knee(s) provided 9 packages (6,578 total downloads, 1,665 unique downloads), see Open Knee(s) download page:
- oks001 version g2-s1-v0.2.0.20150825 (171 unique users as of December 21, 2016)
- oks002 version g2-s2-v0.2.0.20150916 (50 unique users as of December 21, 2016)
- oks003 version g2-s3-v0.2.0.20151013 (25 unique users as of December 21, 2016)
- oks004 version g2-s4-v0.2.0.20151029 (22 unique users as of December 21, 2016)
- oks006 version g2-s6-v0.2.0.20150915 (21 unique users as of December 21, 2016)
- oks007 version g2-s7-v0.2.0.20151021 (22 unique users as of December 21, 2016)
- oks008 version g2-s8-v0.2.0.20151021 (29 unique users as of December 21, 2016)
- oks009 version g2-s9-v0.2.0.20151208 (46 unique users as of December 21, 2016)
Open Knee - Generation 1 versions g1-s1-v1.1.0.391 & g1-s1-v1.0.1.202 (689 unique users as of December 21, 2016):
As of December 21, 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 December 21, 2016, Open Knee(s) website received 4,209 page hits in the past 180 days with 642 unique visitors, see Open Knee(s) project activity.
As of December 21, 2016, Open Knee(s) enabled 21 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 completed:
- Connor Lough, from Saint Louis University, returned back and worked on segmentation and geometry comparison.
- Raghav Malik, from Mentor High School, returned back and worked on software improvements for automated measurement of tissue thickness using a camera-based system.
- Petre Tanska, from University of Eastern Finland, joined the team for three weeks to gain experience in modeling and simulation strategies.
- Jason Halloran and Will Zaylor, from the Cleveland State University, has been attending recurring meetings of the Cleveland Clinic team.
- Ahmet Erdemir provided lectures to promote modeling and simulation biomechanics, which are relevant to Open Knee(s) activities:
Erdemir, A., Democratization of modeling & simulation in biomechanics, BME Seminar Series, June 30, 2016, Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH.
- Erdemir, A., Computational modeling and potential impact on clinical medicine, Cleveland Clinic Orthopaedic Research Center Basic Science Day, June 10, 2016, Lerner Research Institute, Cleveland Clinic, Cleveland, OH.
- Publications
- 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 had publications in peer-reviewed journals related to synergistic activities:
- Erdemir, A., Guess, T. M., Halloran, J. P., Modenese, L., Reinbolt, J. A., Thelen, D. G., and Umberger, B. R. (2016) Commentary on the integration of model sharing and reproducibility analysis to scholarly publishing workflow in computational biomechanics, IEEE Transactions on Biomedical Engineering, 63, 2080-2085.
- Ahmet Erdemir was invited for presentations in scientific conferences related to synergistic activities:
Erdemir, A. Leveraging modeling & simulation in biomechanics for scientific discovery, medical innovation, and clinical care, 8th National Biomechanics Congress with International Participation, October 19-23, 2016, Hacettepe University Beytepe Congress Center, Ankara, Turkey.
- Erdemir, A. Data and data management for finite element analysis in joint biomechanics, XXI Congress of the International Society of Electrophysiology and Kinesiology, July 5-8, 2016, Chicago, IL.
- Drafts of manuscripts on anatomical imaging and joint mechanics testing of the Open Knee(s) - Generation 2 specimens:
- Other
Ahmet and Jason Halloran (Cleveland State University), along with Kevin Shelburne and Peter Laz (University of Denver), Carl Imhauser (Hospital for Special Surgery), and Thor Besier (Auckland Bioengineering Institute), submitted a grant application for potential collaborative work in reproducibility in modeling & simulation of the knee joint.
The grant application to Burroughs Wellcome Fund was not funded. This proposal aimed to expand upon Open Knee(s) through a structured verification & validation study.
Details of activities can be found in past meeting minutes of various teams at RecurringMeetings.
