Computational Cell Biology - User contributions [en]

File:EvaluationCellCycleAndModeling.pdf

2007-05-03T15:20:47Z

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File:EvaluationCellCycleandModeling.pdf

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Tools

2007-05-01T17:59:48Z

WikiAdmin:

==Tools used during the workshop==

[[Tools#Stella|Stella]] | [[Tools#Virtual Cell|Virtual Cell]]

===[http://www.hps-inc.com/softwares/Education/StellaSoftware.aspx 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

===[http://www.nrcam.uchc.edu/ 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.

==Other tools of interest==

JDesigner | JigCell | Excel | MatLab

===[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.

===[http://jigcell.biol.vt.edu/ JigCell]===

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 JigCell site.

Paper on the JigCell Model Builder (PDF)

===Excel===

===MatLab===

===GenMapp===

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 GenMapp site.

Tools

2007-05-01T17:59:04Z

WikiAdmin:

Tools
_______________________________________________________

==Tools used during the workshop==

[[Tools#Stella|Stella]] | [[Tools#Virtual Cell|Virtual Cell]]

===[http://www.hps-inc.com/softwares/Education/StellaSoftware.aspx 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

===[http://www.nrcam.uchc.edu/ 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.

==Other tools of interest==

JDesigner | JigCell | Excel | MatLab

===[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.

===[http://jigcell.biol.vt.edu/ JigCell]===

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 JigCell site.

Paper on the JigCell Model Builder (PDF)

===Excel===

===MatLab===

===GenMapp===

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 GenMapp site.

Tools

2007-05-01T17:58:05Z

WikiAdmin:

Tools
_______________________________________________________

==Tools used during the workshop==

[[Tools#Stella|Stella]] | [[Tools#Virtual Cell|Virtual Cell]]

===[http://www.hps-inc.com/softwares/Education/StellaSoftware.aspx 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

===[http://www.nrcam.uchc.edu/ 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.

==Other tools of interest==

JDesigner | JigCell | Excel | MatLab

===[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.

===JigCell===

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 JigCell site.

Paper on the JigCell Model Builder (PDF)

===Excel===

===MatLab===

===GenMapp===

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 GenMapp site.

Tools

2007-05-01T17:54:52Z

WikiAdmin:

Tools
_______________________________________________________

==Tools used during the workshop==

[[Tools#Stella|Stella]] | [[Tools#Virtual Cell|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.

==Other tools of interest==

JDesigner | JigCell | Excel | MatLab

===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.

===JigCell===

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 JigCell site.

Paper on the JigCell Model Builder (PDF)

===Excel===

===MatLab===

===GenMapp===

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 GenMapp site.

Tools

2007-05-01T17:54:15Z

WikiAdmin:

Tools
_______________________________________________________

==Tools used during the workshop==

[[Tools#Stella]] | [[Tools#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.

==Other tools of interest==

JDesigner | JigCell | Excel | MatLab

===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.

===JigCell===

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 JigCell site.

Paper on the JigCell Model Builder (PDF)

===Excel===

===MatLab===

===GenMapp===

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 GenMapp site.

Tools

2007-05-01T17:53:19Z

WikiAdmin: /* Tools used during the workshop */

Tools
_______________________________________________________

==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.

==Other tools of interest==

JDesigner | JigCell | Excel | MatLab

===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.

===JigCell===

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 JigCell site.

Paper on the JigCell Model Builder (PDF)

===Excel===

===MatLab===

===GenMapp===

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 GenMapp site.

Canisius College Computational Biology Workshop

2007-05-01T17:52:05Z

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*[[About|About]]
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*[[Contact|Contact]]
|style="width:11%;font-size:95%"|
*[[Instructor|Instructor]]
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*[[Resources|Resources]]
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*[[Schedule|Schedule]]
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*[[Tools|Tools]]

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|-
|style="color:#000"|{{Welcome!}}
|-
! <h2 style="margin:0;background:#bbbbaa;font-size:120%;font-weight:bold;border:1px solid #a3bfb1;text-align:left;color:#000;padding:0.2em 0.4em;">Workshop Schedule</h2>
|-
|style="color:#000"|{{Workshop Schedule}}
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! <h2 style="margin:0;background:#bbbbaa;font-size:120%;font-weight:bold;border:1px solid #a3bfb1;text-align:left;color:#000;padding:0.2em 0.4em;">About the Instructor</h2>
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|style="color:#000"|{{About Raquell}}
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MediaWiki:Sidebar

