ISSSB'11 First International Symposium on
Symbolic Systems Biology (ISSSB'11):
Approaches and Applications
Shonan Village Centre, Japan
13-17 November, 2011

Symbolic Systems Biology is a growing area of research involving the application of formal logic-based methods to systems biology and bioinformatics. With biological data being acquired at ever increasing rates, symbolic approaches are being used more and more, in conjunction with numeric techniques, to help formalise expert knowledge and integrate information across different levels of biological abstraction. Recently, a number of symbolic approaches have been developed and usefully applied to a variety of biological problems. Such methods include

  • formal logics (e.g., propositional/first-order/modal frameworks)
  • computational logics (e.g., constraint/logic/answer-set programs)
  • graphical models (e.g., Boolean/Bayesian/Petri nets)
  • synthetic inference (abduction/induction)
  • formal methods (e.g., model checking/pi-calculus/hybrid logic)
  • qualitative reasoning
  • action languages
  • statistical relational learning

While many of these techniques are discussed in various texts on systems biology (see the useful links below), there has been very little inter-comparison these methods and their respective strengths and weaknesses. Instead we find a toolbox of isolated approaches with no conceptual foundations that allow any relationships to be theoretically explored and practically harnessed. Such a study is urgently needed to help to facilitate research in symbolic systems biology by providing a roadmap of which systems are best suited to which problems and allowing more effective exploitation and re-use of algorithms and data.

At the same time, there is also a need for more collaboration between numerical and symbolic biologists. This is necessary to better understand the advantages and drawbacks of the quantitative and qualitative approaches and progress towards a synergistic integration of the two. Ideally this should be done with advice from experimental biologists who are better informed of hot applications and emerging methods of data acquisition. This will help to provide a real context in which symbolic systems biology can be more usefully developed.


The primary aim is to initiate a systematic comparison of symbolic methods and their biological applications to better understand their strengths, weaknesses and supported features. For example, most methods operate upon networks which can be classified functionally (metabolic pathways, protein interactions, signal transduction, gene regulation, etc.) or formally (synchronous/asynchronous, discrete/continuous, deterministic/probabilistic, cyclic/acyclic, with/without feedbacks, etc.). We believe such features will help to construct a roadmap of what been achieved so far and suggest future directions for further research.

A secondary aim is to identify ways in which purely symbolic methods have been or could be combined with numerical techniques and applied to emerging problems in experimental and synthetic biology. We believe it is important to promote a dialogue between qualitative, quantitative, and experimental biologists. For example, it seems symbolic biologists can benefit from a better understanding of flux-based analyses used by numerical biologists; while numerical biologists can benefit from a better understanding of graph-based methods used by symbolic biologists. We believe both views are necessary to better handle real world noise and uncertainty.

Ideally, we will end up constructing a web site which provides an overview and comparison of the above-mentioned methods and applications. We would also hope to begin a discussion (possibly the topic of a future follow-on meeting) on how such methods could employ a standard data format (SBML/SGML) to allow a common specification language for such problems to facilitate inter-operability of the methods. We would also hope to produce some small and larger exemplars that could be used to compare the features offered by the various approaches and estimate their scalability to realistically sized problems. In this way we see the symposium as the first step towards providing a theoretical footing for the field of symbolic systems biology.


The symposium will be hosted by the National Institute of Informatics (NII) in Japan as part of its new series of Shonan meetings which provide a premier Asian location for informatics seminars following the successful European Dagstuhl format. These meetings aim to foster discussion of research and exchange of knowledge between world-class scientists, promising young researchers, and practitioners. They are held in the Shonan Village Center (near Tokyo) which offers a combination of facilities for conferences, training, and lodging in a resort-like setting (with a direct train connection from Narita airport).

We intend to encourage participation from a mix of symbolic biologists, numerical biologists, and experimental biologists. We will encourage these experts to explain their approach, demonstrate their tools, and participate in group discussions aimed at comparing the advantages and disadvantages of each approach and exploring the ways of integrating symbolic and numerical techniques.

