ErdemirA 08:48, 16 August 2010 (EDT) Working Group 6 members, please welcome our new member Reuben Kraft. Reuben showed an interest to our working group after following the IMAG wiki. He leads the Computational Bio-Injury Mechanics Group ath Army Research Laboratory in Aberdeen Proving Ground, MD.
ErdemirA 16:13, 27 July 2010 (EDT) James, this is great to hear. I will definitely be interested in participating. Frankly, with Reporting in FEA, what we try to do is probably a small subset of this. Is there an interest to use such codes and standards for reporting material in Journal of Biomechanical Engineering.
MooreJ The American Society of Mechanical Engineers (ASME) has initiated the process of writing codes and standards for computational biomechanics modeling. The primary goal at this point is to provide guidelines for medical device companies that would like to use computational simulations in their FDA submissions. If anyone is interested in participating, let me know and I will ask permission to post the contact info of the organizer.
ErdemirA 11:24, 27 July 2010 (EDT) Working Group 6 members, please welcome our new member Vijay Rajagopal. Merryn decided to be an observer to the group and nominate Vijay to join us. Vijay's previous research has been in the development of continuum mechanics models for breast tissue deformation, and he has a current interest in quantifying and modelling sub-cellular structures in cardiac cells.
On another note, the outline of Reporting in FEA was drafted and I need help to fill in many of its components. Trent, Jason, and Srinivas has agreed to take care of some, in particular sections on Current state-of-the-art in reporting models and Case Study. If you use finite element analysis as a tool, or rely on others FEA work in your research, or encounter it by any means and have something to say, please do so and help standardize reporting of studies utilizing this great numerical tool.
Jill, relevant to Reporting in FEA, I wonder if American Society of Biomechanics has certain recommendations for its members when reporting computer simulations studies. Any comments?
ErdemirA 12:05, 21 June 2010 (EDT) Trent, myself, Jason, and Srinivas have met at the ASME Summer Bioengineering Conference between June 16-19, 2010. Our planned activities, shaped by our discussions, are summarized below. All Working Group participants are more than welcome to contribute and provide feedback.
- Working on a white paper focusing on reporting of computational modeling studies in biomechanics (see Reporting in FEA)
- Contribution to a white paper from Working Group 10 on modular modeling
- Preparing an IMAG presentation on surrogate modeling. Surrogate modeling is used to approximate response of complex models with the intent to decrease computational cost of coupled problems. This presentation will likely be based on work by Trent's group and by Jason, potentially incorporating Fregly's work, which are used to couple movement simulations with contact and tissue mechanics.
- Following my discussions with Jeff Weiss, an IMAG presentation on FEBio, finite element analysis package for biomechanics, may be a possibility.
ErdemirA 08:58, 7 June 2010 (EDT) Trent, myself, Jason and Srinivas will be at ASME Summer Bioengineering Conference between June 16-19, 2010. We are planning to have an informal meeting to discuss WG6 related issues and future. If you will be at the conference, please join us. Let's try to find each other at the opening reception. For those who need information on how we look like, see IEEE EMBS Article for a mugshot of myself and Trent.
ErdemirA 10:49, 25 November 2009 (EST) I am trying to conduct a mini survey based on some recent discussions in MSM and IMAG. The survey can be found in Survey on Modeling and Simulation. Please contribute by adding your comments below the questions. Add any other questions and items that you see relevant.
ErdemirA 16:24, 27 October 2009 (EDT) There has been a significant amount of e-mail traffic between myself, Trent, Joy Ku (Simbios), Grace Peng (NIH), Luis Ibanez (Kitware), and Philip Bourne (PLoS Computational Biology) on the need and mechanisms to start a journal to disseminate data, models, and software for simulation-based medicine. The discussion is becoming mature, therefore a wiki page is created at Journal for Dissemination.
ErdemirA 16:14, 8 September 2009 (EDT) Trent and I had a chance to meet during the Annual Meeting for the American Society of Biomechanics and discussed various issues relevant to multiscale modeling in tissue mechanics and the working group. Below is a summary, please provide feedback.
