MMBio S Biomedical Technology Research Resource BTRC High

MMBio. S Biomedical Technology Research Resource (BTRC) High Performance Computing for Multiscale Modeling of Biological Systems Salk Overarching biological theme: PSC Spatial organization Temporal evolution of (neuro)signaling systems/events PITT CMU

MMBio. S External Advisory Board Members Harel Weinstein, DSc Maxwell M. Upson Professor of Physiology and Biophysics Chair, Dept of Physiology and Biophysics Director, Institute for Computational Biomedicine Weill Cornell Medical College of Cornell U Tri-Institutional Professor: WCMC, Rockefeller, MSKCC Badrinath "Badri" Roysam, Ph. D Professor and Chair of Electrical and Computer Engineering University of Houston, Martin Meier-Schellersheim, Ph. D Chief, Computational Biology Section, Laboratory of Systems Biology National Institute of Allergy and Infectious Diseases, NIH Scott Acton, Ph. D Professor, Charles L. Brown Electrical and Computer Engineering Department, and Department of Biomedical Engineering Director, Virginia Image and Video Analysis Lab University of Virginia Klaus Schulten, Ph. D Uof Illinois at Urbana-Champaign Les Loew, Ph. D U of Connecticut Health Center Ex-officio Peter Strick, Ph. D Distinguished Professor Chair of Neurobiology U of Pittsburgh, SOM Nathan Urban, Ph. D Prof of Neurobiology CNBC Co-Director Pitt, SOM

MMBio. S BTRC Administration PSC Leadership (Ralph Roskies) PSC System Administration CMU Leadership (Robert Murphy) PI (Pitt) Ivet Bahar Salk Leadership (Terry Sejnowski) Pitt DCSB Financial Administration (Marcia Schwab) Ivet Bahar, Ph. D: John K. Vries Chair and Founder of the Dept of Computational & Systems Biology (CSB), School of Medicine (SOM), U of Pittsburgh (Pitt); co-Founder (with R. F. Murphy) of the Joint Ph. D Program between Pitt and CMU; Associate Director of the University of Pittsburgh Drug Discovery Institute (UPDDI) Terry J. Sejnowski, Ph. D: Francis Crick Professor and Director of the Computational Neurobiology Laboratory at the Salk Institute for Biological Sciences (Salk), Distinguished Professor at UCSD Dept of Neurobiology/ Neurosciences; an investigator with the Howard Hughes Institute and a member of the NAS. Robert F. Murphy, Ph. D: Ray and Stephanie Lane Professor and Head of Computational Biology at Carnegie Mellon University; Professor of Biological Sciences, Bioengineering and Machine Learning; co-founder of Joint Ph. D Program in Comp Bio between Pitt and CMU Ralph Roskies, Ph. D: Co-Founder (with M. Levine, CMU) and Scientific Director of the Pittsburgh Supercomputing Center (PSC); Professor of Physics, School of Arts & Sciences, Pitt; PI of the P 41 National Resource for Biomedical Supercomputing (NRBSC) between 1990 and 2005; Appointed to National Library of Medicine (NIH) Board of Regents in 2011.

MMBio. S BTRC Administration PSC Leadership (Ralph Roskies) PSC System Administration CMU Leadership (Robert Murphy) Salk Leadership (Terry Sejnowski) Pitt DCSB Financial Administration PI (Pitt) Ivet Bahar (Marcia Schwab) Executive Committee (EC) TR&D 1 (Bahar Zuckerman) TR&D 2 (Faeder & Sejnowski) Dan M. Zuckerman Ph. D, Assoc Prof at Comp & Sys Biol Dept (CSB), Pitt, Director of CMU/ Pitt Joint Ph. D Program in Comput Biology; expert in molecular modeling & simulations TR&D 3 (Murphy) James R. Faeder, Ph. D: Assoc Professor at the CSB, expert in rule-based modeling of biochemical networks and signal transduction events, codeveloper of cell mode ling software Bio. Net. Gen Training (Dittrich) Carl Kingsford, Ph. D Associate Prof, Dept of Computational Biology; Carnegie Mellon U; specialized in chromatin structure and assembly, Dissemination and protein interaction networks. (Dittrich) Markus Dittrich, Ph. D: Senior Scientist at the PSC; knowledge on both molecular (MD) and cellular (MCell) simulations; leader of he Natl Res for Biomed Supercomp (NRBSC) at the PSC; Director of PSC Educational activities

MMBio. S External Advisory Board (EAB) BTRC Administration PSC Leadership (Ralph Roskies) PSC System Administration CMU Leadership (Robert Murphy) Salk Leadership (Terry Sejnowski) Pitt DCSB Financial Administration PI (Pitt) Ivet Bahar (Marcia Schwab) Executive Committee (EC) TR&D 3 (Murphy) TR&D 2 (Faeder & Sejnowski) TR&D 1 (Bahar) DBP 1 (Amara & Torres) DBP 3 (Sorkin) Training (Dittrich) DBP 2 (Kennedy) DBP 4 (Wuelfing) DBP 5 (Reid) Dissemination (Dittrich)

