• RecurringMeetings
• 2013-10-28

Recurring Meeting of the Advisory Board

Date(s): October 28 - November 1, 2013

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

• September 16, 2013 - October 28, 2013

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. Scott Sibole

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

Goals of Progress Period

• Organize workload of Cleveland Clinic, Stanford University, and University of Utah teams
• Start recurring meetings with team members
• Establish web based collaboration infrastructure
• Start development of web based computation infrastructure
• Start development of simulation software improvements
• Start development and review of experimentation specifications

For more details, see the proposed timeline of the proposal in attachment:GrantInformation/proposal.pdf.

Activities of Progress Period

• Organization

  • As part of a specifications task entitled Roadmap, a wiki page was created; see [http://wiki.simtk.org/openknee/Roadmap?action=recall&rev=14 Revision as of October 27, 2013] or [:Roadmap: current version]. The document provides centralized access to descriptions of infrastructure, specifications, and development milestones for Open Knee(s) utilities and models.

  • First set of meetings with [:RecurringMeetings/2013-09-30: Cleveland Clinic Core Team], between [:RecurringMeetings/2013-10-07-1700:Cleveland Clinic & Stanford University], and between [:RecurringMeetings/2013-10-07-1300:Cleveland Clinic & University of Utah] were conducted to distribute project workload, clarify expectations, and pinpoint deliverables.

• Recurring meetings

  • A task to establish recurring meetings has been completed by creating a wiki page; see [http://wiki.simtk.org/openknee/RecurringMeetings?action=recall&rev=26 Revision as of October 27, 2013] or [:RecurringMeetings: current version]. The document describes the means to conduct the meetings and also provides access to meeting minutes.

• Web based collaboration infrastructure

  • The project site at https://simtk.org/home/openknee provides the web based collaboration infrastructure for development and dissemination. Please refer to InstructionsForProjectSite to learn specific components of the web site.

  • The wiki at http://wiki.simtk.org/openknee provides the capacity for collaborative development of scientific content, e.g. specifications. Please refer to InstructionsForWiki to get accustomed to using the wiki.

  • The source code repository located at https://simtk.org/svn/openknee provides a version control system and the means for collaborative development of software, data analysis code, and models. Please refer to InstructionsForSourceCodeRepository to learn using this system.

  • The project site, wiki, and source code repository was updated to move the previous Open Knee work as [:GenerationOne:Open Knee - Generation 1].

• Web based computation infrastructure
  • Cleveland Clinic and Stanford University had a conference call to discuss web based computation infrastructure. Please refer to [:RecurringMeetings/2013-10-07-1700: meeting minutes].

  • A specifications task entitled Test workflow for cloud computing prototype was created to provide a simple test problem on the wiki, in order to support development of a cloud computing prototype.

• Simulation software improvements
  • Cleveland Clinic and University of Utah had two conference calls to discuss improvement in simulation software. Please refer to meeting minutes ([:RecurringMeetings/2013-10-07-1300:October 7, 2013] and [:RecurringMeetings/2013-10-23:October 23, 2013]).

  • As part of specifications task entitled Febio feature requests, Cleveland Clinic team provided prioritization of desired FEBio features and a test problem in the wiki; see [http://wiki.simtk.org/openknee/Specifications/FebioFeatures?action=recall&rev=16 Revision as of October 27, 2013] or [:Specifications/FebioFeatures: current version].

  • Details of FEBio, simulation software for finite element analysis, can be found in ["Infrastructure/SimulationSoftware"].
• Experimentation specifications

  • Various specifications tasks were started and corresponding wiki pages have been created to document operation procedures to conduct experimentation on specimens. These pages are aimed to guide anyone to follow up the steps to reach the targeted outcome of a given experimentation procedure. The specifications wiki page lists all these along with an illustration of the overall experimentation workflow, see [http://wiki.simtk.org/openknee/Specifications?action=recall&rev=27 Revision as of October 27, 2013] or [:Specifications: current version].

  • A high priority specification is related to specimens in order to start acquisition of knee samples. A related wiki page is complete; see [http://wiki.simtk.org/openknee/Specifications/Specimens?action=recall&rev=19 Revision as of October 27, 2013] or [:Specifications/Specimens: current version]. An anticipated difficulty in this procedure is the potentially limited access to osteoarthritic knee specimens.

  • Before conducting anatomical imaging and mechanical testing specimens need to be prepared appropriately. Relevant information has been

accumulated in wiki pages related to preparation ([http://wiki.simtk.org/openknee/Specifications/SpecimenPreparation?action=recall&rev=9 Revision as of October 27, 2013] or [:Specifications/SpecimenPreparation: current version]) and registration ([http://wiki.simtk.org/openknee/Specifications/Registration?action=recall&rev=13 Revision as of October 27, 2013] or [:Specifications/Registration: current version]). Anticipated difficulties in these procedures are i) potential redesign of brass components to minimize imaging artifacts, ii) development of new holding fixtures to transport specimens, and iii) redesign of registration markers for femur and tibia.

• Imaging, see [http://wiki.simtk.org/openknee/Specifications/ExperimentationAnatomicalImaging?action=recall&rev=11 Revision as of October 27, 2013] or [:Specifications/ExperimentationAnatomicalImaging: current version].

• Joint testing, see [http://wiki.simtk.org/openknee/Specifications/ExperimentationJointMechanics?action=recall&rev=32 Revision as of October 27, 2013] or [:Specifications/ExperimentationJointMechanics: current version]

• Tissue testing, see [http://wiki.simtk.org/openknee/Specifications/ExperimentationTissueMechanics?action=recall&rev=4 Revision as of October 27, 2013] or [:Specifications/ExperimentationTissueMechanics: current version]

• Other

  • For publication of previous work on Open Knee, various publication tasks were created. An outline and a draft of Open Knee - Generation 1 manuscript can be found in [https://simtk.org/websvn/wsvn/openknee/_gen1/doc/manuscript.odt source code repository].

For a complete list of various tasks (finished or in progress), please refer to https://simtk.org/pm/?group_id=485.

Plans for Next Progress Period (October 29, 2013 - May 2014)

• Complete a prototype of web based computation infrastructure (Stanford University)
• Complete implementation of high priority features in simulation software (University of Utah)
• Complete experimentation (specifications and data collection) for Specimen 001 (Cleveland Clinic)
• Disseminate data from Specimen 001 (Cleveland Clinic)

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

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

• Launch community projects program (reviews, internships, and collaborations) (Cleveland Clinic & Community)

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

For more details, see the proposed timeline of the proposal in attachment:GrantInformation/proposal.pdf.

Meeting Minutes

Date:

Time:

Means:

Attendees:

1. TBD

Agenda:

1. Project description
2. Expectations from Advisory Board
3. Progress update
4. Scheduling of biannual meetings
5. Action items for following meeting
6. Other

Immediate Action Items:

See notes for details.

• TBD

Notes:

1. TBD