Tools

From Computational Cell Biology

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Tools
 
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==Tools used during the workshop==
==Tools used during the workshop==
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Stella |  Virtual Cell
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[[Tools#Stella|Stella]] |  [[Tools#Virtual Cell|Virtual Cell]]
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===Stella===
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===[http://www.hps-inc.com/softwares/Education/StellaSoftware.aspx Stella]===
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===Virtual Cell===
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===[http://www.vcell.org/ Virtual Cell]===
   
   
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Users create models through a graphical user interface or by generating mathematical descriptions using Virtual Cell Math Language. The tool is accessible via the web with user registration.
Users create models through a graphical user interface or by generating mathematical descriptions using Virtual Cell Math Language. The tool is accessible via the web with user registration.
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==Other tools not covered in the workshop==
 
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JDesigner | JigCell | Excel |Paup | Phylip | GenMapp | BRB Array
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'''Virtual Cell Software Guides'''
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[http://www.vcell.org/login/VCell%20Quick%20Start%20Guide.pdf Quick tips][http://www.vcell.org/login/user_guide_4_1.pdf User Guide 4.1]
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==Other tools of interest==
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JDesigner | JigCell | Excel | MatLab | XPP
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===JDesigner===
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===[http://sbw.kgi.edu/software/jdesigner.htm JDesigner]===
   
   
This application is used to draw biochemical networks and export the drawn network as SBML (Systems Biology Markup Language). It can be used as an interface for developing networks that run on Jarnac.
This application is used to draw biochemical networks and export the drawn network as SBML (Systems Biology Markup Language). It can be used as an interface for developing networks that run on Jarnac.
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===JigCell===
 
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This modeling framework makes uses a spreadsheet interface, solves differential equations, allows users to enter their own rate constants and input conditional statements for the simulation.
 
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Because the cell cycle underlies the growth, development, and reproduction of all living organisms, knowledge about its control is central to cell biology and has potential applications in the health care and pharmaceutical industries. We want to develop novel, computational tools, with user-friendly interfaces, for studying complex biochemical regulatory systems in general, and the cell cycle control system in particular.
 
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- exerpted from the JigCell site.
 
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Paper on the JigCell Model Builder (PDF)
 
===Excel===
===Excel===
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===Paup===
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===MatLab===
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This is a tool for inferring and interpreting phylogenetic trees, available for purchase at the company website.
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===Phylip===
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This is a free inference tool for phylogenetic analysis.
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===GenMapp===
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The main features underlying GenMAPP are:
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* Draw pathways with easy to use graphics tools
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* Color genes on MAPP files based on user-imported genomic data
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* Query genomic data against MAPPs and the GeneOntology with MAPPFinder
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- excerpted from the GenMapp site.
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===BRB array===
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BRB ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data.
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===MCell===
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- excerpted from the BRB array site.
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===XPPAUT===

Latest revision as of 14:54, 19 December 2007

Contents

Tools used during the workshop

Stella | Virtual Cell

Stella

This software uses the metaphor of flows and stocks for drafting models of dynamic systems. Model examples and tutorials can be downloaded from the company site.

This software is useful for Mapping and Modeling, Simulation and Analysis, and Communication


Virtual Cell

Users create models through a graphical user interface or by generating mathematical descriptions using Virtual Cell Math Language. The tool is accessible via the web with user registration.

Virtual Cell Software Guides Quick tipsUser Guide 4.1

Other tools of interest

JDesigner | JigCell | Excel | MatLab | XPP

JDesigner

This application is used to draw biochemical networks and export the drawn network as SBML (Systems Biology Markup Language). It can be used as an interface for developing networks that run on Jarnac.


Excel

MatLab

MCell

XPPAUT

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