A vertex base simulation of apoptosis mediated Drosophila leg joints formation
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README.md

README.md

This software is no longer maintained, our development efforts have moved to the tyssue library.

See also those notebooks for the leg-joint formation simulation in tyssue: https://github.com/DamCB/tyssue-notebooks/tree/master/leg_joint

This is the Drosophilia Leg Joint Simulation - or in short just leg-joint

copyright Guillaume Gay - 2012 - 2014 - http://damcb.com

This work is part of a research project which has been publish in Nature:

Apico-basal forces exerted by apoptotic cells drive epithelium folding

Bruno Monier, Melanie Gettings, Guillaume Gay, Thomas Mangeat, Sonia Schott, Ana Guarner, Magali Suzanne Nature (21 January 2015), doi:10.1038/nature14152

This work was done in collaboration with Magali Suzanne group at LBCMCP - Université de Toulouse.

If you're just here for eye candy, you can watch a video of the simulation here There's a short summary of the biology here, and you can ask for the paper itself by e-mail.

Dependencies

  • Python >= 3.3 (might work with minimal effort on 2.7, but it's untested)
  • numpy >= 1.8
  • scipy >= 0.12
  • pandas >= 0.13
  • matplotlib >= 1.3
  • IPython >= 1.0
  • graph_tool >= 2.2.36 warning Due to a bug in version 2.2.35, this version won't work

Installing

The easiest route to install (nearly) all the dependencies is to use Anaconda. For graph-tool follow the link above and the instructions there. The easiest way is to install from the precompiled packaged binaries, if available for your OS. Due to a bug, version 2.2.35 won't work.

Documentation

The best way to approach the simulations work-flow is to have a look (and eventually execute) at the notebooks. You can browse static views of those here: http://nbviewer.ipython.org/github/glyg/leg-joint/tree/master/notebooks/

Acknowledgements

We are grateful to Corinne Benassayag, Emmanuel Farge, Yannick Gachet, Thomas Lecuit, Pierre-François Lenne, François Payre, Ernesto Sanchez-Herrero, Bénédicte Sanson and Sylvie Tournier for comments on the manuscript, to Tiago de Paula Peixoto for providing the graph-tool library, and to Marion Aguirrebengoa for helping us with statistics. MS's lab is supported by an ANR grant, a RITC grant and a grant from the University of Toulouse.