I am computer scientist. I put ideas into programmes to understand. I dedicate my study to biology (check my personal page http://stoma.name to see some tools&models I developed). I am interested in interdisciplinary projects within Developmental Biology, Systems Biology and Synthetic Biology, and in particular:

1. Increasing the inovation by developing tools and methodologies facilitating the research in modern biology:
   1. (founder) Spatio-temporal simulation environment
   2. (core dev.) Openalea
2. Building integrative models:
   1. "Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development", Stoma S, Lucas M, Chopard J, Schaedel M, Traas J, Godin C, PLoS Computational Biology 4(10), 2008: e1000207 doi:10.1371/journal.pcbi.1000207
   2. "Using mechanics in the modelling of meristem morphogenesis", Stoma S, Chopard J, Godin C, Traas J: Functional-structural plant models (FSPM), Napier, New Zealand, November 4-9, 2007.
3. Providing training on the state of the art tools used in modern biology:
   1. mentor at Google School of Code 2011
   2. teaching students?
   3. teaching at workshops 1, 2
4. Popularizing standards for various aspects of modeling work:
   1. "Defining Modeling Strategies for Systems Biology", Mats Jirstrand et al., report for the EU commission, 2011.
5. Building integrative data processing workflows dedicated to Systems Biology based on microscopy data:
   1. I use scripting languages (bash, Python) and image processing tools (Fiji, CellProfiler) to make life of the biologists easier!

Please do not hesitate to contact me if you have any inquiries or collaborative proposals.

Contacts

Address

INRIA Paris-Rocquencourt

Domaine de Voluceau BP 105

Projet CONTRAINTES

Batiment 8

78153 Le Chesnay Cedex

CV

Download PDF with CV: EN DE PL FR ES

Publications

Until the papers are not restricted by copyright of the editor they can be found here:

"STSE: Spatio-Temporal Simulation Environment Dedicated to Biology", Stoma S, Froehlich M, Gerber S, Klipp E, BMC Bioinformatics, BMC Bioinformatics, 2011, 12(1):126.

"Defining Modeling Strategies for Systems Biology", Mats Jirstrand et al., report for the EU commission, 2011.

"Towards modeling of spatial dynamic systems based on microscopy images", Stoma S, Proceedings of 6th Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg, 2010.

"Spatio-Temporal Simulation Environment: A Microscopy Image Based Modelization Framework", Stoma S, Klipp E, Microscopy and Microanalysis, 16 (Suppl. 2) , pp 734-735, 2010.

"Modelling development of shoot apical meristem of Arabidopsis", Stoma S, PhD thesis, Montpellier, France, February, 2009.

"Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development", Stoma S, Lucas M, Chopard J, Schaedel M, Traas J, Godin C, PLoS Computational Biology 4(10), 2008: e1000207 doi:10.1371/journal.pcbi.1000207

"Using mechanics in the modelling of meristem morphogenesis", Stoma S, Chopard J, Godin C, Traas J: Functional-structural plant models (FSPM), Napier, New Zealand, November 4-9, 2007.

Invited talks

• "STSE: a tool for microscopy image-based modeling", Palma, Spain, 2011
• "Systematic model building: modeling in space and time", Prague, Czech Republic, 2011
• "Towards modeling of spatial dynamic systems based on microscopy images", Heidelberg, Germany, 2010
• "Mathematical modeling in the context of aquaporin regulation", Nijmegen, Netherlands, 2009
• "Modeling of meristem development", Lyon, France, 2008

Other important roles

• An external expert invited for the FutureSysBio 2010 (a coordination and support action that aim at shaping and predicting the future development of the field Systems Biology working for the European Commission), 2010
• Member of the Humboldt University Recruitment Commission evaluating candidates for Junior Professorship in Biophysics, 2009
• Author of the cover for PLoS Computational Biology 4(10), 2008
• Reviewer for the PLoS Computational Biology, 2009-present

Organization

• Coordination of the european Aquaglyceroporin meeting in Berlin , (ca. 20 people, 5 countries), 2010
• Co-coordination of the european Sy-stem meeting in Montpellier (ca. 40 people, 10 countries), 2008

Grants

• 2011, Second author of Google Summer School of Code 2011 (we proposed to build tools supporting editing&visualizing pathways in the internet browser using cutting edge technologies - details are here), success
• 2011, Author of individual postdoc grant @ BIOMS, reached finals, rejected
• 2011, First author of grant for the Deployment of New Technologies in Teaching @ Humboldt University: using Moodle platform to prepare interactive teaching materials "Python in scientific applications", rejected
• 2010, Author of the Foundation for Polish Science Homing Plus grant application: STSE development, cooperation between Germany and Poland, value: ca. 0.2 million Euro), finished in top 20, with average mark ,,very good application - should receive funding'', rejected

Conference talks/posters

• First Annual Meeting and Workshop on TB Biology and Modeling, Prague, Czech Republic, 03/2011
• 6th Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg, Germany, 09/2010
• Microscopy and Microanalysis, Portland, USA, 08/2010
• ERAsysBio, Tenerife, Spain, 07/2010
• EMBO Workshop Advanced Light Microscopy Techniques and their Applications (PO), Heidelberg, Germany, 05/2010
• Aquaporins (PM), Berlin, Germany, 05/2010
• Aquaporins (PM), Nijmegen, Netherlands, 12/2009
• Aquaporins (PM), Goettingen, Germany, 05/2009
• Aquaporins (PM) (PO), Aarhus, Denmark, 12/2008
• System Biology MEET (PO), Berlin, Germany, 08/2008
• IBSB (PO), Berlin, Germany, 08/2008
• The understanding and modeling of auxin transport in plants, Nottingham (PO), UK, 05/2008
• Sy-stem (PM), Montpellier, France, 04/2008
• Functional-structural plant models (FSPM), Napier, New Zealand, 11/2007
• Sy-stem (PM), Zurich, Switzerland, 12/2007
• Sy-stem (PM), Ghent, Belgium, 04/2007
• Sy-stem (PM), Katowice, Poland, 11/2006
• Sy-stem (PM), Tubingen, Germany, 03/2006
• Sy-Stem (PM) (PO), Lyon, France, 10/2005

(PO) -- poster presentation (PM) -- project meeting with status reports

My labs

Contraintes (INRIA, France)

Theoretical Biophysics (Humboldt University, Germany)

Virtualplants (INRIA, France)

Reproduction et Développement des Plantes (Ecole Normal Superior, France)

Institute of plant science (University of Wroclaw, Poland)