Abstract

Simtk.org has become a hub for the dissemination of tools related to physics-based simulation in biomedical research, with more than 380 projects and 8000 users. Our future plans are driven by this rapid growth in the number of users of simtk.org, and the feedback we receive from them. Over the next four years, we will build the capabilities of simtk.org to create a sustainable model for support for its many users. Our plan for improved support is based on social networking for peer-support and virtual machines for replication of research results. The rapid expansion of social networks, such as Facebook, is an important development since the NCBC program began in 2004. Some of our software applications have a critical mass of users who want to interact and support one another. Thus, we plan to implement tools based on social networking paradigms to enable peer support. The development of virtual machines provides an opportunity for users of simtk.org to reproduce the results of others. Virtual machines provide a mechanism for an operating system, executable codes, and data sets to be pre-loaded into a binary format that represents an """"""""image"""""""" of a fully functional machine. Our pilot studies have demonstrated the ability to deliver binaries, documentation, models and full simulation trajectories. Thus, going forward, we will improve the ability of simulation scientists to share their work in full detail.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54GM072970-07
Application #
8324538
Study Section
Special Emphasis Panel (ZRG1)
Project Start
Project End
Budget Start
2011-09-01
Budget End
2012-08-31
Support Year
7
Fiscal Year
2011
Total Cost
$114,314
Indirect Cost

  Institution

Name
Stanford University
Department
Type
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305

  Publications

Seth, Ajay; Hicks, Jennifer L; Uchida, Thomas K et al. (2018) OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement. PLoS Comput Biol 14:e1006223
Liu, Tianyun; Ish-Shalom, Shirbi; Torng, Wen et al. (2018) Biological and functional relevance of CASP predictions. Proteins 86 Suppl 1:374-386
Rojas, Enrique R; Billings, Gabriel; Odermatt, Pascal D et al. (2018) The outer membrane is an essential load-bearing element in Gram-negative bacteria. Nature 559:617-621
Rojas, Enrique R; Huang, Kerwyn Casey; Theriot, Julie A (2017) Homeostatic Cell Growth Is Accomplished Mechanically through Membrane Tension Inhibition of Cell-Wall Synthesis. Cell Syst 5:578-590.e6
Budday, S; Sommer, G; Birkl, C et al. (2017) Mechanical characterization of human brain tissue. Acta Biomater 48:319-340
DeMers, Matthew S; Hicks, Jennifer L; Delp, Scott L (2017) Preparatory co-activation of the ankle muscles may prevent ankle inversion injuries. J Biomech 52:17-23
Dodani, Sheel C; Kiss, Gert; Cahn, Jackson K B et al. (2016) Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models. Nat Chem 8:419-25
Sack, Kevin L; Baillargeon, Brian; Acevedo-Bolton, Gabriel et al. (2016) Partial LVAD restores ventricular outputs and normalizes LV but not RV stress distributions in the acutely failing heart in silico. Int J Artif Organs 39:421-430
Shukla, Diwakar; Peck, Ariana; Pande, Vijay S (2016) Conformational heterogeneity of the calmodulin binding interface. Nat Commun 7:10910
Rajagopal, Apoorva; Dembia, Christopher L; DeMers, Matthew S et al. (2016) Full-Body Musculoskeletal Model for Muscle-Driven Simulation of Human Gait. IEEE Trans Biomed Eng 63:2068-79

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