The silicon trypanosome: a test case of iterative model extension in systems biology

Fiona Achcar; Abeer Fadda; Jurgen R Haanstra; Eduard J Kerkhoven; Dong-Hyun Kim; Alejandro E Leroux; Theodore Papamarkou; Federico Rojas; Barbara M Bakker; Michael P Barrett; Christine Clayton; Mark Girolami; R Luise Krauth-Siegel; Keith R Matthews; Rainer Breitling

doi:10.1016/B978-0-12-800143-1.00003-8

The silicon trypanosome: a test case of iterative model extension in systems biology

Adv Microb Physiol. 2014:64:115-43. doi: 10.1016/B978-0-12-800143-1.00003-8.

Authors

Affiliations

¹ Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
² Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany.
³ Department of Pediatrics, Centre for Liver Digestive and Metabolic Diseases, and Systems Biology Centre for Energy Metabolism and Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Molecular Cell Physiology, Faculty of Earth and Life Sciences, VU University Amsterdam, Amsterdam, The Netherlands.
⁴ Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Systems and Synthetic Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
⁵ Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
⁶ Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany.
⁷ The Department of Statistical Science and The Centre for Computational Statistics and Machine Learning University College London, London, United Kingdom.
⁸ Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom.
⁹ Department of Pediatrics, Centre for Liver Digestive and Metabolic Diseases, and Systems Biology Centre for Energy Metabolism and Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
¹⁰ Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom. Electronic address: rainer.breitling@manchester.ac.uk.

Abstract

The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has emerged as a popular model organism in systems biology. A predictive quantitative model of glycolysis in the bloodstream form of the parasite has been constructed and updated several times. The Silicon Trypanosome is a project that brings together modellers and experimentalists to improve and extend this core model with new pathways and additional levels of regulation. These new extensions and analyses use computational methods that explicitly take different levels of uncertainty into account. During this project, numerous tools and techniques have been developed for this purpose, which can now be used for a wide range of different studies in systems biology.

Keywords: Differential equations; Dynamic modelling; Metabolomics; Systems biology; Transcriptomics; Trypanosoma brucei; Uncertainty.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Animals
Glycolysis
Humans
Protozoan Proteins / genetics
Protozoan Proteins / metabolism
Systems Biology*
Trypanosoma brucei brucei / genetics
Trypanosoma brucei brucei / metabolism*
Trypanosomiasis, African / parasitology*

Substances

Protozoan Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding