List of systems biology modeling software information
Systems biology relies heavily on building mathematical models to help understand and make predictions of biological processes. Specialized software to assist in building models has been developed since the arrival of the first digital computers.[1][2][3][4] The following list gives the currently supported software applications available to researchers.
The vast majority of modern systems biology modeling software support SBML, which is the de facto standard for exchanging models of biological cellular processes. Some tools also support CellML, a standard used for representing physiological processes. The advantage of using standard formats is that even though a particular software application may eventually become unsupported and even unusable, the models developed by that application can be easily transferred to more modern equivalents. This allows scientific research to be reproducible long after the original publication of the work.
To obtain more information about a particular tool, click on the name of the tool. This will direct you either to a peer-reviewed publication or, in some rare cases, to a dedicated Wikipedia page.
^Chance, Britton; Higgins, Joseph; Garfinkel, David (1962). Analogue and digital computer representations of biochemical processes. Federation of American Societies for Experimental Biology..: Federation Proceedings, Vol 12. No. 1-2. p. 75.
^Burns, Jim (1 March 1973). Metabolic Control Analysis. Thesis (Thesis). doi:10.5281/zenodo.7240738.
^Garfinkel, David (August 1968). "A machine-independent language for the simulation of complex chemical and biochemical systems". Computers and Biomedical Research. 2 (1): 31–44. doi:10.1016/0010-4809(68)90006-2. PMID 5743538.
and 25 Related for: List of systems biology modeling software information
Systemsbiology is the computational and mathematical analysis and modelingof complex biological systems. It is a biology-based interdisciplinary field...
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships...
The following is a listofsoftware packages and applications for biocybernetics research. SystemsBiology Markup Language (SBML) Biological Pathway Exchange...
theory Listofsystemsbiologymodelingsoftware Reder, Christine (November 1988). "Metabolic control theory: A structural approach". Journal of Theoretical...
representation of an algorithm or a stepwise process. Fundamental Modeling Concepts (FMC) modeling language for software-intensive systems. IDEF is a family of modeling...
Popular software tools used in systemsbiologymodeling include massPy, Cytosim, and PySB. Further examples may be found at Wikipedia's listofsystems biology...
Cancer systemsbiology encompasses the application ofsystemsbiology approaches to cancer research, in order to study the disease as a complex adaptive...
research grants through the National Institutes of Health. Listofsystemsbiologymodelingsoftware Schaff J, Fink CC, Slepchenko B, Carson JH, Loew LM (September...
This listof sequence alignment software is a compilation ofsoftware tools and web portals used in pairwise sequence alignment and multiple sequence alignment...
analysis, system dynamics (feedback control), and optimization methods. SystemsModeling Language (SysML), a modeling language used for systems engineering...
engineering, design, electronic engineering, software engineering, chemical engineering, and systemsbiology. There are many reasons for performing reverse...
silico research. Developing such models has been a task of systemsbiology and mathematical biology. It involves developing efficient algorithms, data structures...
of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to...
Time-sharing operating systems schedule tasks for efficient use of the system and may also include accounting software for cost allocation of processor time,...
Cybernetics and Systems Research. North-Holland. pp. 397–402. ISBN 978-0-444-86488-8. Bozinovski, Stevo (2014) "Modeling mechanisms of cognition-emotion...
team of researchers to work on developing better software infrastructure for computational modeling in systemsbiology. Hamid Bolouri was the leader of the...