1 / 28

Biology & computing

Biology & computing. Franck Delaplace IBISC – Evry University - Genopole BERDER 2012. Synthetic Biology in a Nutshell. Multi disciplinary approach design of synthetic bio-systems Engineering principles. Design  Assembly of BIOBRICKS. Kwok -Nat. 463 Jan. 2010. Modeling.

tamra
Download Presentation

Biology & computing

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Franck Delaplace - Berder 2012 Biology & computing Franck Delaplace IBISC – Evry University - Genopole BERDER 2012

  2. Franck Delaplace - Berder 2012 Synthetic Biology in a Nutshell • Multi disciplinary approach • design of synthetic bio-systems • Engineering principles Design  Assembly of BIOBRICKS Kwok -Nat. 463 Jan. 2010

  3. Franck Delaplace - Berder 2012 Modeling Design

  4. Franck Delaplace - Berder 2012 What I cannot compute, I cannot understand … Computing = Understanding HOPE SO ! <3

  5. Franck Delaplace - Berder 2012 computation Biology Life as model of computation Bio-inspired computation Biology Computing with Life Synthetic Biology Programming Life Systems biology computation model as a model of Life

  6. Franck Delaplace - Berder 2012 Bio-inspired algorithms & models Life as model of computation

  7. Franck Delaplace - Berder 2012 Bio-Inspired algorithms • Computation Framework • For a large class of problems • Meta heuristic • For complex problems • Intractable  NP complete • IA problems (Design) • Common Features • Population, Society • Local operations • Global evaluation • Randomness

  8. Franck Delaplace - Berder 2012 Genetic algorithm - Bridge Design Darwinian Paradigm Funes, Pablo, Lapat, Louis and Pollack, Jordan B. EvoCAD: Evolution-Assisted Design. Artificial Intelligence in Design'00  Agent = Genome coding for a bridge

  9. Franck Delaplace - Berder 2012 Bio-Inspired models Turing machine = “common ancestor” • New computing model • Alternative computation medium • New computing rules • Computational power • Turing universality: Simulation of a computer (universal Turing machine) • Massive parallelism :combinatorial resolution of NP complete problems

  10. Franck Delaplace - Berder 2012 Example Membrane computing • P-System • Non determinism • Evolution strategy  maximal parallel • Application • Sorting • NP complete problem (TSP) • Verification of cryptography protocol Skin Membrane Rules Objects

  11. Franck Delaplace - Berder 2012 Systems biology computation as a model of biological processes

  12. l'une des propriétés fondamentales qui caractérisent tous les êtres vivants sans exception : celle d'être des objets doués d'un projet qu'à la fois ils représentent dans leurs structures et accomplissent par leurs performances . [..] Il est indispensable de la reconnaître comme essentielle à la définition même des êtres vivants. [..] que nous appellerons la téléonomie Franck Delaplace - Berder 2012 computation-inspired framework « De toute évidence, la cohérence fonctionnelle d'une machine chimique aussi complexe, et en outre autonome, exige l'intervention d'un système cybernétique gouvernant et contrôlant l'activité chimique en de nombreux points. » (p. 59) • “Cybernétiquemoléculaire” • Circuit / Network explanatory framework of biological process • Logical Network (R.Thomas)

  13. Franck Delaplace - Berder 2012 Formal models • Discrete dynamics • State based • Formal property analysis • Safety • Reachability / invariance • Explanatory framework • Formalization of Biological process • Phenotype = molecular signature  equilibria Transition State State

  14. Franck Delaplace - Berder 2012 Example - Automata based model a b c 101 111 a b 001 011 100 110 c a = NOT c b = a c = NOT b 000 010 Specification Dynamics

  15. Franck Delaplace - Berder 2012 Synthetic biology Programming/designing living organism

  16. Franck Delaplace - Berder 2012 Design-manufacturing  compilation main(){ Printf (“Hello World”); } Program Compilation Execution Computer SB function Synthesis Synthetic Biology