Sunday 13th November
Monday 14th November
08.55Opening Address
Oliver Ray
Carolyn Talcott: Symbolic Systems Biology: a Perspective
09.45Agenda Discussion
Katsumi Inoue & Oliver Ray
11.00Talk File
Chitta Baral: Using text extraction and reasoning to construct pharmaco-kinetic pathways and further reason with them to discover drug-drug interactions
11.30Talk File
Hiroshi Matsuno: Modelling of signalling pathways based on Petri nets
14.00Talk File
Torsten Schaub: Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming
14.30Talk N/A
Anne Poupon: Inference of Biological Networks from Experimental Data
15.00Talk File
Marcus Tindall: Understanding Intracellular Signalling in Bacterial Chemotaxis
Francois Fages: Formal Cell Biology in BIOCHAM
16.45Talk N/A
Randy Goebel: The diversity of methods relevant to symbolic systems biology
17.15Discussion (Methods)
Carolyn Talcott
Tuesday 15th November
Sriram Iyengar: Multi-layer modelling in systems biology
09.45Talk File
Celine Rouveirol: Some contributions to transcriptomic data analysis and gene regulation learning
10.15Spotlight N/A
Andrei Doncescu: Model of Double Strand Break of DNA in Logic-Based Hypothesis Finding
11.00Talk File
Tatsuya Akutsu: Attractor detection and control of Boolean networks
11.30Discussion (Methods)
Andrew Phillips
13.30Talk File
Marc Craven: Identifying Candidate Pathways to Explain Phenotypes in Genome-Wide Mutant Screens
14.00Talk N/A
Hisao Moriya: Robustness analysis of yeast cell cycle in silico and in vivo
14.30Spotlight N/A
Toyoyuki Takada: Comparative analysis of liver gene expression profiles in mouse C57BL/6J and MSM/Ms strainss
14.45Discussion (Genes)
Marcus Tindall
Ross King: Robot Scientists for Biology
16.45Spotlight File
Wai-Ki Ching: On Construction of Probabilistic Boolean Networks
19.00Discussion (Logic)
Stephen Muggleton
19.30Talk File
Oliver Ray: Biological pathway inference with answer set programming
20.00Talk File
Katsumi Inoue: Abduction in meta-reasoning
Wednesday 16th November
Andrew Phillips: Programming Cells
09.45Spotlight File
Gauvain Bourgne: Decomposition for Reasoning with Biological Networks
10.00Spotlight File
Tomoya Baba: Gene essentialities of bacterial systems
10.15Spotlight N/A
Takehide Soh: Predicting Gene Knockout Effects by Minimal Pathway Enumeration
11.00Talk File
Takeyuki Tamura: Predicting essential genes via impact degree on metabolic networks
11.30Discussion (Networks)
Katsuhisa Horimoto
Thursday 17th November
Stephen Muggleton: Automated Discovery of Food Webs from Ecological Data using Logic-based Machine Learning
10.00Talk File
Henning Christiansen: Complex PRISM models for analyzing very large biological sequence data, plus a few notes on probabilistic abductive logic programming
11.00Closing Discussion
Oliver Ray & Katsumi Inoue

A summary of the symposium with abstracts of the talks are available as a pdf


The following figures derived from the pre-workshop questionnaire (all of which are further explained in the above report) show (i) a clustering of participants based on the applications and methods with which they work and (ii) an association between those applications and the corresponding methods:

n.b. The photograph on the left (taken by Henning. Christiansen) shows the view of Mount Fuji from the conference centre across the bay of Kanagawa. This is presumably a very similar vantage point to the iconic image of Fuji in Hokusai's Great Wave of Kanagawa.

Coach to Kamakura (30 minutes) leaves at 13:30. Guided tour of Kotoku temple (Great Buddha), Hase temple, and Tsurugaoka Hachiman shrine. Coach to restaurant (Japanese style) arrives at 18:00. Banquet. Coach to Shonan (30 minutes) arrives at 20:30.

Oliver Ray
University of Bristol, United Kingdom
Katsumi Inoue
National Institute of Informatics, Japan
Katsuhisa Horimoto
Institute of Advanced Industrial Science and Technology, Japan
  • Takehide Soh, Graduate University for Advanced Studies
  • Junji Oshima, National Institute of Informatics
  • Ayako Sumi, National Institute of Informatics

  • Andrei Doncescu, CNRS
  • Andrew Phillips, Microsoft Research
  • Anne Poupon, CNRS
  • Antonis Kakas, University of Cyprus
  • Carolyn Talcott, SRI International
  • Celine Rouveirol, University Paris 13
  • Chitta Baral, Arizona State University
  • Francois Fages, INRIA Paris-Rocquencourt
  • Gauvain Bourgne, National Institute of Informatics
  • Henning Christiansen, Roskilde University
  • Hiroshi Hosobe, National Institute of Informatics
  • Hiroshi Matsuno, Yamaguchi University
  • Hisao Moriya, RCIS, Okayama University
  • Katsuhisa Horimoto, Institute of Advanced Industrial Science and Technology
  • Katsumi Inoue, National Institute of Informatics
  • Koji Iwanuma, University of Yamanashi
  • Marcus Tindall, University of Reading
  • Mark Craven, University of Wisconsin
  • Oliver Ray, University of Bristol
  • Randy Goebel, University of Alberta
  • Ross King, Aberystwyth University
  • Sriram Iyengar, University of Texas
  • Stephen Muggleton, Imperial College London
  • Taisuke Sato, Tokyo Institute of Technology
  • Takehide Soh, Graduate University for Advanced Studies
  • Takeyuki Tamura, Kyoto University
  • Tatsuya Akutsu, Kyoto University
  • Tomoya Baba, National Institute of Genetics
  • Torsten Schaub, university of Potsdam
  • Toyoyuki Takada, National Institute of Genetics
  • Wai-Ki Ching, University of Hong Kong
  • Yoshitaka Yamamoto, Yamanashi University

img A brand new book that collects together several techniques in the area of symbolic systems biology:

Symbolic Systems Biology: Theory and Methods
M.Sriram Iyengar (Ed.)
Jones and Bartlett Learning, 2011
img A recent book that studies systems biology from a network perspective and discusses the utility of several symbolic techniques:

Biomolecular Networks: Methods and Applications in Systems Biology
L. Chen, R. Wang, X. Zhang
John Wiley and Sons, 2009
img Another recent book that includes several biological applications of symbolic methods:

Elements of Computational Systems Biology
H. Lodhi and S. Muggleton (Eds.)
John Wiley and Sons, 2009
img A recent editorial that highlights the importance of the Dagstuhl and Shonan workshops:

Where have all the workshops gone?
Moshe Y. Vardi
Communications of the ACM 54:1, 2011
img A recent conference exploring the use of algebraic/symbolic and numeric methods in Biology:

Algebraic and Numeric Biology
K. Horimoto, M. Nakatsui and N. Popov (Eds.)
Hagenberg, Austria, 2010

(c) Oliver Ray, last updated 06/04/2012