- Opensim-announcement - SimTK Mailing Lists

OpenSim Workshop, New OpenSim Fellow, and More
by Jennifer Hicks 19 Dec '16

19 Dec '16

*Apply for the Upcoming OpenSim Workshop in Belgium* *February 6-8, 2017 in Leuven, Belgium* The workshop will focus on getting started with OpenSim for new research projects, including data import and using OpenSim’s workflow tools. It is open to beginning and intermediate users. OpenSim experts and fellows Friedl De Groote, Ilse Jonkers, Massimo Sartori, Giordano Valente, Luca Modenese, Dimitra Blana, and Mariska Wesseling will lead the workshop. Applications are being accepted on a rolling basis. Read more and apply <http://web.stanford.edu/group/opensim/support/event_details.html?id=171&tit…> . *Ricardo Matias Becomes Newest OpenSim Fellow* Congratulations to Ricardo Matias on becoming the newest OpenSim Fellow. Ricardo Matias is a senior researcher in the Neuromechanics of Human Movement Research Group at the University of Lisbon in Portugal. He was an OpenSim Visiting Scholar in 2015 and recently ran an introductory OpenSim workshop at the International Shoulder Group Annual Meeting, highlighting uses of the new OpenSim shoulder model <https://simtk.org/projects/scapulothoracic> he helped develop. This honor from the National Center for Simulation in Rehabilitation Research (NCSRR) recognizes a strong commitment to the OpenSim community and a deep expertise in biomechanical modeling and simulation. Read more about the current fellows <http://simtk-confluence.stanford.edu:8080/display/OpenSim/OpenSim+Fellows> and learn how to apply <http://web.stanford.edu/group/opensim/support/fellows.html>. *Apply to the NCSRR/OpenSim Visiting Scholars Program* *Summer 2017 at Stanford UniversityApplications are due on February 3, 2017* The National Center for Simulation in Rehabilitation Research (NCSRR) is now accepting applications for the 2017 Visiting Scholars Program. The program is a unique experience that fosters expertise and collaborations in biomechanical simulations for rehabilitation research. Up to four individuals will be chosen to visit the NCSRR at Stanford University for a 5-week period during the summer of 2017. Read more and learn how to apply <http://web.stanford.edu/group/opensim/support/scholars.html>. *Follow Us on Twitter* To get up-to-the-minute news related to OpenSim, follow us on Twitter <https://twitter.com/OpenSimSU>. We post information about our webinars and other events, relevant grant announcements, conferences of interest to the rehab and simulation communities, fellowship/postdoc opportunities, as well as recent publications that use OpenSim. -- *Jennifer Hicks, Ph.D.* Director of Data Science | Mobilize Center <http://mobilize.stanford.edu> Associate Director | NCSRR <http://www.stanford.edu/group/opensim/about/index.html> R&D Manager | OpenSim <http://opensim.stanford.edu/> Stanford University 650-498-4403 | jenhicks(a)stanford.edu

1 0

Call for Applications - NCSRR/OpenSim Visiting Scholars Program 2017
by Jennifer Hicks 13 Dec '16

13 Dec '16

*Apply for the NCSRR/OpenSim Visiting Scholars Program* *Summer 2017 at the National Center for Simulation in Rehabilitation Research, Stanford University* The National Center for Simulation in Rehabilitation Research (NCSRR) based at Stanford University is now accepting applications for the 2017 Visiting Scholars Program. The program is a unique experience that fosters expertise and collaborations in biomechanical simulations for rehabilitation research. Up to four individuals will be chosen to visit the NCSRR at Stanford University for a 5-week period during the summer of 2017, from mid-June to mid-July. Each visiting scholar will be reimbursed for their travel and living expenses up to $8,000. During their visits, awardees will receive training and mentoring to help them reach their research goals. They will have the opportunity to participate in formal meetings, discussions with OpenSim experts, and brainstorming sessions with their fellow visiting scholars to advance their research and the OpenSim project. The Visiting Scholars Program is intended for faculty members and postdoctoral fellows with exceptional skills in biomechanics, simulation, and computer science, who will advance the field of movement science through the development of new software, biomechanical models, and outstanding research. Applications are due Midnight PST, February 3, 2017. Read more and learn how to apply <http://web.stanford.edu/group/opensim/support/scholars.html>. -- *Jennifer Hicks, Ph.D.* Director of Data Science | Mobilize Center <http://mobilize.stanford.edu> Associate Director | NCSRR <http://www.stanford.edu/group/opensim/about/index.html> R&D Manager | OpenSim <http://opensim.stanford.edu/> Stanford University 650-498-4403 | jenhicks(a)stanford.edu

