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, and the feedback we receive from them. Over the next four years, we will build the capabilities of 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 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.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Specialized Center--Cooperative Agreements (U54)
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Special Emphasis Panel (ZRG1-BST-K)
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Stanford University
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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
Araya, Carlos L; Cenik, Can; Reuter, Jason A et al. (2016) Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nat Genet 48:117-25
Uchida, Thomas K; Hicks, Jennifer L; Dembia, Christopher L et al. (2016) Stretching Your Energetic Budget: How Tendon Compliance Affects the Metabolic Cost of Running. PLoS One 11:e0150378
Seth, Ajay; Matias, Ricardo; Veloso, António P et al. (2016) A Biomechanical Model of the Scapulothoracic Joint to Accurately Capture Scapular Kinematics during Shoulder Movements. PLoS One 11:e0141028
Sahli Costabal, Francisco; Hurtado, Daniel E; Kuhl, Ellen (2016) Generating Purkinje networks in the human heart. J Biomech 49:2455-65
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
Eastman, Peter; Pande, Vijay S (2015) OpenMM: A Hardware Independent Framework for Molecular Simulations. Comput Sci Eng 12:34-39
Wisdom, Katrina M; Delp, Scott L; Kuhl, Ellen (2015) Use it or lose it: multiscale skeletal muscle adaptation to mechanical stimuli. Biomech Model Mechanobiol 14:195-215
Dorn, Tim W; Wang, Jack M; Hicks, Jennifer L et al. (2015) Predictive simulation generates human adaptations during loaded and inclined walking. PLoS One 10:e0121407

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