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MediaWiki:Sidebar

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Relevant Literature

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Template:Relevant Literature

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===Books===
{{Books}}

Template:Resources

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*[[Preliminary Questionnaire]]
*[[Tools#Tools used during the workshop|Tools used during the workshop]]
*[[References for workshop exercises]]
*[[Links to modelling databases]]
----
*[[Tools#Other tools not covered in the workshop but referenced by students|Other software tools not covered in the workshop but referenced by students]]
*[[Literature on teaching approaches]]
*[[Relevant Literature|Other relevant literature]]
----
*[[Links to additional training opportunities]]

Template:Resources

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*[[Preliminary Questionnaire]]
*[[Tools#Tools used during the workshop|Tools used during the workshop]]
*[[Tools#Other tools not covered in the workshop but referenced by students|Other tools not covered in the workshop but referenced by students]]
*[[Relevant Literature]]

Template:Resources

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*[[Preliminary Questionnaire]]
*[[Tools|Software tools we will use]]
*[[Tools#Other tools not covered in the workshop but referenced by students|Other tools not covered in the workshop but referenced by students]]
*[[Relevant Literature]]

Template:Resources

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*[[Preliminary Questionnaire]]
*[[Tools|Software tools we will use]]
*[[Tools#]]
*[[Relevant Literature]]

Tools

2007-04-30T14:51:32Z

WikiAdmin:

Tools
_______________________________________________________

Tools used during the workshop

Stella | JDesigner | Excel | 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

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

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.

Other tools not covered in the workshop but referenced by students
Paup | Phylip | GenMapp | BRB Array | Lotus 1,2,3 | JigCell
Paup

This is a tool for inferring and interpreting phylogenetic trees, available for purchase at the company website.

Phylip

This is a free inference tool for phylogenetic analysis.

GenMapp

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 GenMapp site.

BRB array

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

- excerpted from the BRB array site.

Lotus 1,2,3

Collaborative information management.

JigCell

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 JigCell site.

Paper on the JigCell Model Builder (PDF)

Tools

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Tools

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<TBODY>
<TR>
<TD align=middle height=21><div align="left"></div></TD>
<TD height=21 bgColor=#ffffff><div align="left"></div></TD>
</TR>
<TR>
<TD height=37 colspan="2" align=middle><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"><strong>Tools
used during the workshop</strong></font></div></TD>

</TR>
<TR>
<TD height=21 colspan="2" align=middle> <p align="center"><font size="2" face="Arial, Helvetica, sans-serif"><a href="#stella">Stella</a>
| <a href="#JDes">JDesigner</a> | <a href="#excel">Excel</a>
| <a href="#virt">Virtual Cell</a></font></p></TD>
</TR>

<TR>
<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>
<TD width=381 height=29 bgColor=#ffffff><div align="left"></div></TD>
</TR>
<TR>
<TD height=84 colspan="2" align=middle> <p align="left"><font size="2" face="Arial, Helvetica, sans-serif"><font color="#000000">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.</font></font></p>
<p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">This
software is useful for Mapping and Modeling, Simulation
and Analysis, and Communication</font></p>

<hr align="left" width="381"> </TD>
</TR>
<TR>
<TD align=middle height=22><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
<TD height=22 bgColor=#ffffff><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
</TR>
<TR>
<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>

<TD height=22 bgColor=#ffffff><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
</TR>
<TR>
<TD height=23 colspan="2" align=middle><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"><font color="#000000">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.</font></font>
</div>
<hr align="left" width="381"></TD>
</TR>
<TR>
<TD align=middle height=21><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"><a name="excel"></a>Excel</font></div></TD>

<TD height=21 bgColor=#ffffff><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
</TR>
<TR>
<TD height=21 colspan="2" align=middle><p align="left"> </p>
<hr align="left"> </TD>
</TR>
<TR>
<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
Cell</a></font></div></TD>
<TD height=21 bgColor=#ffffff><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>

</TR>
<TR>
<TD height=21 colspan="2" align=middle><p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">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.</font></p>
<hr align="left"> </TD>
</TR>
<TR>
<TD height=21 colspan="2" align=middle><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font>
</div>
<hr align="left"> <div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>

</TR>
<TR>
<TD height=36 colspan="2" align=middle><div align="left"><strong>Other
tools not covered in the workshop but referenced by
students</strong></div></TD>
</TR>
<TR>
<TD height=21 colspan="2" align=middle><div align="center"><font size="2" face="Arial, Helvetica, sans-serif"><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></font></div></TD>

