Advanced Computing in Cell Biology:

Workshop in Computational Biology

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Tools used during the workshop

Stella | JDesigner | Excel | Virtual Cell


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



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.




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

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

This is a free inference tool for phylogenetic analysis.


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

- excerpted from the BRB array site.

Collaborative information management.

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


This material is based upon work supported by the National Science Foundation under Grant No. 0439204. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. If you have a question about materials on these pages please send us an email.