TOM Fall Schedule

Tentative schedule for Fall session 2016

Date Presenter       Title of presentation
31.08 Abhishekh Gupta SGNS2: a tool for systems modeling
21.09 Tuomo Hartonen Transcription factor binding site discovery from ChIP-exo/Nexus data
19.10 Gopal Peddinti COBRA: Constraint Based Modeling for Genome scale metabolic networks
16.11 Teemu Kivioja Integer Linear Programming
14.12 Boris Vassiliev

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TOM – 31.08.2016

Venue: Biomedicum 1, Seminar room 1-2

Timing: 16:00 onwards

Presenter: Abhishekh Gupta, Post-doc, Group Aittokallio, FIMM

SGNS2: a tool for systems modeling

To move beyond the trajectory of traditional scientific efforts focused on studying individual genes or single mutation and its relationship with a phenotype, we need to channel efforts to integrate information from various technologies (omics datasets) to enable a holistic view of biological systems (my current research focus is on Cancer systems). Therefore, what I will be presenting to you can be categorized into the area of Cancer Systems Biology.


Interactions in biological systems differ from physical and chemical systems, as biological processes are mostly stochastic in nature and involve a low copy numbers of interacting species (for ex: mRNA, proteins, substrate). Transcriptional regulation of gene expression is a dynamic process, and inherently noisy due to the fluctuations in number of biomolecules involved in such processes. This dynamic behavior of transcriptomic landscape can have a significant effect on the overall cellular response to a given stimulus, for instance, how a cancer cell responds to a drug. For such systems, a stochastic formulation is usually preferred.

I will be presenting how the tool SGNS2 can be used in systems biology project. SGNS2 is an open-source simulator of chemical reaction systems according to the Stochastic Simulation Algorithm (SSA). SGNS2 is based on an enhanced Next Reaction Method, one of the efficient sampling procedures of the SSA. The simulator also uses the concepts of dynamic compartments. The simulator is optimized for simulation of models with large number interacting species.

Lloyd-Price J, Gupta A, Ribeiro AS. SGNS2: a compartmentalized stochastic
chemical kinetics simulator for dynamic cell populations. Bioinformatics. 2012
Nov 15;28(22):3004-5.