1 0

Webinar on Probabilistic Analyses, New OpenSim Simulation Resources, and More
by Jennifer Hicks 07 Nov '16

07 Nov '16

*Webinar: Enabling Stochastic Simulations of Movement with High Throughput Computing* *Wednesday, November 17, 2016 at 10:00 a.m. Pacific Standard Time* Colin Smith and Darryl Thelen from the University of Wisconsin-Madison will describe a framework that enables the probabilistic analyses of simulation results on high throughput computing systems. They will also demo how to run OpenSim simulations on the Open Science Grid. Learn more and register <http://opensim.stanford.edu/support/event_details.html?id=169>. *Solving Inverse Kinematics and Inverse Dynamics in Real-Time* Claudio Pizzolato, David Lloyd, and Luca Modenese from Griffith University, Australia and Monica Reggiani from University of Padua, Italy have recently published their new methods on computing inverse kinematics and inverse dynamics in real-time in Computer Methods in Bioengineering and Biomedical Engineering <http://www.tandfonline.com/doi/full/10.1080/10255842.2016.1240789>. This extension, called the Real-Time OpenSim Extension (RTOSIM), can connect OpenSim to different devices and perform those calculations on a frame-by-frame basis. RTOSIM is available on SimTK <https://simtk.org/projects/rtosim>. *Simulating Ideal Assistive Devices to Reduce the Metabolic Cost of Running* Thomas Uchida and colleagues at Stanford University published a paper in PLOS One <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163417> where they simulated running with different ideal assistive devices to examine the predicted changes in muscle recruitment patterns and metabolic power consumption. The data underlying the findings are freely available at https://simtk.org/home/idealassist_run. *Announcing New OpenSim Fellow* Dimitra Blana from Keele University in the United Kingdom is our newest OpenSim Fellow. The OpenSim Fellows Program recognizes OpenSim experts who will collectively advance and help grow the field of neuro-musculoskeletal modeling and simulation. Dr. Blana is experienced in musculoskeletal modeling of the upper limb, particularly the shoulder, as well as in real-time simulation and optimal control. She was selected as an OpenSim Visiting Scholar in 2015 and has made significant contributions to the OpenSim community through her research and dissemination efforts. Learn more and/or apply <http://opensim.stanford.edu/support/fellows.html> to the OpenSim Fellows Program *Diverse Projects Advanced through Recent OpenSim Virtual Workshop* Last week a group of 35 U.S. and international scholars gathered virtually and advanced their OpenSim projects during the 2nd OpenSim Virtual Workshop. Projects covered a range of topics in rehabilitation science (e.g., tibia loading in children with myelomeningocele, deltoid activation post-reverse shoulder arthroplasty, and wheelchair propulsion), as well as new technical developments (e.g., a robotic linear actuator, integration of automatic differentiation, and OpenSim-finite element simulation pipelines). Learn more <https://docs.google.com/presentation/d/1NASW24LapmGHHFOnLh-Y-Qz59fGx13O-5tm…> about the workshop projects and what they accomplished *Follows Us on Twitter* To get up-to-the-minute news related to OpenSim, follow us on Twitter <https://twitter.com/OpenSimSU>. We post information about our webinars and other events, relevant grant announcements, conferences of interest to the rehab and simulation communities, fellowship/postdoc opportunities, as well as recent publications that use OpenSim. -- *Jennifer Hicks, Ph.D.* Director of Data Science | Mobilize Center <http://mobilize.stanford.edu> Associate Director | NCSRR <http://www.stanford.edu/group/opensim/about/index.html> R&D Manager | OpenSim <http://opensim.stanford.edu/> Stanford University 650-498-4403 | jenhicks(a)stanford.edu

