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

The linguistic cell

Sentence parsing Bacteria Team Sweden (G¨

• teborg)

Chalmers Technical University G¨

• teborg University

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• teborg) (G¨
• teborg)

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Outline

Table of contents

1

Introduction Project Idea Grammar Finite State Automaton

2

Modeling Design Challenges The Mathematical Model The Biological Model Plasmids

3

Further Work Generalized Model

4

Summary

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Introduction Project Idea

Project Idea

Sentence ⇓ External input into the bacteria ⇓ The bacteria checks the order of words ւ Correct ց Incorrect

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Introduction Grammar

Language & Grammar

Grammar S → NP VP NP → (det) (adj) N VP → V (NP) Examples in English correct The small boy walks the big dog. incorrect Let the boy go. Regular Expression (det)(adj) N V ((det)(adj) N) S NP det The adj small N boy VP V walks NP det the adj big N dog.

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Introduction Finite State Automaton

Finite State Automaton

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Modeling Design Challenges

Design Challenges & Solutions

1

Repeated input (e.g. det det) ② Counter with interval state & intermediate input a

2

Wrong input (e.g. det adj N adj) ② Specificially set inhibitions

aETH iGEM 2005

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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 ODE dydti = syni

• j∈i
• actj,

if j activates i repj, if j inhibits i − degi Hill function h+(xj, Θj, m) =

(xjΘj)m 1+(xjΘj)m

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Modeling The Biological Model

The linguistic cell – The Model

Correct Example [ ] The small boy walks.

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• teborg) (G¨
• teborg)

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Modeling The Biological Model

The linguistic cell – The Model

Correct Example The small boy walks.

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• teborg) (G¨
• teborg)

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Modeling The Biological Model

The linguistic cell – The Model

Correct Example The [ ] small boy walks.

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• teborg) (G¨
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Modeling The Biological Model

The linguistic cell – The Model

Correct Example The small boy walks.

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• teborg) (G¨
• teborg)

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Modeling The Biological Model

The linguistic cell – The Model

Correct Example The small [ ] boy walks.

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• teborg) (G¨
• teborg)

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Modeling The Biological Model

The linguistic cell – The Model

Correct Example The small boy walks.

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• teborg) (G¨
• teborg)

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Modeling The Biological Model

The linguistic cell – The Model

Correct Example The small boy [ ] walks.

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• teborg) (G¨
• teborg)

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Modeling The Biological Model

The linguistic cell – The Model

Correct Example The small boy walks.

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• teborg) (G¨
• teborg)

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Modeling The Biological Model

The linguistic cell – The Model

Correct Example The small boy walks[ ].

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• teborg) (G¨
• teborg)

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Modeling The Biological Model

The linguistic cell – The Model

Correct Example The small boy walks.

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• teborg)

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Modeling The Biological Model

Result – Correct sentence

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• teborg)

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Modeling The Biological Model

The linguistic cell – The Model

Incorrect example [ ] Let the boy go.

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Modeling The Biological Model

The linguistic cell – The Model

Incorrect example Let the boy go.

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• teborg)

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Modeling The Biological Model

Result – Incorrect sentence

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• teborg) (G¨
• teborg)

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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 . . . )

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Further Work Generalized Model

Generalization

Input Arbitrary adjacency matrix Output Biological model

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• teborg) (G¨
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Summary

Summary

biological model of a FSA bacteria parses sentences novel idea 1st example of FSA in cell

• ne-way system

discrete state system

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• teborg) (G¨
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Summary

Thanks to . . .

Our Supervisors Sven Nelander Per Sunnerhagen Master programs Bioinformatics & Systems Biology Olle Nerman Biotechnology Calle Franz´ en Missing members Naser Monsefi Laleh Kazemzadeh Intakhar Ahmad Tanvir Ahamed

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