</TR>
<TR>
<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>
<TD height=21 bgColor=#ffffff><div align="left"><font size="2" face="Arial, Helvetica, sans-serif"> </font></div></TD>
</TR>
<TR>
<TD height=74 colspan="2" align=middle> <p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">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>.</font> </p>

<hr align="left" width="381"></TD>
</TR>
<TR>
<TD align=middle height=21><div align="left"></div></TD>
<TD height=21 bgColor=#ffffff><div align="left"></div></TD>
</TR>
<TR>
<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>
<TD height=25 bgColor=#ffffff><div align="left"></div></TD>

</TR>
<TR>
<TD height=25 colspan="2" align=middle> <div align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">This
is a free inference tool for phylogenetic analysis.</font>
</div>
<hr align="left" width="381"> <div align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif"> 
</font></div></TD>
</TR>
<TR>
<TD align=middle height=21><div align="left"></div></TD>

<TD height=21 bgColor=#ffffff><div align="left"></div></TD>
</TR>
<TR>
<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>
<TD height=37 bgColor=#ffffff><div align="left"></div></TD>
</TR>
<TR>
<TD height=154 colspan="2" align=middle> <p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">The
main features underlying GenMAPP are:<br>

<br>
- Draw pathways with easy to use graphics tools <br>
- Color genes on MAPP files based on user-imported
genomic data<br>
- Query genomic data against MAPPs and the GeneOntology
with MAPPFinder </font><font color="#000000" face="Arial, Helvetica, sans-serif"><br>
<br>
<font size="1">- excerpted from the <a href="http://www.genmapp.org/">GenMapp
site</a>.</font></font> </p>

<hr align="left" width="381"></TD>
</TR>
<TR>
<TD align=middle height=21><div align="left"></div></TD>
<TD height=21 bgColor=#ffffff><div align="left"></div></TD>
</TR>
<TR>
<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
array</font></a></div></TD>
<TD height=39 bgColor=#ffffff><div align="left"></div></TD>

</TR>
<TR>
<TD height=106 colspan="2" align=middle> <p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">BRB
ArrayTools is an integrated package for the visualization
and statistical analysis of DNA microarray gene expression
data.</font><font color="#000000" face="Arial, Helvetica, sans-serif"><br>
<br>
<font size="1">- excerpted from the <a href="http://linus.nci.nih.gov/BRB-ArrayTools.html">BRB
array site</a>.</font></font> </p>
<hr align="left" width="381"> </TD>

</TR>
<TR>
<TD align=middle height=21><div align="left"></div></TD>
<TD height=21 bgColor=#ffffff><div align="left"></div></TD>
</TR>
<TR>
<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
1,2,3</font></a></div></TD>
<TD height=24 bgColor=#ffffff><div align="left"></div></TD>
</TR>

<TR>
<TD height=39 colspan="2" align=middle> <p align="left"><font color="#000000" size="2" face="Arial, Helvetica, sans-serif">Collaborative
information management. </font> </p>
<hr align="left" width="381"> </TD>
</TR>
<TR>
<TD align=middle height=21><div align="left"></div></TD>
<TD height=21 bgColor=#ffffff><div align="left"></div></TD>
</TR>

<TR>
<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>
<TD height=28 bgColor=#ffffff><div align="left"></div></TD>
</TR>
<TR>
<TD height=81 colspan="2" align=middle><div align="left"><font face="Arial, Helvetica, sans-serif"><font color="#000000" size="2">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.</font></font><br>
<br>
<font color="#000000" size="2" face="Arial, Helvetica, sans-serif">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. <br>

- <font size="1">exerpted from the <a href="http://jigcell.biol.vt.edu/">JigCell
site</a>.<br>
<font size="2"><a href="docs/ModelBuilderJigCell.pdf"><br>
Paper on the JigCell Model Builder</a> (PDF)</font></font></font></div></TD>
</TR>
<TR>
<TD height=21 colspan="2" align=middle><div align="left"></div></TD>