1 0

Webinar on Musculoskeletal Modeling, Code for Solving Muscle Redundancy Problem, and More
by Joy P. Ku 12 Oct '16

12 Oct '16

Webinar: Musculoskeletal Models Deconstructed Wednesday, October 19, 2016 at 10:00 a.m. Pacific Daylight Time Apoorva Rajagopal from the OpenSim team will provide an overview of OpenSim model components and describe how different modeling choices affect the simulated dynamics. Learn more and register<http://opensim.stanford.edu/support/event_details.html?id=167> Video at JavaOne 2016 Conference Features OpenSim OpenSim is featured in a video that was part of the keynote for the JavaOne 2016 Conference last month. The video will also be shown at regional JavaOne events over the next 9 months. View video<https://youtu.be/_AlZuUCoXGY> (the OpenSim portion begins ~1:55). Robust, Computationally Efficient Formulations for Solving Dynamic Optimization Problems Using Direct Collocation Friedl De Groote from KU Leuven, Belgium and BJ Fregly from the University of Florida have recently published their results in the Annals of Biomedical Engineering<http://link.springer.com/article/10.1007%2Fs10439-016-1591-%E2%80%8B9> comparing different direct collocation optimal control formulations for solving the muscle redundancy problem. Their MATLAB code, together with OpenSim models and experimental data to solve the muscle redundancy problem in the leg during walking and running, is available on SimTK<https://simtk.org/projects/optcntrlmuscle>. Medical Rehabilitation Research Resource (MR3) Network The National Center for Simulation in Rehabilitation Research (NCSRR), which supports OpenSim, is one of six resource centers from across the United States that are part of the MR3 Network<https://ncmrr.org/>. MR3 Network centers provide infrastructure and access to expertise, technologies, and resources to support medical rehab research, focusing on areas such as clinical trial design, neuromodulation, regenerative medicine, large data research, and translation. To stay connected and receive the latest announcements about funding opportunities, training, conferences, and meetings available through the MR3 Network, sign-up for e-mail updates<https://ncmrr.org/join/>. --- Joy P. Ku, PhD Project Manager, SimTK<http://simtk.org/> Director of Communications & Training, NCSRR<http://opensim.stanford.edu/> Director of Communications & Engagement, Mobilize Center<http://mobilize.stanford.edu/> Stanford University (w) 650.736.8434, (f) 650.723.7461 Email: joyku(a)stanford.edu

1 0

Virtual Workshop Applications Due Friday
by Jennifer Hicks 20 Sep '16

20 Sep '16

*Apply for the Next Virtual Workshop for Advanced OpenSim Users* *October 24 -28, 2016* *Applications Due September 23*Building on the success of our first virtual workshop this spring, we are pleased to announce the next event will take place over the course of one week in October. The goal of the workshop is to accelerate the research projects of OpenSim community members. Participants will work on their projects, with support and advice from the Stanford University OpenSim team and each other. The event will span one week, including two video conference meetings, along with daily chat forum support. It is expected that participants have already begun to use OpenSim for their project. Teams of applicants are highly encouraged. Learn more and apply <http://opensim.stanford.edu/support/event_details.html?id=165&title=Virtual…> . *OpenSim Part of Course on Open Source Tools for Biomechanics* Last week the OpenSim team, led by Chris Dembia of Stanford University, participated in a one-day course <http://ieeeboston.org/open-source-tools-computational-biomechanics/> on open-source software for biomechanics, organized by Kevin Moerman at the MIT Media Lab. Approximately 25 individuals attended and gained hands-on experience with the OpenSim application and MATLAB scripting interface. You can download the slides here <http://stanford.edu/~dembia/IEEEBostonCourseOpenSimSlides.pdf>. Attendees also learned how to use FEBio <http://febio.org/> and GIBBON <http://www.gibboncode.org/>. A number of attendees were interested in combining OpenSim with finite element analyses. -- *Jennifer Hicks, Ph.D.* Director of Data Science | Mobilize Center <http://mobilize.stanford.edu> Associate Director | NCSRR <http://www.stanford.edu/group/opensim/about/index.html> R&D Manager | OpenSim <http://opensim.stanford.edu/> Stanford University 650-498-4403 | jenhicks(a)stanford.edu

