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      “Essentially, all models are wrong, but some are useful”—a cross-disciplinary agenda for building useful models in cell biology and biophysics

      Biophysical Reviews

      Springer Science and Business Media LLC

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          The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

          Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. The specification of SBML Level 1 is freely available from http://www.sbml.org/
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            COPASI--a COmplex PAthway SImulator.

            Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods. Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features. We discuss numerical issues with these features; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation. The complete software is available in binary (executable) for MS Windows, OS X, Linux (Intel) and Sun Solaris (SPARC), as well as the full source code under an open source license from http://www.copasi.org.
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              A modular design for the clathrin- and actin-mediated endocytosis machinery.

              Endocytosis depends on an extensive network of interacting proteins that execute a series of distinct subprocesses. Previously, we used live-cell imaging of six budding-yeast proteins to define a pathway for association of receptors, adaptors, and actin during endocytic internalization. Here, we analyzed the effects of 61 deletion mutants on the dynamics of this pathway, revealing functions for 15 proteins, and we analyzed the dynamics of 8 of these proteins. Our studies provide evidence for four protein modules that cooperate to drive coat formation, membrane invagination, actin-meshwork assembly, and vesicle scission during clathrin/actin-mediated endocytosis. We found that clathrin facilitates the initiation of endocytic-site assembly but is not needed for membrane invagination or vesicle formation. Finally, we present evidence that the actin-meshwork assembly that drives membrane invagination is nucleated proximally to the plasma membrane, opposite to the orientation observed for previously studied actin-assembly-driven motility processes.
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                Author and article information

                Journal
                Biophysical Reviews
                Biophys Rev
                Springer Science and Business Media LLC
                1867-2450
                1867-2469
                December 2018
                November 12 2018
                December 2018
                : 10
                : 6
                : 1637-1647
                Article
                10.1007/s12551-018-0478-4
                © 2018

                http://www.springer.com/tdm

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