CSBE Dr Laurence Loewe

9 February 2010

Dr Laurence Loewe

Dr Laurence Loewe
Contact Details
Centre for Systems Biology at Edinburgh
The University of Edinburgh
CH Waddington Building, Room 2.04
King's Buildings Campus
Mayfield Road
Edinburgh
Scotland, UK

Telephone: +44 (0)131 651 9017
E-mail: laurence.loewe[a]ed.ac.uk

Research Interests

My research centres on computer models that integrate biological knowledge. Such models regularly struggle with the complexity of intracellular biochemical reaction networks. To facilitate the analysis of more complex models, I work with Prof. Jane Hillston on extending the applicability of the Bio-PEPA process algebra.

A process algebra is a compositional, formal system description technique that is supported by formal reasoning and model manipulation methods. The formality means that a software tool can apply these methods automatically in order to help with the analysis of a model. Bio-PEPA has recently been developed in order to model intracellular biochemical reaction networks.

I am currently working on the following applied and methodological projects together with other researchers in CSBE:

Apply Bio-PEPA to model the cholesterol synthesis pathway.
Apply Bio-PEPA to model circadian clocks.
Explore the use of Approximate Bayesian Computation for estimating parameters in biochemical models from experimental data.
Attempt to extend the applicability of Bio-PEPA models by investigating some underlying mechanistic assumptions.

Having quality modelling tools that are applicable to a wide range of systems biology problems is important. For example, such tools can facilitate analyses of robustness that are based on a mechanistic understanding in corresponding models. Robustness is a pervasive feature of biological systems that needs to be understood for many other questions, including effective drug design and how systems evolve. I also have an interest in how systems biology might interact with evolutionary genetics (see the evolutionary systems biology website). My long-term research homepage is here.

Selected Publications

Loewe, L. 2009. A framework for evolutionary systems biology. BMC Systems Biology 3:27. Abstract; PDF

Loewe, L., and J. Hillston. 2008. The distribution of mutational effects on fitness in a simple circadian clock. pp. 156-175 in: M. Heiner, and A. M. Uhrmacher, eds. Computational Methods in Systems Biology CMSB-08. Springer, Rostock, Germany. Lecture Notes in Bioinformatics 5307:156-175. PDF

Loewe, L., and J. Hillston. 2008. Meeting report: Computational models in systems biology. Genome Biol 9:328. PDF

Loewe, L. 2008. Designing a Front-End for Bio-PEPA in S. Gilmore, ed. Proceedings of the 7th Workshop on Process Algebra and Stochastically Timed Activities, 30-31 July 2008, Edinburgh, UK. PDF

Duguid A, Gilmore S, Guerriero ML, Hillston J & Loewe L (2009) “Design and development of software tools for Bio-PEPA”, Proceedings of the 2009 Winter Simulation Conference (WSC’09), eds.: Rossetti RMD, Hill RR, Johansson B, Dunkin A & Ingalls RG. Austin, Texas, to appear in December. PDF

Loewe L., Moodie S., Hillston J. 2009. Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA. Proceedings of the "2nd International Workshop on Computational Models for Cell Processes" (CompMod 2009). Abstract | PDF

Loewe L., Moodie S., Hillston J. 2009. Technical Report: Defining a textual representation for SBGN Process Diagrams and translating it to Bio-PEPA for quantitative analysis of the MAPK signal transduction cascade. Technical Report EDI-INF-RR-1334, School for Informatics, University of Edinburgh. PDF

Selected software prototypes

SBGNtext2BioPEPA: translating from SBGN to quantitative analysis in Bio-PEPA

SBGNtext2BioPEPA is a tool that automatically translates from a textual representation of SBGN Process Diagrams to the process algebra Bio-PEPA to facilitate quantitative analysis. While the ready-to-download code is tailored towards generating Bio-PEPA code, the underlying principles are general and can help translate to other quantitative analysis formalisms too. This work has also led to a possible textual representation of SBGN Process Diagrams that is formally defined by a BNF grammar. For more details, see the dedicated SBGNtext2BioPEPA site.

Why construct translators? Ever since the invention of computers, people have been developing schemes for simplifying the process of programming. While textual programming languages at various levels of abstraction are much simpler to use than binary machine code, many biologists feel that visual representations of biochemical reaction networks are simpler to produce and to understand than textual (or mathematical) representations. This drives the development of graphical notations for the description of biochemical systems, the latest of which is known as SBGN (Systems Biology Graphics Notation). Work on translators is needed to develop approaches for including quantitative details and automatically translating the corresponding information into input for modelling frameworks such as Bio-PEPA.