1 0

Apply for the Next Virtual Workshop and More OpenSim News
by Jennifer Hicks 01 Sep '16

01 Sep '16

*Apply for the Next Virtual Workshop for Advanced OpenSim Users* *October 24 -28, 2016* Building on the success of our first virtual workshop this spring, we are pleased to announce the next event to take place over the course of one week in October. The goal of the workshop is to accelerate the research projects of OpenSim community members. Participants will work on their projects, with support and advice from the Stanford University OpenSim team and each other. The event will span one week, including two video conference meetings, along with daily chat forum support. It is expected that participants have already begun to use OpenSim for their project. Teams of applicants are highly encouraged. Learn more and apply <http://opensim.stanford.edu/support/event_details.html?id=165&title=Virtual…> . *New Discrete Model of the Knee Enables Cosimulation* Anne Schmitz and colleagues have developed and validated a discrete model of the knee that includes both ligaments and cartilage contact. This enables it to be used in cosimulation experiments, coupling musculoskeletal dynamics with soft tissue mechanics. The article “Development of an Open-Source, Discrete Element Knee Model <http://ieeexplore.ieee.org/document/7501488/?arnumber=7501488>” in *IEEE Transactions on Biomedical Engineering* describes the model and its validation against cadaveric data. The model is freely available for download at https://simtk.org/projects/kneemodel. A co-simulation framework for the knee is also available at https://simtk.org/projects/uwcosim. *Openings at Oregon State University’s Robotics and Human Control Systems Lab* OpenSim Fellow Ravi Balasubramanian at Oregon State University has openings for graduate students and postdocs to work on projects to augment or restore human function in manipulation and locomotion tasks by designing implantable mechanisms. Learn more <http://biomch-l.isbweb.org/threads/29222-Robotics-biomechanics-Seeking-post…> . *Course on Open-Source Tools for Computational Biomechanics* *Thursday, September 15, 2016MIT Media Lab, Cambridge, MA* This course introduces participants to three open-source tools: GIBBON for image segmentation; FEBio for finite element analysis; and OpenSim for musculoskeletal modeling and simulation. The OpenSim portion will include a discussion of using OpenSim for predictive simulation and muscle activity estimation, and a survey of research studies integrating OpenSim with finite element modeling. Participants will also have the opportunity to work hands on with each software package. Learn more and register <http://ieeeboston.org/open-source-tools-computational-biomechanics/>. -- *Jennifer Hicks, Ph.D.* Director of Data Science | Mobilize Center <http://mobilize.stanford.edu> Associate Director | NCSRR <http://www.stanford.edu/group/opensim/about/index.html> R&D Manager | OpenSim <http://opensim.stanford.edu/> Stanford University 650-498-4403 | jenhicks(a)stanford.edu

1 0

Workshop in Boston Area, New Full Body Model, and Postdoc Openings
by Joy P. Ku 17 Aug '16