- Recruiting New Working Group Members: The more the merrier. Additional members with relevant research in multiscale musculoskeletal and tissue mechanics will likely stimulate our knowledge and establish new collaboration pathways by providing different perspectives. If anyone knows someone at this capacity and who is interested in discussions with our working group, please let me know. Someone that I am interested in inviting is Jess Snedeker from University of Zurich, http://www.biomechanics.ch/.
- Presentations by Software Developers: Open source development is continuing at a high pace and we have now access to many model development and simulations. Two relevant examples are FEBio and IA-FEMESH. We can invite the leading investigators in these projects (Jeff Weis, University of Utah and Nicole Grosland, University of Iowa) to provide MSM webinars.
- Advertising MSM webinars on Biomch-L: We can increase visibility of MSM webinars relavant to musculoskeletal biomechanics and tissue mechanics by advertising them at BIOMCH-L listserver. Is attendance to webinars from anyone in the community allowed? I notice that bandwidth maybe a problem.
- Article on Art of Modeling: Trent and I discussed about many tips and tricks that we employ in modeling but are not necessarily learned in a scientific manner. I.e., why tetrahedral elements work in some simulations and they do not in others? There are many such knowledge we gain through trial and error and or through word-of-mouth from the experience of previous generations. How can we document such knowledge that it can be more accessible?
- Journal Data, Model, and Software Dissemination: It appears that dissemination of data, model and software is rather slow and incomplete when compared to amount of work we conduct. A major reason for that is we all need to wait until we get our publications out and get credit for doing the work, which is only possible if a scientific question is addressed. In addition, bringing the data into a usable form more or less accessible by others can be a long and tedious process. While a scientific publication is focused on the research problem, it does not necessarily detail relevant data specifications nor provide a complete data set with full documentation. Can starting a journal designed for dissemination in simulation-based medicine expedite this process? It will definitely have different review criteria (more or less a certification process and a quick one) but it should definitely provide mechanisms to cite data, model or software, e.g. a doi number, and be incorporated into literature databases, e.g. PubMed. Any comments? Should we pass this idea to the MSM consortium?
Working Group 6: Tissue Mechanics
Working Group Leads:
Goals and Objectives
- determine computational priorities and challenges related to multi-scale modeling (MSM), specifically MSM of tissue mechanics and biomechanics,
- explore solutions for model sharing, and
- provide a forum for discussion of issues related to MSM and biomechanics
Working Group 6 Participants
- Bindi Brook
- Daniel Einstein
- Ahmet Erdemir (co-lead), Media:erdemir-research_area.pdf
- Trent Guess (co-lead), Media:WG_6_Guess.pdf
- Jason Halloran
- Anthony Hunt Media:Research_Description_for_MSM04May10.pdf
- Reuben Kraft
- Jill McNitt-Gray
- James Moore Media:MooreLymphModelingBackground.pdf
- Tina Morrison Tina's Website
- Peter Pivonka, Media:ECB-research-description.pdf
- Vijayaraghavan Rajagopal Vijay's Profile
- Jeff Reinbolt
- Jess Snedeker, Media:snedeker-research_area.pdf
- Srinivas Tadepalli, Srinivas Tadepalli's Profile
- Jeff Bischoff
- Ching-Long Lin
- Anil Misra
- James Glazier
- Merryn Tawhai
For participant details, see Working Group 6 Participants.
Friday June 26, 2009 4-5pm EDT - Ahmet Erdemir, Merryn Tawhai, Trent Guess
Multiscale Modeling in Computational Biomechanics
Abstract Biomechanics is broadly defined as the scientific discipline that investigates the effects of forces acting on and within biological structures. The realm of biomechanics includes the circulatory and respiratory systems, tissue mechanics and mechanotransduction, and the musculoskeletal system and motor control. As in many other biological phenomena, many spatial scales are crossed by biomechanics research: intracellular, multicellular, and extracellular matrices; and tissue, organ, and multiorgan systems. It is well established that the effect of forces at higher scales influence behavior at lower scales and that lower-scale properties influence higher-scale response. However, computational methods that incorporate these interactions in biomechanics are relatively rare. In general, computational models that include representation of multiple spatial or temporal scales are loosely defined as multiscale. The fact that multiscale modeling is not well defined lends the term to a variety of scenarios within the computational physiology community. In biomechanics, multiscale modeling may mean establishing a hierarchical link between the spatial and temporal scales, while the output of a larger-scale system is passed through a finely detailed representation at a lower scale (e.g., body-level movement simulations that provide net joint loading for tissue-level stress analysis). In reality, multiscale modeling may require more intricate representation of interactions among scales. A concurrent simulation strategy is inevitable to adequately represent nonlinear associations that have been known for decades.
