From szymon stoma

Biol: Biol

I am interested in applying Computer Science to interdisciplinary projects within all areas, with special focus on Life Science:

1. A man behind scenes in:
   1. Image and Data Analysis Unit of ScopeM ETH Zurich
   2. MicroscopeIT
   3. Histopixel
   4. Cat-astrophe games
2. Building/validating integrative models:
   1. "STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification", Stoma S, Donze A, Bertaux F, Maler O, Batt G, PLoS Computational Biology 9(5), 2013.
   2. "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
   3. "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. Increasing the inovation by developing tools and methodologies facilitating the research in modern biology:
   1. (cofounder) Essential Vision
   2. (cofounder) Taxonify
   3. (founder) Yeast Image Toolkit
   4. (founder) Spatio-temporal simulation environment
   5. (core dev.) Openalea
   6. (founder) Systems Biology Model Checker
4. Providing training on the state of the art tools used in modern biology:
   1. managing software development: STSE | YIT | SBMC
   2. mentor at Google School of Code 2011
   3. teaching students
   4. teaching at workshops 1, 2, 3
5. Popularizing standards for various aspects of science:
   1. Call4help
   2. "Bridging the gaps in Systems Biology", Cvijovic M et al., Molecular Genetics and Genomics, 2014.
6. 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! I supported image processing in various projects in:
      1. Edda Klipps Lab@TBP::Humboldt University Berlin
      2. Ron Weiss Lab@Synthetic Biology::MIT
      3. Francois Fages Group@Contraintes::INRIA

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

Past projects

post-doc@Syne2arti (2011-2014)

Syne2arti is a project plunged in the context of synthetic biology, or bioengineering, which aims at designing and constructing in vivo biological systems that perform novel, useful tasks. This is achieved by reingeneering existing systems. In contrast to traditional biotechnology, the focus is on developing biological or computational tools that help with an efficient construction of new systems.

The project is developed mainly between two institutions: INRIA (France) and MIT (USA).

founder@Spatio-Temporal Simulation Environment (STSE) dedicated to biology (2010-2015)

This is a project which allows me to follow my dream: an automatic build up of computer simulations based on microscopy imaging. The overall goal of this project is to provide the software platform: a set of tools used to perform spatio-temporal simulations in discrete structures, preferably based on microscopy data. The framework contains modules to digitize, represent, analyze, and model spatial distributions of molecules in static and dynamic structures (e.g. growing). A strong accent is put for the experimental verification of biological models by actual, spatio-temporal data acquired using microscopy techniques.

It is a project driven by my passion, since currently it is not supported officially by any institution (however it is supported by many individuals which I am most grateful). My main responsibilities for the project are planning&coordination of its development (in terms of choice of methodology, biological applications and IT development), promoting and representing the project and since recently checking for funding possibilities.

post-doc@Aquaglyceroporins (2008-2010)

The overall goal of this project was to provide high-level training to early-stage researchers and experienced researchers in integrated analysis of cell physiology by performing interdisciplinary analyses of the role, structure, function and regulation of aquaporins, thereby advancing this field and contribute to structuring the area within Europe.This Research training network combined concepts and techniques from molecular cell biology; physiology and systems biology of cell, tissue and animal models; clinical studies; model organisms; protein production, purification and crystallisation; structural biology by atomic force microscopy, electron crystallography and X-ray crystallography; computational biology via molecular dynamics simulation and mathematical modelling; rational molecular design, organic chemistry and combinatorial chemistry.

PhD@Sy-Stem (2005-2008)

SY-STEM was clearly inter- and multi-disciplinary, and builded new bridges between biology, mathematics, statistics and computer modeling. It used genetic, molecular and cellular approaches, imaging techniques, as well as large-scale genomic techniques to generate sets of data describing SAMs regulations and organ initiation in the model plant Arabidopsis thaliana. Therefore, adapted mathematical and informatics approaches were required to integrate the growing body of knowledge in such a way that it could advance the level of understanding in the field by computational modeling of the apical meristem. Check my contribution to Sy-Stem here.