17 Aug '16

Course on Open-Source Tools for Computational Biomechanics Thursday, September 15, 2016 MIT Media Lab, Cambridge, MA This course introduces participants to three open-source tools: GIBBON for image segmentation; FEBio for finite element analysis; and OpenSim for musculoskeletal modeling and simulation. The OpenSim portion will include a discussion of using OpenSim for predictive simulation and muscle activity estimation, and a survey of research studies integrating OpenSim with finite element modeling. Participants will also have the opportunity to work hands on with each software package. Learn more and register<http://ieeeboston.org/open-source-tools-computational-biomechanics/>. New Full Body Model Available Apoorva Rajagopal and colleagues at Stanford University have developed and validated a new full body model. The model has a muscle force distribution reflective of those of a young, healthy population, includes a new knee model to accurately represent internal forces, and has increased performance due to simplified muscle-wrapping surfaces. The associated publication<http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7505900> will appear in a special issue of IEEE Transactions on Biomedical Engineering on reproducible research. The model is freely available for download at https://simtk.org/projects/full_body. Reflex Controller Models Contracture and Spasticity in Children with Cerebral Palsy Past Visiting Scholar Marjolein van der Krogt (VU University Medical Center) and colleagues have recently published the article "Neuro-musculoskeletal Simulation of Instrumented Contracture and Spasticity Assessment in Children with Cerebral Palsy"<https://jneuroengrehab.biomedcentral.com/articles/10.1186/s12984-016-0170-5> in the Journal of NeuroEngineering and Rehabilitation. The study utilizes a reflex controller model implemented in OpenSim to study the role of altered passive muscle stiffness in contracture and of velocity-dependent stretch reflex in spasticity. The controller is available for download at https://simtk.org/projects/spasticitymodel. Workshop at International Shoulder Group Annual Meeting Past Visiting Scholars Dimitra Blana and Ricardo Matias ran a successful workshop at the International Shoulder Group's Annual Meeting<https://www.zhaw.ch/de/engineering/institute-zentren/imes/conference-of-the…> in July. Approximately 30 individuals participated, gaining hands-on experience with scaling and running inverse kinematics using the new shoulder model<https://simtk.org/projects/scapulothoracic> from Seth and Matias. You can download the slides, as well as the files and instructions for the hands-on examples, by visiting the workshop webpage<http://simtk-confluence.stanford.edu:8080/display/OpenSim/International+Sho…>. Postdoctoral Openings at University of Washington's Ability & Innovation Lab OpenSim Fellow Kat Steele at the University of Washington has two postdoctoral openings for individuals with a background in engineering, computer science, or a closely related field. One project is to study neuromuscular control in cerebral palsy using muscle synergy analysis and OpenSim simulations. The second project is the creation of mobile technology to track and train muscle activity after stroke. Learn more<http://depts.washington.edu/uwsteele/get-involved/> --- Joy P. Ku, PhD Director, Simbios<http://simbios.stanford.edu/> Director of Communications & Training, NCSRR<http://opensim.stanford.edu/> Director of Communications & Engagement, Mobilize Center<http://mobilize.stanford.edu/> Stanford University (w) 650.736.8434, (f) 650.723.7461 Email: joyku(a)stanford.edu

1 0

Webinar on Jogging Biomechanics and OpenSim Pilot Project Grants
by Announcements of OpenSim releases and updates 16 Jun '16

16 Jun '16

*Participate in Our Next Webinar: Investigating Jogging Biomechanics using the Full-Body Lumbar Spine Model* *Thursday, June 23, 2016 at 10:00am, Pacific Daylight Time* Ajit Chaudhari and Margaret Raabe (The Ohio State University) will describe the development and validation of a new full-body lumbar spine model. They will describe how they applied the model to address the biomechanical consequences of running with core muscle weakness. Read more and register <http://web.stanford.edu/group/opensim/support/event_details.html?id=161>. *Apply for an OpenSim Pilot Project Grant up to $40,000* *Applications Due July 20, 2016* The National Center for Simulation in Rehabilitation Research (NCSRR) and OpenSim project at Stanford seek proposals for our pilot project program. The program awards seed grants to innovative and meritorious projects that will accelerate the use of simulation in rehabilitation research. Pilot project awardees may request funding (up to $40,000) for their research. Find more information and the application packet <http://opensim.stanford.edu/support/pilot.html>. -- *Jennifer Hicks, Ph.D.* Director of Data Science | Mobilize Center <http://mobilize.stanford.edu> Associate Director | NCSRR <http://www.stanford.edu/group/opensim/about/index.html> R&D Manager | OpenSim <http://opensim.stanford.edu/> Stanford University 650-498-4403 | jenhicks(a)stanford.edu

1 0

Webinar on Shoulder Modeling, Pilot Projects, Visiting Scholars Selected, and More
by Announcements of OpenSim releases and updates 02 Jun '16