Plans for Next Progress Period (December 30, 2016 - May 2017)
Launch cloud computing at SimTk.org (Stanford University)
- Upgrade Open Knee(s) - Generation 1 to reflect meniscal constraints and in situ ligament strains (Cleveland Clinic)
- Continue implementing additional convenience features for simulation of joint mechanics using FEBio (University of Utah)
- Continue 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)
- 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. The project slowed down following departure of personnel. It is anticipated that a no cost extension will be requested to continue project related activities for another year.
Meeting Minutes
Date, Time, Means:
- December 22, 2016, 11:00 AM EST, Skype (AE,TG)
- December 29, 2016, 10:00 AM EST, phone call (AE,JA,YD)
- January 5, 2017, 9:00 AM EST, Skype (AE,RK)
Attendees:
- Ahmet Erdemir (Cleveland Clinic)
- Jack Andrish (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.
Ongoing Action Items:
See notes for details.
Cleveland Clinic
- Continue tissue mechanics testing of Open Knee(s) specimens.
- Continue development of Open Knee(s) models.
- Review and submit publications on Open Knee(s) data.
Stanford University
- Launch and support cloud computing for Open Knee(s).
University of Utah
- Implement additional convenience features in FEBio for Open Knee(s) simulations.
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 with individual members of the Advisory Board. In each of these, he provided a summary of progress and plans for the upcoming year. He reported that he slowed down the project and he will likely ask for a no cost extension to continue for another year. He summarized the ongoing activities as tissue testing, segmentation, and model development. He emphasized the automated model assembly approach, which will facilitate modeling once segmented geometries become available. He provided an update on past, recent, and future grant applications for the expansion of Open Knee(s). Other highlights from the individual meetings are noted below.
- Trent and Ahmet mostly discussed tissue testing, segmentation, and model development. Trent mentioned his interest in meniscus data for some his potential projects. He may contact Ahmet in this regard in a few months. Ahmet noted that he would be happy to provide more detailed information when needed.
- Jack asked about publications. Ahmet noted that while Open Knee(s) publications were delayed, there were other groups who utilized the first generation model in their studies and published. He also mentioned his interest to increase usability of Open Knee(s) models by providing them in different formats.
- Yasin encouraged Ahmet to document and potentially organize a conference session on lessons learned during development of free and open source virtual knee specimens. Ahmet indicated at he already had presented work in relevance to science of modeling and simulation. He would be interested in aforementioned activities in future but he would need to prioritize. He recommended to chat with Yasin in more detail in the upcoming Multiscale Modeling Consortium meeting in March, 2017.
- Yasin was also interested in testing of tissue for other scientific reasons, e.g. to characterize cartilage plasticity. Ahmet noted that the Open Knee(s) project has kept all the tissues from the specimens. Some of these specimens are not necessarily part of Open Knee(s) tissue testing protocol. Others will be kept after tissue testing for additional characterization, when and if requested. Yasin asked if Ahmet would be interested in other investigators visiting Cleveland Clinic to conduct such tests. Ahmet indicated that this would be a possibility. Yasin recommended Ahmet to devise a formal protocol to accomplish this.
- Ahmet informed Yasin about the strategy implemented for comparison of geometries segmented by different people on the same knee and tissue. This project emerged from previous discussions and a dashboard on the status of this activity can be found in the Roadmap.
- Rami and Ahmet mostly discussed tissue testing, particularly pre-conditioning strategies. Ahmet indicated that current testing protocols of Open Knee(s) utilizes 1000 cycles at 2 Hz for pre-conditioning to establish a repeatable tissue response.
- Rami and Ahmet also discussed Petri's work on cell scale modeling and how to move it forward. Petri visited the Open Knee(s) team just recently and spent three weeks on modeling and simulation.
- Recap of previous meeting minutes.
- The discussions mainly focused on progress and future plans (see item above).
- Action items for following meeting.
- Most action items were related to the ongoing agenda items, see above.
- Other.
- Refer to notes above for the agenda item on progress update.