J
James C. Schaff
Researcher at University of Connecticut Health Center
Publications - 51
Citations - 6777
James C. Schaff is an academic researcher from University of Connecticut Health Center. The author has contributed to research in topics: SBML & Software. The author has an hindex of 28, co-authored 49 publications receiving 6343 citations. Previous affiliations of James C. Schaff include University of Connecticut.
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Journal ArticleDOI
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Michael Hucka,Andrew Finney,Herbert M. Sauro,Hamid Bolouri,Hamid Bolouri,John Doyle,Hiroaki Kitano,Adam P. Arkin,Benjamin Bornstein,Dennis Bray,Athel Cornish-Bowden,Autumn A. Cuellar,S. Dronov,E. D. Gilles,Martin Ginkel,V. Gor,Igor Goryanin,W. J. Hedley,T. C. Hodgman,J.-H.S. Hofmeyr,Peter Hunter,Nick Juty,J. L. Kasberger,Andreas Kremling,Ursula Kummer,N Le Novère,Leslie M. Loew,D. Lucio,Pedro Mendes,E. Minch,Eric Mjolsness,Yoichi Nakayama,Melanie R. Nelson,Poul M. F. Nielsen,T. Sakurada,James C. Schaff,Bruce E. Shapiro,Thomas S. Shimizu,H. D. Spence,Jörg Stelling,Koichi Takahashi,Masaru Tomita,John Wagner,J. Wang +43 more
TL;DR: This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
Journal ArticleDOI
The Virtual Cell : a software environment for computational cell biology
Leslie M. Loew,James C. Schaff +1 more
TL;DR: The Virtual Cell is a computational environment designed for cell biologists as well as for mathematical biologists and bioengineers that serves to aid the construction of cell biological models and the generation of simulations from them.
Journal ArticleDOI
Cell Shape and Negative Links in Regulatory Motifs Together Control Spatial Information Flow in Signaling Networks
Susana R. Neves,Panayiotis Tsokas,Anamika Sarkar,Elizabeth A. Grace,Padmini Rangamani,Stephen M. Taubenfeld,Cristina M. Alberini,James C. Schaff,Robert D. Blitzer,Ion I. Moraru,Ravi Iyengar +10 more
TL;DR: A mechanism by which cellular geometry, the presence of regulatory loops with negative regulators, and key reaction rates all together control spatial information transfer and microdomain characteristics within cells is suggested.
Journal ArticleDOI
A general computational framework for modeling cellular structure and function
TL;DR: The "Virtual Cell" provides a general system for testing cell biological mechanisms and creates a framework for encapsulating the burgeoning knowledge base comprising the distribution and dynamics of intracellular biochemical processes.
Journal ArticleDOI
Quantitative cell biology with the Virtual Cell.
TL;DR: This review summarizes how a Virtual Cell model is assembled and describes the physical principles underlying the calculations that are performed, to illustrate the power of this paradigm for elucidating cell biology.