BioBricks Model Generator for electronic simulator How to generate - - PowerPoint PPT Presentation

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BioBricks Model Generator for electronic simulator How to generate - - PowerPoint PPT Presentation

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Biobricks model generator for electronics simulator Vincent Wlotzko Martin Andraud BioBricks Model Generator for electronic simulator How to generate Biobrick models understandable by conventional electronic simulators Biobricks model

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Biobricks model generator for electronics simulator

BioBricks’ Model Generator for electronic simulator

How to generate Biobrick models understandable by conventional electronic simulators

Martin Andraud Vincent Wlotzko

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Biobricks model generator for electronics simulator Biobricks’ model generator usable by a electronic simulator

Overview

  • I. Introduction

Team presentation

Project introduction

  • II. Background

Context Project overview This year

  • III. Software

Principle How it works

  • IV. Demonstration
  • V. Future
  • VI. Acknowledgements

11/6/2011 2/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator Biobricks model generator for electronics simulator

Team Presentation

Students:

Andraud Martin Vincent Wlotzko

Advisor:

J.Haiech Yves Gendrault Christophe Lallement Morgan Madec

Instructors:

  • I. Introduction

Our team Project

  • II. Background
  • III. Models
  • IV. Software
  • V. Demo
  • VI. Future
  • VI. Thank you

11/6/2011 3/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator Biobricks model generator for electronics simulator

Introduction

  • There is no Automated Design Tool yet

in biology

  • This type of tool could be helpfull for

biologists because:

– More and more complex systems = more and more difficult to design – Building a system is time and money consuming

This type of tool already exists in electronics

  • I. Introduction

Our team Project

  • II. Background
  • III. Models
  • IV. Software
  • V. Demo
  • VI. Future
  • VI. Thank you

11/6/2011 4/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator Biobricks model generator for electronics simulator

Context

  • Electronics:

– For over 40 years, strong experience in building more and more complex systems

First microprocessor Intel 4004 (1971) 2300 transistors Nowadays processor Intel Xeon (2010) 2 billion transistors

Improvements of the design flow and the technology, creation of automated and reliable tools to help designers to build extremely complex systems

  • I. Introduction
  • II. Background

Context Elec VS Bio Our goals Global project This year

  • III. Software
  • IV. Demo
  • V. Future
  • VI. Thank you

11/6/2011 5/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator Biobricks model generator for electronics simulator

  • Two analogies are possible between

electronics and biology

Electronics VS Biology

Biobrick Part Device BioSystem Transistor Gate Processor

Biology Electronics

  • Level 1: Design approach
  • Level 2: Electronic and Biologic mechanisms can be

modeled by ODE (Ordinary Differential Equations)

  • I. Introduction
  • II. Background

Context Elec VS Bio Our goals Global project This year

  • III. Software
  • IV. Demo
  • V. Future
  • VI. Thank you

11/6/2011 6/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator Biobricks model generator for electronics simulator

Our project - aims

  • Adapting the powerfulness of electronic

tools for biologists in creating a complete automation design tool

  • I. Introduction
  • II. Background

Context Elec VS Bio Our Goals Global project This year

  • III. Software
  • IV. Demo
  • V. Future
  • VI. Thank you

Source : http://blog.mckuhn.de

11/6/2011 7/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator

Idea

Designing your best biosystem’s diagram Finding the best BioBricks Simulate your best Biosystem

Our project

Biosystem’s function & requirements System’s specifications

Increase the level of abstraction

  • of
  • I. Introduction
  • II. Background

Context Elec VS Bio Our Goals Global project This year

  • III. Software
  • IV. Demo
  • V. Future
  • VI. Thank you

11/6/2011 8/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator

Idea

Designing your best biosystem’s diagram Finding the best BioBricks Simulate your best Biosystem

Our project

Biosystem’s function & requirements System’s specifications

One function = several biobricks You have to find the most suitable BioBrick assembly for your application

  • of
  • I. Introduction
  • II. Background

Context Elec VS Bio Our Goals Global project This year

  • III. Software
  • IV. Demo
  • V. Future
  • VI. Thank you

11/6/2011 9/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator

Idea

Designing your best biosystem’s diagram Finding the best BioBricks Simulate your best Biosystem

Our project

Biosystem’s function & requirements System’s specifications

To validate the proof

  • f concept of your

system, you need a qualitative and a quantitative simulation Powerfull electronic tools can help you

  • I. Introduction
  • II. Background

Context Elec VS Bio Our Goals Global project This year

  • III. Software
  • IV. Demo
  • V. Future
  • VI. Thank you

11/6/2011 10/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator

Biosystem’s function & requirements System’s specifications

Idea

BioBrick parts registry BioBrick Assembly BioBricks Compiler ‘0’-or-’1’ Behavioral Model Simulation Results (Qualitative) Behavioral Simulator Conservative Model Simulation Results (Quantitative) Continuous – time simulator Model Synthetizer BIOLOGY ELECTRONICS

