Tools

From Computational Cell Biology

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)