About Morphogénie


Biology is both complex and complicated. Biologists face unexpected behaviour and natural variability at the bench every day. What they observe has often not been looked at before (or not like that!).

Creating a dynamical and physicaly accurate simulation of the oserved biological system can ease the integration of the quantitative data collected.

Our goal is to lower the activation energy between the biological issue and its numerical representation. Openness is essential to allow fluid information and software sharing between ourselves and our users, and is complemented by a litterate programming approach. The core of our software is thus open source, and we rely on open source technologies.

We also understand that physicists, computational biologists and computer scientists don’t always have time nor strong intensives to produce documented and easy to maintain code. By taking care of these aspects through continuous integration, we help interdisciplinary work focus on understanding each other - which is of course the hardest part!

Our main product is the tyssue library. You can follow our open source developement work at github.com/DamCB page.

The society

Morphogénie Logiciels SAS is a free and open source software editor founded in 2016 by Guillaume Gay. Our area of expertise is in the development of tailored data driven modeling of living organisms, from the single cell to the epithelium.

We consider that our value lies in our expertise, and Morphogénie is financed through both public and private collaborations.

About Guillaume

A photo of me

Guillaume Gay is a free software user and developer. He mostly uses the Python programming language, with the wonderfull Numpy and friends libraries.

GG studied physics and chemistry in Bordeaux, Strasbourg and Toulouse, France. During his PhD, he worked on experiments trying to combine laser cooled atoms and light fields generated by small apertures in metallic films, called surface plasmon polaritons. He defended his PhD. thesis in june 2006, and shortly after made a small jump to another building of my alma mater university in Toulouse and found myself in a cell biology lab, in Sylvie Tournier’s team. He was hired to work on a FRAP and micro-discection apparatus on a wide field microscope. The data he was gathering gave sufficient information for modeling purposes, so he developed a model of chromosome segregation in fission yeast (JCB 2009).

Parallel to this, he worked with V. Lobjois and C. Lorenzo, who are know part of the IP3D team at ITAV, to build a Selective Plane Imaging Microscope (or SPIM) to study proliferation in 3D cancer cell cultures. In 2008, he spent a semester at Los Andes University in Bogotá, Colombia as an invited professor in the biophysics group, where he worked on giant unilamellar vesicles sedimentation, taught basic physics to biology and medecine students, and learned Spanish.

Principal publications

B. Monier, M. Gettings, G. Gay, T. Mangeat, S. Schott, A. Guarner, M. Suzanne 2015, Apico-basal forces exerted by apoptotic cells drive epithelium folding, Nature vol. 518 7538:245-248

Gay, G., Courtheoux, T., Reyes, C., Tournier, S., and Gachet, Y. 2012. A stochastic model of kinetochore–microtubule attachment accurately describes fission yeast chromosome segregation. The Journal of Cell Biology 196:757-774 .

Courtheoux, T., Gay, G., Gachet, Y., and Tournier, S. 2009. Ase1/Prc1-dependent spindle elongation corrects merotely during anaphase in fission yeast. Journal of Cell Biology 187:399–412.

Gay, G., Alloschery, O., de Lesegno, B. V., Weiner, J., and Lezec, H. J. 2006. Surface wave generation and propagation on metallic subwavelength structures measured by Far-Field interferometry. Physical Review Letters 96:213901+.

Gay, G., Alloschery, O., Viaris de Lesegno, B., O/’Dwyer, C., Weiner, J., and Lezec, H. J. 2006. The optical response of nanostructured surfaces and the composite diffracted evanescent wave model. Nature Physics 2:262–267.

Lorenzo, C., Frongia, C., Jorand, R., Fehrenbach, J., Weiss, P., Maandhui, A., Gay, G., Ducommun, B., and Lobjois, V. 2011. Live cell division dynamics monitoring in 3D large spheroid tumor models using light sheet microscopy. Cell Division 6:22+.

Suarez, I. A. R., Gay, G., Ladino, A., Gonzalez Mancera, A., and Leidy, C. 2010. Dynamics of sedimentation and deformation of GUVs under different tonicity conditions. In Biohyscial Society 54th Annual Meeting, volume 98, pp. 491a+.

For a full list of my publications, please visit citeUlike