Skip to main content

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.




Labels:

Comments

Post a Comment

Popular posts from this blog

Information Retreival Systems in Bioinformatics: Entrez

Currently many biological databases have been developed and became an important toolbox for every scientist in research and academic purpose. Searching a sequence homologue of either Protein, DNA or to know the novelty of a sequence, one needs to do a sequence search against available databases. Similarly, searching for Open Reading Frame, structure, functional, regulatory sequences and repeated elements, we also need to search our query against different available databases. As biological data is increasing with the passage of time, its tremendous growth requires a searching and access system to retrieve useful information. In biological data, three retrieval systems are widely used relevant to a scientific need, it includes: Entrez, Sequence Retrieval System also known as SRS and DBGET. These retrieval systems let its user a text search against multiple molecular databases and also provides useful relevant information in the forms of links either internal or external to our qu...
Post a Comment
Read more

Comparison between Shared memory architecture and Shared nothing architecture

Shared-Memory Architecture: This architecture connects different processor under one operating system through high speed interconnections (cross-bar switch or high speed bus etc). Query response time is reduced by dividing workload to any connected processor with least or no workload. This architecture provides two main advantages over other architectures as it manages load in a perfect manner and easy to manage. It uses least busy processors and allocates new tasks to it so that query processing is done at a fast speed. But along with two major advantages it has three basic disadvantages too. These are low availability, any fault or problem may affect most of the processors making less availability, high cost to link processors and third, limited extensible. Performance   Shared memory architecture provides a good performance as compared to shared nothing architecture by balancing query load on a processor with less or no work load. So...
Post a Comment
Read more

Centrifugal field flow fractionation:

Centrifugal field flow fractionation: Centrifugal FFF is basically a new name given to Sedimentation FFF after further developments in it. The specialty of this Centrifugal FFF is that it involves the use of centrifugal force as the externally applied force which is the basic element required in the separation of the analyte particles. Channel used in this technique is in the form of a ring which spins at 4900 rpm.  This technique is effective in the separation, characterization and purification of micron-sized particles of any type of analyte. It allows for the separation of particles with only a 5% difference in size. Mode of elution In Centrifugal or sedimentation FFF the elution is carried out by hyperlayer mode. The other two modes of elution fail to explain that for the particles having the size less than 1 µm the retention ratio increases with the increase in velocity of flow. In other words the transport velocity is variable for the particles whose size i...
Post a Comment
Read more