Validation Proof of concept

DESIGNER BIOBRICK FINDER SIMULATOR

Block diagram of elementary function Automatic Synthesizer System Analyzer

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Biobricks model generator for electronics simulator

Biosystem’s function & requirements System’s specifications

Idea

BioBrick parts registry BioBrick Assembly BioBricks Compiler ‘0’-or-’1’ Behavioral Model Simulation Results (Qualitative) Behavioral Simulator Conservative Model Simulation Results (Quantitative) Continuous – time simulator Model Synthetizer BIOLOGY ELECTRONICS

Validation Proof of concept

DESIGNER BIOBRICK FINDER SIMULATOR

Block diagram of elementary function Automatic Synthesizer System Analyzer Biosystem’s function & requirements

DESIGNER

Block diagram of elementary function Automatic Synthesizer System Analyzer

Behavioral model

[OUT] [B] [C] [AB] [E] [A]

  • Based on boolean algebra (

logic description)

  • Written in VHDL (electronic

description language)

  • Each block is linking to each
  • ther by the names of the

species

  • Quantitative information
  • nly
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Biobricks model generator for electronics simulator

Biosystem’s function & requirements System’s specifications

Idea

BioBrick parts registry BioBrick Assembly BioBricks Compiler ‘0’-or-’1’ Behavioral Model Simulation Results (Qualitative) Behavioral Simulator Conservative Model Simulation Results (Quantitative) Continuous – time simulator Model Synthetizer BIOLOGY ELECTRONICS

Validation Proof of concept

DESIGNER BIOBRICK FINDER SIMULATOR

Block diagram of elementary function Automatic Synthesizer System Analyzer

Conservative model

  • Based on ODE and analogy SYNTH

SYNTHETIC BIO ELEC

  • Written in VHDL-AMS (electronic

description language)

  • Qualitative information

(concentrations)

     

mX d A K k dt mX d

mX n R tr

        

1

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Biobricks model generator for electronics simulator

Our first year

  • Convincing the biologist’s community

that electronics and biology can be combined to improve biosystem’s design

  • Creating a software which simulates a

biosystem as an electrical circuit

  • I. Introduction
  • II. Background

Context Elec VS Bio Our Goals Global project This year

  • III. Software
  • IV. Demo
  • V. Future
  • VI. Thank you

11/6/2011 14/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator

Graphical User Interface

‘0’-or-’1’ Behavioral Model Simulation Results (Qualitative) Behavioral Simulator Conservative Model Simulation Results (Quantitative) Continuous- time Simulator Block diagram of elementary function

Input species Output species Mechanisms

  • Inhibition
  • Association
  • Synthesis

Reactions parameters

Model Synthetizer BIOLOGY ELECTRONICS Using of an electronic description language in the automatic code generator

11/6/2011 15/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator Biobricks model generator for electronics simulator Software core written in C++ Qt framework for the Graphic User Interface

Software

Two BioSystem models’ generator with one architecture

  • I. Introduction
  • II. Background
  • III. Software

Tools

  • IV. Demo
  • V. Future
  • VI. Thank you

11/6/2011 16/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator

11/6/2011 iGEM 2011 World Jamboree ENSPS Strasbourg 17/19

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Biobricks model generator for electronics simulator Biobricks’ model generator usable by a electronic simulator

SYSTEM MECH. SPECIES Main Window Graphical User Interface Manager Engine Pattern files Syst.vhd Entities.vhd TestBench.vhd Simulation file

Software

11/6/2011 18/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator Biobricks model generator for electronics simulator

Demonstration

  • I. Introduction
  • II. Background
  • III. Software
  • IV. Demo
  • V. Future
  • VI. Thank you

Video available on our wiki

11/6/2011 19/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator

Next Version

  • I. Introduction
  • II. Background
  • III. Software
  • IV. Demo
  • V. Future

Next version Perspectives

Achievements

  • VI. Thank you

11/6/2011 20/19 iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator

What we have done yet

Perspectives

11/6/2011 21/19

  • I. Introduction
  • II. Background
  • III. Software
  • IV. Demo
  • V. Future

Next version Perspectives

Achievements

  • VI. Thank you

iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator

Achievements

Showing the usefulness of the electronics for synthetic biology Building models and analogy between the two fields Allowing the biologists to simulate their systems before creating it Suggesting an Automated Design Tool project for synthetic biology

11/6/2011 22/19

  • I. Introduction
  • II. Background
  • III. Software
  • IV. Demo
  • V. Future

Next version Perspectives

Achievements

  • VI. Thank you

iGEM 2011 World Jamboree ENSPS Strasbourg

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Biobricks model generator for electronics simulator

Acknowledgements

  • I. Introduction
  • II. Background
  • III. Software
  • IV. Demo
  • V. Future
  • VI. Thank you

11/6/2011 23/19 iGEM 2011 World Jamboree ENSPS Strasbourg