</TR>
<TR>
<TD height=21 colspan="2" align=middle> <p align="left"> </p></TD>
</TR>
</TBODY>
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<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">Welcome to [[Wikipedia]],</div>
<div style="top:+0.2em; font-size:95%;">the free encyclopedia that [[Wikipedia:Introduction|anyone can edit]].</div>
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*[[Portal:Arts|Arts]]
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*[[Portal:History|History]]
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*[[Portal:Society|Society]]
*[[Portal:Technology|Technology]]
*'''[[Portal:List of portals|All portals]]'''
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|style="font-size:95%; padding:10px 0; margin:0px; text-align:left; white-space:nowrap; color:#000;"| [[Wikipedia:About|Overview]] '''·''' [[Wikipedia:Tutorial|Editing]] '''·''' [[Wikipedia:Questions|Questions]] '''·''' [[Help:Contents|Help]]
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! <h2 style="margin:0; background:#cef2e0; font-size:120%; font-weight:bold; border:1px solid #a3bfb1; text-align:left; color:#000; padding:0.2em 0.4em;">Today's featured article</h2>
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{| width="100%" cellpadding="2" cellspacing="5" style="vertical-align:top; background:#f5faff;"
! <h2 style="margin:0; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;">In the news</h2>
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|style="color:#000;"| {{In the news}}
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! <h2 style="margin:0; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;">On this day...</h2>
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! <h2 style="margin:0; background:#ddcef2; font-size:120%; font-weight:bold; border:1px solid #afa3bf; text-align:left; color:#000; padding:0.2em 0.4em;">Today's featured picture</h2>
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Main Page

2007-04-30T14:07:03Z

WikiAdmin:

<div id="mainpage"></div>
{| style="width:100%; background:#fcfcfc; margin-top:+.9em; border:1px solid #ccc;"
|style="width:56%; color:#000"| 
{| style="width:280px; border:solid 0px; background:none;"
|style="width:280px; text-align:center; white-space:nowrap; color:#000;"|
<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">Welcome to [[Wikipedia]],</div>
<div style="top:+0.2em; font-size:95%;">the free encyclopedia that [[Wikipedia:Introduction|anyone can edit]].</div>
<div id="articlecount" style="width:100%; text-align:center; font-size:85%;">[[Special:Statistics|{{NUMBEROFARTICLES}}]] articles in English</div>
|}
|style="width:11%; font-size:95%; color:#000;"|
*[[Portal:Arts|Arts]]
*[[Portal:Biography|Biography]]
*[[Portal:Geography|Geography]]
|style="width:11%; font-size:95%;"|
*[[Portal:History|History]]
*[[Portal:Mathematics|Mathematics]]
*[[Portal:Science|Science]]
|style="width:11%; font-size:95%;"|
*[[Portal:Society|Society]]
*[[Portal:Technology|Technology]]
*'''[[Portal:List of portals|All portals]]'''
|}
{|style="width:100%; background:none; margin:-.8em 0 -.7em 0;"
|style="font-size:95%; padding:10px 0; margin:0px; text-align:left; white-space:nowrap; color:#000;"| [[Wikipedia:About|Overview]] '''·''' [[Wikipedia:Tutorial|Editing]] '''·''' [[Wikipedia:Questions|Questions]] '''·''' [[Help:Contents|Help]]
|style="font-size:95%; padding:10px 0; margin:0px; text-align: right; white-space:nowrap; color:#000;"|
[[Wikipedia:Contents|Contents]] '''·''' [[Wikipedia:Categorical index|Categories]] '''·''' [[Wikipedia:Featured content|Featured content]] '''·''' [[Wikipedia:Quick index|A–Z index]]
|}
{{Main Page banner}}
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! <h2 style="margin:0; background:#cef2e0; font-size:120%; font-weight:bold; border:1px solid #a3bfb1; text-align:left; color:#000; padding:0.2em 0.4em;">Today's featured article</h2>
|-
|style="color:#000;"| {{Wikipedia:Today's featured article/{{CURRENTMONTHNAME}} {{CURRENTDAY}}, {{CURRENTYEAR}}}}
|-
! <h2 style="margin:0; background:#cef2e0; font-size:120%; font-weight:bold; border:1px solid #a3bfb1; text-align:left; color:#000; padding:0.2em 0.4em;">Did you know...</h2>
|-
|style="color:#000;"| {{Did you know}}
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{| width="100%" cellpadding="2" cellspacing="5" style="vertical-align:top; background:#f5faff;"
! <h2 style="margin:0; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;">In the news</h2>
|-
|style="color:#000;"| {{In the news}}
|-
! <h2 style="margin:0; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;">On this day...</h2>
|-
|style="color:#000;"| {{Wikipedia:Selected anniversaries/{{CURRENTMONTHNAME}} {{CURRENTDAY}}}}
|-
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{| style="border-spacing:8px; margin:-8px -8px;"
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|-
|style="color:#000;"| {{POTD protected}}
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