1. Symbolic Systems Biology: a Roadmap (or, lessons from ISSSB’11) Oliver Ray 1 Marcus Tindall 2 1 University of Bristol, UK 2 University of Reading, UK LDSSB’12, Bristol, UK 24 th September 2012

2. Motivation “conceptual and technological tools developed within computer science are, for the first time, starting to have wide-ranging applications outside the subject in which they originated.”... “computer science is poised to become as fundamental to science, and in particular the natural sciences, as mathematics has become to science, and in particular the physical sciences.” The 2020 Science Group S. Emmott et al. (eds.) Towards 2020 Science Microsoft Corp, 2006 (p.8)

3. Focus  Symbolic  Systems  Biology

4. Focus  Symbolic  formal methods: software and hardware development  Systems  holistic thinking: interacting parts, emergent behaviour  Biology  aims to increase our understanding of living systems

5. Distinction  Symbolic Systems Biology  Computational Systems Biology

6. Distinction  Symbolic Systems Biology  formal methods + systems biology  systems modelling and analysis  Computational Systems Biology  numerical methods + systems biology  data pre-processing + visualisation

7. Relevance  Phenomena of life as information processing  amenable to methods for studying algorithms  Phenomena of life at multiple levels of abstraction  amenable to methods for hard/software develop.  Scientific inference as abduction/deduction/induction  amenable to methods from formal logic  multi-semantic / meta-logical reasoning !  Logic as “Glue”  observations, hypotheses, background knowledge  alternative viewpoints, testable assertions

8. (Rather Sketchy) History  2003Lincoln coins the term (RTA’03)  2004Lincoln and Tiwari write first paper (HSCC’04) Idekar et al. hold first session (PSB’04)  2005Anai and Horimoto hold first conference (AB’05)  20062020 Science Group  2007(AB’07)  2008first summer school (FSM’08) (AB’08)  2009first Dagstuhl seminar (formal methods in mol. bio.)  2010(ANB’10) first book (M.S. Iyengar ed.)  2011first international symposium (ISSSB’11)

9. Methods Book rewrite logics (Pathway Logic) probabilistic model checking} (PRISM) graphical models (Petri-nets) State-charts (GemCell) process calculi (SPiM) Symposium text processing (Baral); answer set programming} (Schaub CLASP, Ray XHAIL) temporal logic (Fages BIOCHAM Itemset mining (Rouveirol HANCIM) Induction (Doncescu SOLAR, Muggleton PROGOL) Boolean Networks (Akutsu) Integer programming (Craven) Abduction (Inoue) Consequence Finding (Bourgne SOLAR) Other qualitative reasoning, equation discovery,... action languages, statistical relational learning,...

10. Applications ? Network Inferencesimulation/completion/revision metabolic signalling genetic food webs ??? Multi-scale modelling ??? Parameter estimation equation discovery stochastic logic programs ??? Model reduction ??? Automated Science Robot Scientist

11. Applications ? Network Inferencesimulation/completion/revision metabolic signalling genetic food webs ??? Multi-scale modelling ??? Parameter estimation equation discovery stochastic logic programs ??? Model reduction ??? Automated Science Robot Scientist Reincarnation?

12. Discussion