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| - | <TD align=middle height=21><div align="left"></div></TD>
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| - | <TD height=37 colspan="2" align=middle><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"><strong>Tools
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| - | used during the workshop</strong></font></div></TD>
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| - | <TD height=21 colspan="2" align=middle> <p align="center"><font size="2" face="Arial, Helvetica, sans-serif"><a href="#stella">Stella</a>
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| - | | <a href="#JDes">JDesigner</a> | <a href="#excel">Excel</a>
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| - | | <a href="#virt">Virtual Cell</a></font></p></TD>
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| - | <TD align=middle width=131 height=29> <p align="left"><a name="stella"></a><a href="http://www.hps-inc.com/softwares/Education/StellaSoftware.aspx">Stella</a></p></TD>
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| - | <TD width=381 height=29 bgColor=#ffffff><div align="left"></div></TD>
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| - | <TD height=84 colspan="2" align=middle> <p align="left"><font size="2" face="Arial, Helvetica, sans-serif"><font color="#000000">This
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| - | software uses the metaphor of flows and stocks for
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| - | drafting models of dynamic systems. Model examples
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| - | and tutorials can be downloaded from the company site.</font></font></p>
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| - | <p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">This
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| - | software is useful for Mapping and Modeling, Simulation
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| - | and Analysis, and Communication</font></p>
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| - | <TD align=middle height=22><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
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| - | <TD height=22 bgColor=#ffffff><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
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| - | <TD align=middle height=22> <p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif"><a name="JDes"></a><a href="http://sbw.kgi.edu/software/jdesigner.htm">JDesigner</a></font></p></TD>
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| - | <TD height=22 bgColor=#ffffff><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
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| - | <TD height=23 colspan="2" align=middle><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"><font color="#000000">This
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| - | application is used to draw biochemical networks and
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| - | export the drawn network as SBML (Systems Biology
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| - | Markup Language). It can be used as an interface for
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| - | developing networks that run on Jarnac.</font></font>
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| - | </div>
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| - | <TD align=middle height=21><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"><a name="excel"></a>Excel</font></div></TD>
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| - | <TD height=21 colspan="2" align=middle><p align="left"> </p>
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| - | <TD align=middle height=21><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"><a name="virt"></a><a href="http://www.nrcam.uchc.edu/">Virtual
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| - | Cell</a></font></div></TD>
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| - | <TD height=21 bgColor=#ffffff><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
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| - | <TD height=21 colspan="2" align=middle><p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">Users
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| - | create models through a graphical user interface or
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| - | by generating mathematical descriptions using Virtual
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| - | Cell Math Language. The tool is accessible via the
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| - | web with user registration.</font></p>
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| - | <hr align="left"> </TD>
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| - | <TD height=21 colspan="2" align=middle><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font>
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| - | </div>
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| - | <hr align="left"> <div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
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| - | <TD height=36 colspan="2" align=middle><div align="left"><strong>Other
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| - | tools not covered in the workshop but referenced by
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| - | students</strong></div></TD>
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| - | <TD height=21 colspan="2" align=middle><div align="center"><font size="2" face="Arial, Helvetica, sans-serif"><a href="#Paup">Paup</a>
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| - | | <a href="#phylip">Phylip</a> | <a href="#genmapp">GenMapp</a>
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| - | | <a href="#BRB">BRB Array</a> | <a href="#lotus">Lotus
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| - | 1,2,3</a> | <a href="#jigcell">JigCell</a></font></div></TD>
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| - | <TD align=middle height=21><div align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif"><a name="Paup"></a><a href="http://paup.csit.fsu.edu/">Paup</a></font></div></TD>
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| - | <TD height=21 bgColor=#ffffff><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
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| - | </TR>
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| - | <TD height=74 colspan="2" align=middle> <p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">This
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| - | is a tool for inferring and interpreting phylogenetic
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| - | trees, available for purchase at the <a href="http://paup.csit.fsu.edu/">company
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| - | website</a>.</font> </p>
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| - | <TD align=middle height=25><div align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif"><a name="phylip"></a><a href="http://evolution.genetics.washington.edu/phylip.html">Phylip</a></font></div></TD>
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| - | <TD height=25 colspan="2" align=middle> <div align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">This
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| - | is a free inference tool for phylogenetic analysis.</font>
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| - | </div>
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| - | </font></div></TD>
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| - | <TD align=middle height=37><div align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif"><a name="genmapp"></a><a href="http://www.genmapp.org/">GenMapp</a></font></div></TD>
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| - | <TD height=154 colspan="2" align=middle> <p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">The
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| - | main features underlying GenMAPP are:<br>
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| - | <br>
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| - | - Draw pathways with easy to use graphics tools <br>
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| - | - Color genes on MAPP files based on user-imported
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| - | genomic data<br>
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| - | - Query genomic data against MAPPs and the GeneOntology
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| - | with MAPPFinder </font><font color="#000000" face="Arial, Helvetica, sans-serif"><br>
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| - | <br>
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| - | <font size="1">- excerpted from the <a href="http://www.genmapp.org/">GenMapp
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| - | site</a>.</font></font> </p>
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| - | <TD align=middle height=39><div align="left"><a name="BRB"></a><a href="http://linus.nci.nih.gov/BRB-ArrayTools.html"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">BRB
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| - | array</font></a></div></TD>
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| - | <TD height=106 colspan="2" align=middle> <p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">BRB
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| - | ArrayTools is an integrated package for the visualization
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| - | and statistical analysis of DNA microarray gene expression
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| - | data.</font><font color="#000000" face="Arial, Helvetica, sans-serif"><br>
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| - | <br>
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| - | <font size="1">- excerpted from the <a href="http://linus.nci.nih.gov/BRB-ArrayTools.html">BRB
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| - | array site</a>.</font></font> </p>
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| - | <TD align=middle height=24><div align="left"><a name="lotus"></a><a href="http://www-306.ibm.com/software/lotus/"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">Lotus
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| - | 1,2,3</font></a></div></TD>
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| - | <TD height=24 bgColor=#ffffff><div align="left"></div></TD>
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| - | <TD height=39 colspan="2" align=middle> <p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">Collaborative
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| - | information management. </font> </p>
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| - | <TD align=middle height=28><div align="left"><a name="jigcell"></a><a href="http://jigcell.biol.vt.edu/"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">JigCell</font></a></div></TD>
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| - | <TD height=28 bgColor=#ffffff><div align="left"></div></TD>
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| - | <TD height=81 colspan="2" align=middle><div align="left"><font face="Arial, Helvetica, sans-serif"><font color="#000000" size="2">This
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| - | modeling framework makes uses a spreadsheet interface,
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| - | solves differential equations, allows users to enter
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| - | their own rate constants and input conditional statements
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| - | for the simulation.</font></font><br>
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| - | <br>
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| - | <font color="#000000" size="2" face="Arial, Helvetica, sans-serif">Because
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| - | the cell cycle underlies the growth, development,
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| - | and reproduction of all living organisms, knowledge
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| - | about its control is central to cell biology and has
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| - | potential applications in the health care and pharmaceutical
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| - | industries. We want to develop novel, computational
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| - | tools, with user-friendly interfaces, for studying
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| - | complex biochemical regulatory systems in general,
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| - | and the cell cycle control system in particular. <br>
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| - |
| |
| - | - <font size="1">exerpted from the <a href="http://jigcell.biol.vt.edu/">JigCell
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| - | site</a>.<br>
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| - | <font size="2"><a href="docs/ModelBuilderJigCell.pdf"><br>
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| - | Paper on the JigCell Model Builder</a> (PDF)</font></font></font></div></TD>
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