MMBio. S External Advisory Board (EAB) BTRC Administration PSC Leadership (Ralph Roskies) PSC System Administration Salk Leadership CMU Leadership (Robert Murphy) (Terry Sejnowski) Pitt DCSB Financial Administration PI (Pitt) Ivet Bahar (Marcia Schwab) Executive Committee (EC) DBP 2 DBP 4 Driving Biomedical Projects Leaders (Wuelfing) (Kennedy) TR&D 2 (Faeder & Sejnowski) TR&D 1 (Bahar) DBP 1 (Amara & Torres) Susan G. Amara, Ph. D Scientific Director, National Institute of Mental Health, NIH Mary B. Kennedy, Ph. D The Allen and Lenabelle Davis Professor of Biology, Caltech DBP 3 (Sorkin) TR&D 3 (Murphy) DBP 5 Training (Dittrich) (Reid) DBP 2 (Kennedy) Alexander (Sasha) Sorkin, Ph. D, Professor and Richard Beatty Mellon Chair, Dept of Cell Biology & Physiology, (Wuelfing) Pitt DBP 4 Christoph Wuelfing, Ph. D Professor, School of Cellular and Molecular Medicine University of Bristol, UK DBP 5 (Reid) R. Clay Reid, MD, Ph. D Senior Investigator, Neural Coding, Allen Institute for Brain Science, Seattle

MMBio. S DBPs

MMBio. S External Advisory Board (EAB) BTRC Administration PSC Leadership (Ralph Roskies) Salk Leadership CMU Leadership (Robert Murphy) PSC System Administration (Terry Sejnowski) Pitt DCSB Financial Administration PI (Pitt) Ivet Bahar (Marcia Schwab) Executive Committee (EC) (Sorkin) (Kennedy) DBP 5 (Reid) DBP 4 (Wuelfing) C&S 12 (Dittrich) C&S 11 (Dittrich) C&S 10 (Murphy) C&S 8 C&S 7 C&S 6 C&S 5 DBP 2 Dissemination C&S 15 DBP 3 C&S 4 C&S 16 (Amara & Torres) Training C&S 14 C&S 18 C&S 2 C&S 17 C&S 1 DBP 1 C&S 19 (Faeder & Sejnowski) (Bahar) TR&D 3 C&S 13 TR&D 2 TR&D 1 Training & Dissemination Activities

MMBio. S C&SP 1 C&SP 2 C&SP 4 C&SP 5 C&SP 6 Ingo Greger, James Kreiger, Ivet Bahar, Jiyoung TR&D 1 Using generative models of cell organization to investigate tumor cell heterogeneity High-throughput scanning EM for neural structure C&SP 10 C&SP 11 C&SP 13 C&SP 16 C&SP 17 C&SP 18 C&SP 19 Structure and Function of Voltage-Gated Calcium Channels Modeling Dendritic Sparks at Dendritic Branch Points TR&D 2 James Faeder, William Hlavacek, Bridget Wilson Kristin Harris, Terrence Sejnowski, Tom Bartol TR&D 3 Robert Friedlander, Mark Schurdak, Andrew Stern, Lans Taylor, Diane Carlisle, Ivet Bahar, Bing Liu Peter Wipf, Stephen Meriney, Ivet Bahar, Mary H. Cheng Dr. Qing. De Wang (PI, UPMC), Ivet Bahar, Mary H Cheng M. H. Ellisman (PI; UCSD), TJ. Sejnowski, TM. Bartol TR&D 3 Florian Engert, David Hildebrand, Art Wetzel Hauke Busch, Melanie Boerries, Robert F. Murphy, Gustavo K. Rohde Julie Theriot, Gustavo K. Rohde, Dejan Slepcev TR&D 2 l TR&D 3 Paraskevi Giannakakou, Robert F. Murphy Regulating synaptic transmission by ADAR Stephen D. Meriney, Markus Dittrich Klaus Palme, Robert F. Murphy Actin filament patterns and cell motility Reconstructing zebrafish neural circuits controlling visually induced behaviors Latent Factor Models for Identification of Novel Neuroprotectives for Huntington’s Disease Lee, Anindita Dutta, Indira Shrivastava Steven Altschuler, Lani Wu, Robert F. Murphy, Gustavo K. Rohde Jeff Lichtman, Josh Morgan, Art Wetzel C&SP 14 C&SP 15 Generative models of plant organelle distribution and differentiation Microtubule pattern analysis and drug sensitivity Michael Hucka, Steve Andrews, Ion Moraru, James Schaff, Les Loew, Roger Brent, Markus Dittrich, Gustavo K. Rohde, Robert F. Murphy Morphological and regulatory models of neuronal differentiation C&SP 12 TR&D 1 Interfacing Image-derived Generative Models with Cell Simulation Engines C&SP 8 Corresponding BTRR Unit Calcium Entry and Transmitter Release at the Neuromuscular Junction Modeling the dynamic FcεRI membrane landscape for signaling and endocytosis Distance-dependent structure and function of neuronal dendrites Investigators Relationship between structural dynamics and Sequence Evolution; Application to molecular machines such as Amnon Horovitz, Lila Gierasch, Russ Altman, Mandy Blackburn, I. General, Ivet Bahar, Cihan Kaya bacterial chaperonins and HSP 70 chaperones AMPA and NMDA receptors structural dynamics C&SP 7 Title C&SPs Subprojects TR&D 1 TR&D 2

Accomplishments by numbers 64 NCBI-listed papers published in 20132015, which acknowledged the MMBio. S BTRR (+ 4 accepted, in press). Pro. Dy software downloaded ~ 86, 334 times, and MCell/Cell Blender/Cell Organizer more than 10, 000 times, in May 2014 - May 2015 22 active subprojects (5 DBP + 17 C&SP)