Bio Synth modeling tools

[Colm Herbert]

I am looking for some software that will model how synthetic genes behave. What do you guys use? Are there any decent open source solutions?

Thanks,
Colm

[Thawfeek Mohammed Varusai]

Hi Colm,

   I'm doing my PhD in Systems Biology. Here we use a lot of software to model cell activities. If your system is small (which would mostly be the case with synthetic genes), you can use COPASI. For more complicated systems, software like MATLAB and Mathematica can be used.

   MATLAB and Mathematica are not free but COPASI can be used for free (check the link) and COPASI is also user-friendly. I work mainly with Mathematica but I've some experience with COPASI. So, if you have issues I may be able to help you.

http://www.copasi.org/tiki-index.php?page=downloadnoncommercial

Hope that was helpful.

Cheers,

Thawfeek

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[Cathal Garvey]

For a free (in both senses of the word) alternative to MATLAB also
consider MatPlotLib, which was designed to mimic and extend matlab while
being compatible with the rest of Python:
https://en.wikipedia.org/wiki/Matplotlib

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T: @onetruecathal, @IndieBBDNA
P: +353876363185
W: http://indiebiotech.com

[Gary Mulder]

Check out R:

http://www.r-project.org/

It seems that all the ex-Matlab statisticians I know have moved to it...

Regards,

Gary

[Nathan McCorkle]

matplotlib is only for plotting though... for a matlab replacement (as
good as it can be for free) there is octave.

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-Nathan