Slides Media:Imag June 2009.pdf
Tuesday March 3, 2009 3-4pm EST - Scott Delp, Stanford University
OpenSim - an Open-Source Application for Musculoskeletal Modeling and Movement Simulations
Abstract: OpenSim is an open-source software application with a graphical user interface that allows users to develop models of musculoskeletal structures and create dynamic simulations of movement. First released in August 2007, OpenSim has already been downloaded by over 2000 users from a wide range of fields. In this talk, I will provide an overview of OpenSim and discuss the built-in tools, such as for computing inverse kinematics and muscle excitations. I will give some examples of how OpenSim has been used for studying gait, show some of the related resources that have been developed by the OpenSim community, and touch on some of the new features that are currently being incorporated into OpenSim.
OpenSim can be downloaded from http://simtk.org/home/opensim.
Speaker: Scott Delp is a professor in bioengineering at Stanford University and co-PI for Simbios, the NIH National Center for Biomedical Computing on physics-based simulation on biological structures. His research focuses on understanding the mechanisms involved in the production of movement, and spans the gamut from developing new simulation tools and algorithms, to working on novel experimental and imaging techniques, to addressing specific clinical questions related to cerebral palsy, stroke, Parkinson's disease, and osteoarthritis.
Working Group Issues
Working Group Name
Any thoughts on changing the working group name from Tissue Mechanics to Biomechanics? Based on our IEEE EMBS submission, this broader title might better align with our collective research areas.
Changing the name from Tissue Mechanics to Biomechanics may work better to cover all our research areas.
Multiscale Modeling in Tissue Mechanics
Multiscale Modeling Definition
Multi-scale typically means models that span multiple length and/or time scales. Is there a need to define computational multi-scale modeling specific to biomechanics? How would this be defined? Discussion on defining Multiscale Modeling in Biomechanics
- Musculoskeletal biomechanics
- Respiratory system
- Cardiovascular system
- Structure function/tissue mechanics
Biological Scales atomic, molecular, molecular complexes, sub-cellular, cellular, multi-cell systems, tissue, organ, multi-organ systems, organism, population, and behavior
E-mail regarding the purpose and goals of the computational tools working document was sent on 7/31/07: Media:July 31 e-mail.txt.
- It is difficult to get funding to support infrastructural projects.
- Devoting time to such projects can lead to an initial decrease in concrete research outputs.
- Software development is costly; dissemination, maintenance and support even more so.
- Developing, maintaining, and coordinating open source tools should be a priority
Discussion details can be found in the following document: Media: WG_discussion_Aug_07.txt
Modeling Issues in Multiscale Biomechanics is adapted from the working document on modeling issues related to computational biomechanics (multiscale, tissue mechanics, musculoskeletal biomechanics): Media:Modeling Issues.doc
WG discussion from the 2007 ASME SBC Media:ASME SBC 2007.txt
- Media:Group 6 minutes April 1 2006.doc
- Media:Group 6 minutes May 1 2006.doc
- Media:Group 6 minutes June 1 2006.doc
- Media:Group 6 minutes July 1 2006.doc
- Media:Group 6 minutes August 1 2006.doc
- Media:Group 6 minutes September 1 2006.doc
- Media:Group 6 minutes October 2006.doc
- Media:Group 6 minutes November 2006.doc
- Media:Group 6 minutes December 2006.doc
- Media:Group 6 minutes January 2007.doc
- Media:Group 6 minutes February 2007.doc
- Media:Group 6 minutes March 2007.doc