COPASI---a COmplex PAthway SImulator
Stefan Hoops,Sven Sahle,Ralph Gauges,Christine Lee,Jürgen Pahle,Natalia Simus,Mudita Singhal,Liang Xu,Pedro Mendes,Ursula Kummer +9 more
Reads0
Chats0
TLDR
COPASI is presented, a platform-independent and user-friendly biochemical simulator that offers several unique features, and numerical issues with these features are discussed; 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.Abstract:
Motivation: 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.
Results: 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.
Availability: 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.
Contact: mendes@vbi.vt.eduread more
Citations
More filters
Journal ArticleDOI
The Perseus computational platform for comprehensive analysis of (prote)omics data.
Stefka Tyanova,Tikira Temu,Pavel Sinitcyn,Arthur Carlson,Marco Y. Hein,Tamar Geiger,Matthias Mann,Jürgen Cox +7 more
TL;DR: The Perseus software platform was developed to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data and it is anticipated that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.
Journal ArticleDOI
Rhodium-Catalyzed C-C Bond Formation via Heteroatom-Directed C-H Bond Activation
TL;DR: This review focuses on Rh-catalyzed methods for C-H bond functionalization, which have seen widespread success over the course of the last decade and are discussed in detail in the accompanying articles in this special issue of Chemical Reviews.
Journal ArticleDOI
Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis
Valerian E. Kagan,Gaowei Mao,Feng Qu,José Pedro Friedmann Angeli,Sebastian Doll,Claudette M. St. Croix,Haider H. Dar,Bing Liu,Vladimir A. Tyurin,Vladimir B. Ritov,Alexandr A. Kapralov,Andrew A. Amoscato,Jianfei Jiang,Tamil S. Anthonymuthu,Dariush Mohammadyani,Qin Yang,Bettina Proneth,Judith Klein-Seetharaman,Simon C. Watkins,Ivet Bahar,Joel S. Greenberger,Rama K. Mallampalli,Brent R. Stockwell,Yulia Y. Tyurina,Marcus Conrad,Hülya Bayır +25 more
TL;DR: It is discovered that ferroptosis involves a highly organized oxygenation center, wherein oxidation in endoplasmic-reticulum-associated compartments occurs on only one class of phospholipids (phosphatidylethanolamines (PEs) and is specific toward two fatty acyls-arachidonoyl (AA) and AdA (AdA).
Journal ArticleDOI
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades
Lulu Qian,Erik Winfree +1 more
TL;DR: This work experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays.
Journal ArticleDOI
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
Markus J. Herrgård,Neil Swainston,Paul D. Dobson,Warwick B. Dunn,K.Yalçın Arga,Mikko Arvas,Nils Blüthgen,Simon Borger,Roeland Costenoble,Matthias Heinemann,Michael Hucka,Nicolas Le Novère,Peter Li,Wolfram Liebermeister,Monica L. Mo,Ana Paula Oliveira,Dina Petranovic,Stephen Pettifer,Evangelos Simeonidis,Kieran Smallbone,Irena Spasic,Dieter Weichart,Roger Brent,David S. Broomhead,Hans V. Westerhoff,Betul Kirdar,Merja Penttilä,Edda Klipp,Bernhard O. Palsson,Uwe Sauer,Stephen G. Oliver,Pedro Mendes,Jens Nielsen,Douglas B. Kell +33 more
TL;DR: This work describes how it has produced a consensus metabolic network reconstruction for S. cerevisiae, and places special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning.
References
More filters
Book
Genetic Algorithms + Data Structures = Evolution Programs
TL;DR: GAs and Evolution Programs for Various Discrete Problems, a Hierarchy of Evolution Programs and Heuristics, and Conclusions.
Journal ArticleDOI
A method for the solution of certain non – linear problems in least squares
TL;DR: In this article, the problem of least square problems with non-linear normal equations is solved by an extension of the standard method which insures improvement of the initial solution, which can also be considered an extension to Newton's method.
Journal ArticleDOI
Determining Lyapunov exponents from a time series
TL;DR: In this article, the authors present the first algorithms that allow the estimation of non-negative Lyapunov exponents from an experimental time series, which provide a qualitative and quantitative characterization of dynamical behavior.
Journal ArticleDOI
A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions
TL;DR: In this paper, an exact method is presented for numerically calculating, within the framework of the stochastic formulation of chemical kinetics, the time evolution of any spatially homogeneous mixture of molecular species which interreact through a specified set of coupled chemical reaction channels.
Related Papers (5)
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