  17. Franck Delaplace - Berder 2012 CAD Environment (ideal) Overview High level Program Low level Program Sequence Interface Translator/ Compiler Validation/ Optimization Synthesis Parts Dedicated Specification Genetic Engineering Database Dynamics Analysis Safety Security Checking Simulator Trace Report Integrated view from the current states of art

  18. Franck Delaplace - Berder 2012 Compilation principles in a nutshell MEMORY + LDC 3, R5 ADD R5,R6,R7 LDC 4,R2 LD &K, R1 / III LD V,Rx ST V,Ry LDC 3, R5 DIV R4,R3,R6 MUL R2,R1,R4 REGISTER LD R3, &J J * LD R3, &J MUL R2,R1,R4 ADD R5,R6,R7 UAL IV K LDC 4,R2 LD &K, R1 OP R1,R2,R3

  19. Franck Delaplace - Berder 2012 Languages for SB  Structural description (GEC [Pedersen,Plotkin]) r0040:prom;b0034:rbs;c0040:prc;X:ter • Program =sequence description • Usual in language & CAD Env. • Genocad, GEC, Kera • Clotho, Eugène, Tinker Cell, … • Grammar rules = guide of design • Structural description • Low level (DNA sequence) R0040 c0040 b0034 X (Genocad[Peccoud] ) GENE CODING SEQ PROM START RBS PROT STOP

  20. Franck Delaplace - Berder 2012 Structural vs. behavioral description Hardware Description Language Verilog - VHDL • Structure • component assembly description • Low level of description • Back end • Behavior/function • Process design • Functional  safety • High level of description • Specification/document Generate Oil Y when X X Y r0040:prom;b0034:rbs;.. ATG|AAA|TTG|… Toy example

  21. Franck Delaplace - Berder 2012 Compilation  Part assembly = behavior assembly • Component description = behavior description • Bio system design = behavior description • The program describes the expected “function” • The issue is to define a compilation method assembling parts such that the behavior of the assembly is “similar” to the behavior of the designed function. • Problem - Reliability  guaranty on the assembly • i.e. formal guaranty that each step is correct w.r.t. to the behavioral “similarity”. Correct translation (compilation) ? Prom X Y b0034 b0015 X Y Program Assembly

  22. Franck Delaplace - Berder 2012 Behavior compilation for SB - 2 possible ways Dessinemoi un canard ! State = Situation Axioms Behavior of components Event-driven transition Proof Theorem Behavior ofthe function State = Situation

  23. Franck Delaplace - Berder 2012 Model & theory in logic Is a formula true ? Model Theory Completeness Correction Interpretation Deduction system ()

  24. Franck Delaplace - Berder 2012 Correction of the assembly Correction of assembly = observational behavior inclusion Compilation = Proof  find a behavior assembly s.t. the behavior of the designed function is included Part A Part B + AATGCGTTTATAGCCCCATGG.. AATTGGAAGCC

  25. Franck Delaplace - Berder 2012 Remarks • Functional/behavioral programming • 1 function  n structures – e.g. inhibition - • Document function  Safety analysis capability • Proof framework • Safe design  formal method + safety analysis • Functional/qualitative description  Specification, resolution principles • Quantitative description  Strategy of the resolution, tuning • Hierarchy of the components Organization for organisms • Functionality • Inter-operability • GUBS project - Adrien Basso Blandin – Franck Delaplace • Behavioral language • Compiler

  26. Franck Delaplace - Berder 2012 Synbiotic : Tower of languages GUBS Nature 434: Basu S & al.

  27. Franck Delaplace - Berder 2012 Conclusion Life as model of computation Bio-inspired • Function • Process computation Biology Computing with Life Synthetic Biology Programming Life Behavioral Language for synthetic biology Systems biology computation model as a model of Life

  28. Franck Delaplace - Berder 2012 l Thank you !

More Related