jigcell.cs.vt.edu

JigCell Project Homepage

Models and Use Cases. Welcome to the JigCell project. JigCell is a joint effort by members of the Departments of Biological Sciences. Our goal is to advance the state of the art for modeling in Systems Biology. Our team provides a unique synergy between biologists and computer scientists. Our philosophy is that this synergy is an important driver for advancing the state-of-the-art in systems biology. By creating advanced software tools, computer scientists can help biologists to become more produ...

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JigCell Project Homepage | jigcell.cs.vt.edu Reviews

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Models and Use Cases. Welcome to the JigCell project. JigCell is a joint effort by members of the Departments of Biological Sciences. Our goal is to advance the state of the art for modeling in Systems Biology. Our team provides a unique synergy between biologists and computer scientists. Our philosophy is that this synergy is an important driver for advancing the state-of-the-art in systems biology. By creating advanced software tools, computer scientists can help biologists to become more produ...

<META> KEYWORDS

1 jigcell homepage

2 frog egg extract

3 budding yeast

4 generic model

5 circadian rhythms

6 software documentation

7 project manager

8 model builder

9 run manager

10 comparator

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JigCell Project Homepage | jigcell.cs.vt.edu Reviews

https://jigcell.cs.vt.edu

Models and Use Cases. Welcome to the JigCell project. JigCell is a joint effort by members of the Departments of Biological Sciences. Our goal is to advance the state of the art for modeling in Systems Biology. Our team provides a unique synergy between biologists and computer scientists. Our philosophy is that this synergy is an important driver for advancing the state-of-the-art in systems biology. By creating advanced software tools, computer scientists can help biologists to become more produ...

INTERNAL PAGES

jigcell.cs.vt.edu

1

JigCell Project Links Page

http://jigcell.cs.vt.edu/links.php

Models and Use Cases. Links to Related Sites. JigCell is funded in part by the DARPA BioSPICE. JigCell is a joint effort by members of the Departments of Biology. Much of this work is done in the Tyson Lab. JigCell is one of several projects related to Problem Solving Environments ( PSE. Research at Virginia Tech. JigCell uses the Systems Biology Markup Language ( SBML. As its native input/output language for models. An alternative model description language to SBML is CellML.

2

The Budding Yeast Cell Cycle

http://jigcell.cs.vt.edu/budyeastUC.php

Models and Use Cases. The Budding Yeast Cell Cycle. A wiring diagram) of the regulatory network. We show in the budding yeast website. And the companion paper. That a computational model, built on the consensus picture of regulatory network derived from reductive biochemical studies and genetic manipulations, is largely successful (predicting 120 out of 133 cases) in explaining the phenotypes of currently characterized mutants of the regulatory system. Highlights of the website include:.

3

Frog Egg Extract Model, Use Case, and Walkthrough

http://jigcell.cs.vt.edu/frogeggUC.php

Models and Use Cases. Frog Egg Extract Model, Use Case, and Walkthrough. Note: Most figures on this page can be clicked on to open a larger version.]. Whose purpose is to illustrate how the JigCell software is used. The model developed in this use case is based on the biochemistry of M-phase promoting factor (MPF) in Xenopus oocyte extracts (frog egg extract). It is a simpler model based on an earlier work by Marlovits, Tyson, Novák, and Tyson (1998). The next step in creating a model is to sketch out th...

4

JigCell Software Distribution Page

http://jigcell.cs.vt.edu/distribution.php

Models and Use Cases. Run the BioPack Demo. A batch system for simulating ODE systems with varying parameters on each simulation. The result of a Param Batch run is a PDF or PS file containing plots of all the simulations. A link to the BioPack directory. Documentation for the BioSPICE dashboard Comparator Analyzer. Documentation for the BioSPICE dashboard Model Builder Analyzer. Page last modified on: September 09 2009 12:40:51. Any questions regarding website may be directed to Cliff Shaffer .

5

JigCell Developer's Notes

http://jigcell.cs.vt.edu/develop.php

Models and Use Cases. This page primarily contains information of interest to the internal JigCell development team. JigCell system performance requirements. JigCell version control system notes. Page last modified on: September 09 2009 12:42:02. Any questions regarding website may be directed to Cliff Shaffer .

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jigcell.cs.vt.edu

JigCell Project Homepage

Models and Use Cases. Welcome to the JigCell project. JigCell is a joint effort by members of the Departments of Biological Sciences. Our goal is to advance the state of the art for modeling in Systems Biology. Our team provides a unique synergy between biologists and computer scientists. Our philosophy is that this synergy is an important driver for advancing the state-of-the-art in systems biology. By creating advanced software tools, computer scientists can help biologists to become more produ...

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