Tools

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Tools used during the workshop

<a href="#stella">Stella</a> 

                           | <a href="#JDes">JDesigner</a> | <a href="#excel">Excel</a>
| <a href="#virt">Virtual Cell</a>

<a name="stella"></a><a href="http://www.hps-inc.com/softwares/Education/StellaSoftware.aspx">Stella</a>

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
 
 

<a name="JDes"></a><a href="http://sbw.kgi.edu/software/jdesigner.htm">JDesigner</a>
 
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.
<a name="excel"></a>Excel
 

 
<a name="virt"></a><a href="http://www.nrcam.uchc.edu/">Virtual Cell</a>
 

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.
 
 
Other 
                           tools not covered in the workshop but referenced by
students
<a href="#Paup">Paup</a> 
                           | <a href="#phylip">Phylip</a> | <a href="#genmapp">GenMapp</a> 
                           | <a href="#BRB">BRB Array</a> | <a href="#lotus">Lotus
1,2,3</a> | <a href="#jigcell">JigCell</a>
<a name="Paup"></a><a href="http://paup.csit.fsu.edu/">Paup</a>
 

This 

                           is a tool for inferring and interpreting phylogenetic 
                           trees, available for purchase at the <a href="http://paup.csit.fsu.edu/">company
website</a>.

<a name="phylip"></a><a href="http://evolution.genetics.washington.edu/phylip.html">Phylip</a>
This 
                           is a free inference tool for phylogenetic analysis.
 
<a name="genmapp"></a><a href="http://www.genmapp.org/">GenMapp</a>

The 

                           main features underlying GenMAPP are:


                           

                           - Draw pathways with easy to use graphics tools 

                           - Color genes on MAPP files based on user-imported 
                           genomic data

                           - Query genomic data against MAPPs and the GeneOntology 
                           with MAPPFinder 

                           

                           - excerpted from the <a href="http://www.genmapp.org/">GenMapp
site</a>.

<a name="BRB"></a><a href="http://linus.nci.nih.gov/BRB-ArrayTools.html">BRB array</a>

BRB 

                           ArrayTools is an integrated package for the visualization 
                           and statistical analysis of DNA microarray gene expression 
                           data.

                           

                           - excerpted from the <a href="http://linus.nci.nih.gov/BRB-ArrayTools.html">BRB
array site</a>.

<a name="lotus"></a><a href="http://www-306.ibm.com/software/lotus/">Lotus 1,2,3</a>

Collaborative information management.

<a name="jigcell"></a><a href="http://jigcell.biol.vt.edu/">JigCell</a>
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.

                           

                           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. 


                           - exerpted from the <a href="http://jigcell.biol.vt.edu/">JigCell 
                           site</a>.

                     <a href="docs/ModelBuilderJigCell.pdf">
Paper on the JigCell Model Builder</a> (PDF)

 
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