Observatorio de I+D+i UPM

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Other publications:
Extending the features and improving the performance of gro simulator: new bacterial conjugation and gene expression module
Year:2015
Research Areas
  • Computational biology
Information
Abstract
gro is a flexible cell programming language and powerful Agent-based Model (AbM) tool developed in Klavins Lab for simulating bacterial colony growth and cell-cell communication. It is used as a prototyping tool in synthetic biology. Here, we present some extensions made to gro to: 1) improve its performance (a new shoving algorithm and a new genetic expression module) and 2) add new functionalities (bacterial conjugation and nutrient uptake). The increase in performance is achieved mainly by the shoving algorithm that seeks to minimise calculations for relocating and reorienting simulated bacteria in the colony. The new genetic module also speeds up execution by calculating protein concentrations in each bacterium using a model based on Boolean networks with delays.
International
Si
Entity
Place
Pages
Reference/URL
Publication type
Poster contribution
Participants
  • Autor: Martín Gutiérrez Pescarmona (UPM)
  • Autor: Guillermo Pérez del Pulgar Frowein (UPM)
  • Autor: Paula Gregorio Godoy (UPM)
Research Group, Departaments and Institutes related
  • Creador: Grupo de Investigación: Grupo de Inteligencia Artificial (LIA)
  • Departamento: Inteligencia Artificial
S2i 2020 Observatorio de investigación @ UPM con la colaboración del Consejo Social UPM
Cofinanciación del MINECO en el marco del Programa INNCIDE 2011 (OTR-2011-0236)
Cofinanciación del MINECO en el marco del Programa INNPACTO (IPT-020000-2010-22)