Cellerator

cellerator.org
Cellerator Home | Publications | Gallery | Models | Download

What is Cellerator?

Cellerator™ is a Mathematica® package designed to facilitate biological modeling via automated equation generation. Cellerator was designed with the intent of simulating at least the following essential biological processes:

signal transduction networks (STNs);
cells that are represented by interacting signal transduction networks; and
multi-cellular tissues that are represented by interacting networks of cells that may themselves contain internal STNs.

One of the big advantages of Cellerator is the ability to represent biochemical networks using an arrow-based reaction notation inside of a symbolic mathematical notebook interface (i.e., Mathematica). Cellerator provides automatic translation of reactions to ordinary differential equations; native Mathematica functions provide a simulation and analysis tool set. Cellerator provides front-end functionality that supplements the native interface and eases the simulation process. Cellerator is open source and freely available to academic users. Details are available in the Bioinformatics Paper (Free full text) on Cellerator. Full Citation: Shapiro BE, Levchenko A, Meyerowitz EM, Wold BJ, Mjolsness ED. (2003) "Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations." Bioinformatics. 2003 Mar 22;19(5):677-8. Google Scholar Search on Cellerator

What is xCellerator?

xCellerator (also called xlr8r) is the second-generation of cellerator. It is separately funded and lgpl licensed. More information on xlr8r is available at xcellerator.info. This web page is only for Cellerator, and not for xCellerator.

Typical Cellerator Arrows

Cellerator Arrow	ODE Terms Generated

Typical Cellerator Palettes

Frequently Asked Questions

How do I get a copy of Cellerator™?
See the Click on the Download link at the top of this page
What operating systems does Cellerator™ run on?
It will run on any computer that has Mathematica 4.0 or higher installed. Cellerator™ has been tested on Mac, Windows, Unix and Linux systems. It has been tested through Mathematica version 5.2.
Does Cellerator™ have a macro-language so that its arrows can be embedding in larger simulations?
Yes! It's Mathematica. Cellerator is implemented as a Mathematica notebook and Cellerator functions can be run from within virtually any Mathematica program by including the Cellerator package.
Can I see some examples of Cellerator™ notebooks?
Yes. Click on the "models" link at the top of this page. There is one notebook that can be read in any web browser; the others require Mathematica or Mathreader (a free Mathematica notebook reader that is available from Wolfram Research).
Can I get Cellerator™ from Wolfram?
No.
Can I run Cellerator™ without Mathematica?
No.
Is Cellerator™ avialble on a WebMathematica server?
No; nor do we have any plans to do so in the forseeable future.
Is there a MatLab, Octave, R, C, or (insert language of choice here) Version?
No.
Does Cellerator™ assume Michaelis-Menten or steady state Kinetics?
NO. It solves the complete set of equations predicted by the Law of Mass Action. Michaelis-Menten reaction arrows are also available. It also has a number of transcriptional regulation models that are not Michaelis-Menten.
Is there a GUI?
Check out Sigmoid
If I send you my list of chemical reactions will you run Cellerator™ for me and give me the results?
Time permitting, yes, with the understanding that if interesting results occur we can refer to them in a subsequent publication. We are looking for exciting new applications to test Cellerator™ with.
Is Cellerator SBML compatible?
Cellerator can write SBML level 1 files. It can not write level 2 files, nor can it read any form of SBML. xCellerator can read and write SBML level 2 files utilizing MathSBML.
What is SBML?
Systems Biology Markup Language, an XML-based protocal for systems biology information interchange. See the SBML web page at http://www.sbml.org for further information.
Does Cellerator™ support stochastic simulations?
The xCellerator plugin module "SSA" implements Gillespie's stochastic simulation algorithm utilizing a Cellerator arrow notation. SSA is a stand-alone notebook or can be used in conjunction with xCellerator. There are no plans at this time to incorporate SSA into cellerator as it is already part of xCellerator.
Can I make a sugestion for a change in Cellerator™?
We are currently focusing on xCellerator development and are only implementing bug fixes in Cellerator at the present time. However, we will gladly welcome suggestions for things to be included in xCellerator. Send an email to bshapiro at caltech dot edu.
Where can I learn more about mathematical biology/signal transduction/differential equations/etc?
Click here to see our unofficial suggested reading list
Who are you guys?
Cellerator was originally conceived and developed by Eric Mjolsness, Andre Levchenko, and Bruce Shapiro. Eric Mjolsness is currently Associate Professor of Computer Science at the University of California, Irvine; Andre Levchenko is currently an Assistant Professor of Biomedical Engineering at Johns Hopkins University; and Bruce Shapiro is currently a Visiting Associate in Biology at the California Institute of Technology.
Who paid for cellerator development and maintenance?
Support during various stages of the project has been generously provided by the Caltech President's Fund; the Whittier Foundation; the Beckman Institute at Caltech; the Biomolecular Sensor Research Program at NASA; the NASA Fundamental Biology Program; the National Cancer Institute; the National Science Foundation; the ERATO Kitano Symbiotic Systems Project; and the University of California at Irvine.

Cellerator

Cellerator :: تعاليق

Cellerator