9 February 2010
Home History Research Software Funding Opportunities Management Members Outreach & Events Commercialisation Experimental Facilities Computational Facilities Infrastructure Vacancies & Studentships Internal Wikis Contact For further information, in particular to explore research collaboration with CSBE, please contact csbe[a]ed.ac.uk	Dr Laurence Loewe Contact Details Centre for Systems Biology at Edinburgh The University of Edinburgh CH Waddington Building, Room 2.04 King's Buildings Campus Mayfield Road Edinburgh Scotland, UK Telephone: +44 (0)131 651 9017 E-mail: laurence.loewe[a]ed.ac.uk Research Interests My research centres on computer models that integrate biological knowledge. Such models regularly struggle with the complexity of intracellular biochemical reaction networks. To facilitate the analysis of more complex models, I work with Prof. Jane Hillston on extending the applicability of the Bio-PEPA process algebra. A process algebra is a compositional, formal system description technique that is supported by formal reasoning and model manipulation methods. The formality means that a software tool can apply these methods automatically in order to help with the analysis of a model. Bio-PEPA has recently been developed in order to model intracellular biochemical reaction networks. I am currently working on the following applied and methodological projects together with other researchers in CSBE: Apply Bio-PEPA to model the cholesterol synthesis pathway. Apply Bio-PEPA to model circadian clocks. Explore the use of Approximate Bayesian Computation for estimating parameters in biochemical models from experimental data. Attempt to extend the applicability of Bio-PEPA models by investigating some underlying mechanistic assumptions. Having quality modelling tools that are applicable to a wide range of systems biology problems is important. For example, such tools can facilitate analyses of robustness that are based on a mechanistic understanding in corresponding models. Robustness is a pervasive feature of biological systems that needs to be understood for many other questions, including effective drug design and how systems evolve. I also have an interest in how systems biology might interact with evolutionary genetics (see the evolutionary systems biology website). My long-term research homepage is here. Selected Publications Loewe, L. 2009. A framework for evolutionary systems biology. BMC Systems Biology 3:27. Abstract; PDF Loewe, L., and J. Hillston. 2008. The distribution of mutational effects on fitness in a simple circadian clock. pp. 156-175 in: M. Heiner, and A. M. Uhrmacher, eds. Computational Methods in Systems Biology CMSB-08. Springer, Rostock, Germany. Lecture Notes in Bioinformatics 5307:156-175. PDF Loewe, L., and J. Hillston. 2008. Meeting report: Computational models in systems biology. Genome Biol 9:328. PDF Loewe, L. 2008. Designing a Front-End for Bio-PEPA in S. Gilmore, ed. Proceedings of the 7th Workshop on Process Algebra and Stochastically Timed Activities, 30-31 July 2008, Edinburgh, UK. PDF Duguid A, Gilmore S, Guerriero ML, Hillston J & Loewe L (2009) “Design and development of software tools for Bio-PEPA”, Proceedings of the 2009 Winter Simulation Conference (WSC’09), eds.: Rossetti RMD, Hill RR, Johansson B, Dunkin A & Ingalls RG. Austin, Texas, to appear in December. PDF Loewe L., Moodie S., Hillston J. 2009. Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA. Proceedings of the "2nd International Workshop on Computational Models for Cell Processes" (CompMod 2009). Abstract \| PDF Loewe L., Moodie S., Hillston J. 2009. Technical Report: Defining a textual representation for SBGN Process Diagrams and translating it to Bio-PEPA for quantitative analysis of the MAPK signal transduction cascade. Technical Report EDI-INF-RR-1334, School for Informatics, University of Edinburgh. PDF Selected software prototypes SBGNtext2BioPEPA: translating from SBGN to quantitative analysis in Bio-PEPA SBGNtext2BioPEPA is a tool that automatically translates from a textual representation of SBGN Process Diagrams to the process algebra Bio-PEPA to facilitate quantitative analysis. While the ready-to-download code is tailored towards generating Bio-PEPA code, the underlying principles are general and can help translate to other quantitative analysis formalisms too. This work has also led to a possible textual representation of SBGN Process Diagrams that is formally defined by a BNF grammar. For more details, see the dedicated SBGNtext2BioPEPA site. Why construct translators? Ever since the invention of computers, people have been developing schemes for simplifying the process of programming. While textual programming languages at various levels of abstraction are much simpler to use than binary machine code, many biologists feel that visual representations of biochemical reaction networks are simpler to produce and to understand than textual (or mathematical) representations. This drives the development of graphical notations for the description of biochemical systems, the latest of which is known as SBGN (Systems Biology Graphics Notation). Work on translators is needed to develop approaches for including quantitative details and automatically translating the corresponding information into input for modelling frameworks such as Bio-PEPA.
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