02 Jun '16

*Participate in Our Next Webinar: A Novel Scapulothoracic Joint Model* *Thursday, June 9, 2016 at 9:30am. Pacific Daylight Time*Ajay Seth (Stanford University) and Ricardo Matias (University of Lisbon) will describe the development and validation of a new scapulothoracic joint model and show how it can be used to examine shoulder motions during activities of daily living. Read more and register <http://web.stanford.edu/group/opensim/support/event_details.html?id=159>. *Apply for an OpenSim Pilot Project Grant up to $40,000* *Applications Due July 20, 2016* The National Center for Simulation in Rehabilitation Research (NCSRR) and OpenSim project at Stanford seek proposals for our pilot project program. The program awards seed grants to innovative and meritorious projects that will accelerate the use of simulation in rehabilitation research. Pilot project awardees may request funding (up to $40,000) for their research. Find m <http://opensim.stanford.edu/support/pilot.html>ore information and the application packet <http://opensim.stanford.edu/support/pilot.html>. *Congratulations to the 2016 NCSRR Visiting Scholars* The NCSRR will host its fifth group of Visiting Scholars this summer. We selected four exceptional candidates from a large and highly competitive pool of applicants based on their outstanding scientific potential, strong computational skills, and past contributions in modeling and simulation. The 2016 Scholars include Xiao Hu, Brad Humphreys, Colin Smith, and Ju Zhang. Read more about the scholars and their projects here <http://www.stanford.edu/group/opensim/support/scholars.html#2016Scholars>. *Inaugural Virtual OpenSim Workshop a Success* Over 30 international researchers participated in our first Virtual Workshop, coming together over two weeks to share their expertise, successes, and challenges using OpenSim for research. Virtual poster presentations afforded participants the opportunity to show off their research and discuss shared challenges in modeling and simulation. Using video conferencing, participants discussed their projects with the OpenSim team--getting advice on how to use software tools to address their research questions. A specialized forum served as a gathering place to ask questions and have discussions about approaches to difficult problems. We look forward to having additional virtual events in the future, and we hope many more of you will be able to participate. Read more on the workshop wiki <http://simtk-confluence.stanford.edu:8080/display/OpenSim/Virtual+Workshop+…> . -- *Jennifer Hicks, Ph.D.* Director of Data Science | Mobilize Center <http://mobilize.stanford.edu> Associate Director | NCSRR <http://www.stanford.edu/group/opensim/about/index.html> R&D Manager | OpenSim <http://opensim.stanford.edu/> Stanford University 650-498-4403 | jenhicks(a)stanford.edu

1 0

Call for Applications: NCSRR/OpenSim Pilot Projects 2016
by Announcements of OpenSim releases and updates 20 May '16

20 May '16

The National Center for Simulation in Rehabilitation Research (NCSRR) and OpenSim project at Stanford seek proposals for our pilot project program. The program awards seed grants to innovative and meritorious projects that will accelerate the use of simulation in rehabilitation research. Our intent is to engage rehabilitation research experts to demonstrate the use of biomechanical simulations in novel areas and to help enhance the OpenSim software for rehabilitation science. Pilot project awardees may request funding (up to $40,000) for their research. In addition, the program launches awardees into leadership roles within the NCSRR network. Projects should have a strong scientific component and demonstrate a clear alignment with the NCSRR’s mission <http://www.stanford.edu/group/opensim/about/index.html>. Research proposals (up to 3 pages) should provide a scientific description of the project to be performed and convey the impact on rehabilitation and the biomechanical simulation community. Applications must also include a description of funding and other support requested. More information and the application packet can be found at the following website: http://opensim.stanford.edu/support/pilot.html All application materials must be received by midnight on July 20, 2016. Winners will be announced by October 2016 with funding to start in late 2016. 1) Written proposals and supporting materials should be sent electronically, preferably as a single PDF, to opensim(a)stanford.edu 2) You must also complete the online application/registration form <https://docs.google.com/forms/d/1SACxr3IP3khr_s0-_sZkeqw0tFe1QDC9u81cgQRoZb…> . We look forward to reviewing another excellent set of proposals for the pilot project program. Best Wishes, Jen Hicks -- *Jennifer Hicks, Ph.D.* Director of Data Science | Mobilize Center <http://mobilize.stanford.edu> Associate Director | NCSRR <http://www.stanford.edu/group/opensim/about/index.html> R&D Manager | OpenSim <http://opensim.stanford.edu/> Stanford University 650-498-4403 | jenhicks(a)stanford.edu

1 0