Reading Group : Process Algebraic and Agent-based Modeling of Biological Systems

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We read, present, and discuss selected articles concerned largely with process algebraic or agent-based techniques (i.e., as opposed to ODE-based) for modelling biological systems at the molecular level, be that for the purpose of knowledge-sharing, simulation, analysis, computation, etc.

Each time, one attendee makes

  • a small presentation (say around 15 min); main aim - to refresh the main results of the paper(s) for all attendees,
  • including at least three suggested topics/questions for discussion based on the material read.

Afterwards we all discuss the paper(s).

Note: Every attendee of the reading group, signs up for making at least one small presentation, and for reading the papers.

Contents

Organizer

Troels Damgaard

How to sign up

Email to Troels: tcd -at- itu -dot- dk

Room and Place

Room: 4A09 at the IT University of Copenhagen.

Schedule

Note: Schedule is tentative and may be subject to changes.

Week Date Time Presenter Topic Papers Extra materials
21 Mon 19 May 13.00-14.30 Troels Damgaard The kappa-calculus

[1] The reference journal version.
[2] Recent material on self-assembly.
[1] Danos and Laneve: Formal Molecular Biology. Volume 325, Issue 1, 28 September 2004, pages 69-110. Computational Systems Biology. (Locally hosted)

[2] Supplementary reading: Curien, Danos, Krivine, and Zhang: Computational Self Assembly. To appear in TCS.

Slides;

Lac Operon: The Movie;
Wikipedia: Lactose Operon.

22 Mon 26 May 13.00-14.30 No lecture No lecture Cancelled due to overlap with PhD Seminar on Modern Virtual Machines, Meta-Programming, F#
23 Mon 2 Jun 13.00-14.30 Arne Glenstrup The stochastic kappa-calculus

[1] Efficient simulation.
[2] A large model.
[1] Danos et al.: Scalable Simulation of Cellular Signaling Networks. APLAS 2007: 139-157. (Paper on Krivine's webpage)

[2] Supplementary reading: Danos et al.: Rule-based Modelling of Cellular Signaling. CONCUR 2007: 17-41.

24 Mon 9 Jun 13.00-14.30 Søren Debois Pi-calculus for biology

[1] The reference paper.
[2+3] Using stochastic pi.
[1] Regev, Silverman and Shapiro: Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra. Pacific Symposium on Biocomputing 2001: 459–470.

[2] Priami et al.: Application of a Stochastic Name-passing Calculus to Representation and Simulation of Molecular Processes. Information Processing Letters. 80, 25-31. 2001.
[3] Supplementary reading: Priami: Stochastic pi-calculus. Comput. J. 38(7): 578-589 (1995)

25 Mon 16 Jun 13.00-14.30 Hugo A. López Brane Calculi

[1] The reference paper.
[1] Cardelli: Brane Calculi - Interactions of Biological Membranes. Computational Methods in Systems Biology, International Conference CMSB 2004, Paris, France, May 26-28, 2004. (Link to paper is for latest revised version.)

Slides by Cardelli
Course on Artificial Biochemistry

26 Mon 23 Jun 13.00-14.30 Ebbe Elsborg Beta-binders

[1] The reference paper. [2] Stochastic Beta binders.
[3+4] Tool.
[1] Priami and Quaglia: Beta Binders for Biological Interactions. In Proceedings of "Computational methods in system biology (CMSB04)", Parigi 2004 2005 308221-34.
[2] Degano, Prandi, Priami and Quaglia: Beta-binders for Biological Quantitative Experiments. ENTCS, Vol. 164(3), 2006.
[3] Dematté, Priami and Romanel: The Beta Workbench. TR-03-2007.
[4] Dematté, Priami and Romanel: The BlenX Tutorial. TR-09-2008.
27 Mon 30 Jun 13.00-14.30 Cancelled
28 Mon 7 Jul 13.00-14.30 Henrik Pilegaard Biology for beginners +
BioAmbients

[1] The reference paper.

[1] Regev, Panina, Silverman, Cardelli, and Shapiro: BioAmbients: An Abstraction for Biological Compartments. TCS, special issue on Comp. Meth. in Sys. Bio. 2004.

28 Mon 14 Jul 13.00-14.30 Henrik Pilegaard Continued from July 7th. As above. (Extra reading - see Suggested Background Reading.)
29-32 Summer break
33 Mon 11 Aug 13.00-14.30 Jorge A. Pérez
(guest star)
Timed Concurrent Constraint Programming for Biological Systems

Abstract of talk
[1] Arbeláez, Gutiérrez and Pérez: Timed Concurrent Constraint Programming in Systems Biology. ALP Newsletter, Vol. 19 n. 4, November/December 2006.
[2] Gutiérrez, Pérez, Rueda and Valencia: Timed Concurrent Constraint Programming for Analysing Biological Systems. Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC 06) (Part of ICALP'06).
Foundational reading, [3] Olarte, Rueda and Valencia: Concurrent Constraint Programming: Calculi, Languages and Emerging Applications.
34-36 Break
37 Mon 8 Sep 13.00-14.30 Thomas Hildebrandt Cancelled
38 Mon 15 Sep 13.00-14.30 Thomas Hildebrandt PRISM for biology Probabilistic Model Checking of Complex Biological Pathways. John Heath a)

Marta Kwiatkowska b) Gethin Norman b) David Parker b) Oksana Tymchyshyn c)

a) School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom

b) Oxford University Computing Laboratory, Wolfson Building, Parks Road, Oxford OX1 3QD, United Kingdom

c) School of Computer Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom

39 Mon 22 Sep 13.00-14.30 Your name here Subject


The semester has begun and we meet weekly.

List of possible papers for later reading includes the supplementary papers above and the following list:

Bitonal systems The most recent membrane calculus from Cardelli. Cardelli: Bitonal Membrane Systems - Interactions of Biological Membranes. To appear in Theoretical Computer Science, Elsevier, 2008.
Bio-PEPA A quite complete introduction to recent work on Bio-PEPA-variant of PEPA. Ciocchetta and Hillston: Bio-PEPA: a framework for the modelling and analysis of biological systems. 2008.
BIOCHAM The Biochemical Abstract Machine Chabrier, Fages and Soliman: The Biochemical Abstract Machine BIOCHAM. LNCS, Vol. 3082/2005, Computational Methods in Systems Biology, 2005.
Abstract Machines for Bio Abstract Machines of Systems Biology Cardelli: Abstract Machines of Systems Biology. Trans. on Comput. Syst. Biol. III, LNBI 3737, pp. 145-168, 2005.

Suggested Background Reading

  • NCBI: What is a Cell: A Science Primer from National Center for Biotechnology Information (NCBI).

Participants

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