The linguistic cell Sentence parsing Bacteria Team Sweden (G - PowerPoint PPT Presentation

The linguistic cell Sentence parsing Bacteria Team Sweden (G¨ oteborg) Chalmers Technical University G¨ oteborg University Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 1 / 15

Outline Table of contents Introduction 1 Project Idea Grammar Finite State Automaton Modeling 2 Design Challenges The Mathematical Model The Biological Model Plasmids Further Work 3 Generalized Model Summary 4 Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 2 / 15

Introduction Project Idea Project Idea Sentence ⇓ External input into the bacteria ⇓ The bacteria checks the order of words ւ ց Correct Incorrect Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 3 / 15

Introduction Grammar Language & Grammar Grammar S → NP VP S NP → (det) (adj) N VP → V (NP) NP VP Examples in English det adj N V NP correct The small boy walks the big dog. The small boy walks det adj N incorrect Let the boy go. the big dog. Regular Expression (det)(adj) N V ((det)(adj) N) Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 4 / 15

Introduction Finite State Automaton Finite State Automaton Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 5 / 15

Modeling Design Challenges Design Challenges & Solutions Repeated input (e.g. det det) 1 ② Counter with interval state & intermediate input a Wrong input (e.g. det adj N adj) 2 ② Specificially set inhibitions a ETH iGEM 2005 Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 6 / 15

Modeling The Mathematical Model The linguistic cell – The Theory Assumptions State I1 is active at t = 0 Every inhibition has the same strength Introduction of ”stop” signal Mathematical Model � act j , if j activates i ODE dydt i = syn i � − deg i if j inhibits i rep j , j ∈ i ( x j Θ j ) m Hill function h + ( x j , Θ j , m ) = 1+( x j Θ j ) m Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 7 / 15

Modeling The Biological Model The linguistic cell – The Model Correct Example [ ] The small boy walks. Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 8 / 15

Modeling The Biological Model The linguistic cell – The Model Correct Example The small boy walks. Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 8 / 15

Modeling The Biological Model The linguistic cell – The Model Correct Example The [ ] small boy walks. Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 8 / 15

Modeling The Biological Model The linguistic cell – The Model Correct Example The small boy walks. Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 8 / 15

Modeling The Biological Model The linguistic cell – The Model Correct Example The small [ ] boy walks. Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 8 / 15

Modeling The Biological Model The linguistic cell – The Model Correct Example The small boy walks. Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 8 / 15

Modeling The Biological Model The linguistic cell – The Model Correct Example The small boy [ ] walks. Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 8 / 15

Modeling The Biological Model The linguistic cell – The Model Correct Example The small boy walks . Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 8 / 15

Modeling The Biological Model The linguistic cell – The Model Correct Example The small boy walks[ ]. Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 8 / 15

Modeling The Biological Model The linguistic cell – The Model Correct Example The small boy walks . Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 8 / 15

Modeling The Biological Model Result – Correct sentence Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 9 / 15

Modeling The Biological Model The linguistic cell – The Model Incorrect example [ ] Let the boy go. Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 10 / 15

Modeling The Biological Model The linguistic cell – The Model Incorrect example Let the boy go. Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 10 / 15

Modeling The Biological Model Result – Incorrect sentence Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 11 / 15

Modeling Plasmids Plasmid suggestions for E.coli Input plasmids five exogenous activators (e.g. Met, Gal, zinc, copper, iron) target gene (e.g. MetR, ZntR, GalR, CusR, fnr) Internal Plasmids 10 different repressor binding sites (e.g. metJ, Nral, Hu . . . ) 10 different ways to inactivate repressors (proteolysis, Lac . . . ) Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 12 / 15

Further Work Generalized Model Generalization Input Arbitrary adjacency matrix Output Biological model Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 13 / 15

Summary Summary biological model of a FSA bacteria parses sentences novel idea 1 st example of FSA in cell one-way system discrete state system Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 14 / 15

Summary Thanks to . . . Our Supervisors Sven Nelander Missing members Per Sunnerhagen Naser Monsefi Laleh Kazemzadeh Master programs Intakhar Ahmad Bioinformatics & Systems Biology Tanvir Ahamed Olle Nerman Biotechnology Calle Franz´ en Team Sweden (G¨ oteborg) (G¨ oteborg) The linguistic cell 15 / 15