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Important softwares in modelling and simulation

 

BioSPICE Dashboard

Bio-SPICE, an open source framework and software toolset for Systems Biology, is intended to assist biological researchers in the modeling and simulation of spatio-temporal processes in living cells. In addition, our goal is to develop and serve a user community committed to using, extending and exploiting these tools to further our knowledge of biological processes.



 





BioUML

BioUML is Java framework for systems biology. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization and simulations.

 





CADLIVE

CADLIVE is a system for constructing large-scale biological networks (metabolic and gene regulatory networks) using GUI (Graphic User Interface) and saving them as regulator reaction equations in a database in the format compatible to a simulator. It has been developed by H. Kurata at the Kyushu Institute of Technology together with staffs at Mitsui Knowledge Industry Co., Ltd.

PROTON

PROTON is an Integrative Modeling System (IMS). It has been initiated by the project MARG sponsored by the German Research Council (DFG). The purpose of the system is to support the modeling of large-scale systems by using integrative methods.




Simpathica

Simpathica is a set of tools capable of simulating and analyzing biological pathways. It consists of a front end and a back end. The front end is a pathway editor which generates a set of Ordinary Differential Equations, which are in turn simulated using Octave. The back end, also known as XSSYS, is a temporal logic analysis tool which can answer queries about the time course behavior of a set of pathways. Developed by NYU Courant Institute of Mathematical Sciences.

StochSim

StochSim is a stochastic simultor for biological processes. StochSim was written by Carl Firth (formerly Carl Morton-Firth)

Aipotu 

         It is a BioQUEST software simulation that integrates genetics, biochemistry, molecular       biology, and evolution to study a biological phenomenon. It is designed to show students the connections between these three key disciplines of modern molecular genetics. It is based on "Botstein's Triangle"; (Science 240:1439 (1988)) shown below:





That is:
  • Life can be explained in terms of The Individual Functions of Living Things.
  • Genetics explains The Individual Functions of Living Things in terms of Genes.
  • Biochemistry explains The Individual Functions of Living Things in terms of Proteins.
  • Molecular Biology connects Genetics and Biochemistry by explaining how Genes encode Proteins.
  • Evolution provides a context that explains how these features changed over time to become what they are.




The phenomenon under study - the Individual function of this living thing - is the color of a simulated flower (see below).
You are provided with a starting set of flowers in the Greenhouse; these organisms are saved as organism files, each of which contains two DNA sequences. These organisms are loaded into the Greenhouse when the program starts.




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