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 generator usable by a Biobricks model generator for electronics simulator electronic simulator Overview I. Introduction III. Software Team presentation Principle How it works Project introduction IV. Demonstration II. Background Context V. Future Project overview This year VI. Acknowledgements iGEM 2011 World Jamboree 11/6/2011 2/19 ENSPS Strasbourg
Biobricks model generator for Biobricks model generator for electronics simulator electronics simulator Team Presentation I. Introduction Instructors: Students: Our team Andraud Martin Christophe Lallement Project II. Background III. Models IV. Software V. Demo Yves Gendrault Morgan Madec VI. Future Vincent Wlotzko VI. Thank you Advisor: J.Haiech iGEM 2011 World Jamboree 11/6/2011 3/19 ENSPS Strasbourg
Biobricks model generator for Biobricks model generator for electronics simulator electronics simulator Introduction • There is no Automated Design Tool yet I. Introduction Our team in biology Project • This type of tool could be helpfull for II. Background III. Models biologists because: IV. Software – More and more complex systems = more V. Demo VI. Future and more difficult to design VI. Thank you – Building a system is time and money consuming This type of tool already exists in electronics iGEM 2011 World Jamboree 11/6/2011 4/19 ENSPS Strasbourg
Biobricks model generator for Biobricks model generator for electronics simulator electronics simulator Context • Electronics: I. Introduction – For over 40 years, strong experience in II. Background Context building more and more complex systems Elec VS Bio Our goals Improvements of the design flow and the Global project technology, creation of automated and reliable This year III. Software tools to help designers to build extremely complex systems IV. Demo V. Future VI. Thank you First microprocessor Nowadays processor Intel 4004 (1971) Intel Xeon (2010) 2300 transistors 2 billion transistors iGEM 2011 World Jamboree 11/6/2011 5/19 ENSPS Strasbourg
Biobricks model generator for Biobricks model generator for electronics simulator electronics simulator Electronics VS Biology • Two analogies are possible between I. Introduction electronics and biology II. Background Context - Level 1: Design approach Elec VS Bio - Level 2: Electronic and Biologic mechanisms can be Our goals modeled by ODE (Ordinary Differential Equations) Global project This year III. Software Biology Device Biobrick Part BioSystem IV. Demo V. Future VI. Thank you Electronics Transistor Gate Processor iGEM 2011 World Jamboree 11/6/2011 6/19 ENSPS Strasbourg
Biobricks model generator for Biobricks model generator for electronics simulator electronics simulator Our project - aims • Adapting the powerfulness of electronic I. Introduction tools for biologists in creating a complete II. Background automation design tool Context Source : http://blog.mckuhn.de Elec VS Bio Our Goals Global project This year III. Software IV. Demo V. Future VI. Thank you iGEM 2011 World Jamboree 11/6/2011 7/19 ENSPS Strasbourg
Biobricks model generator for electronics simulator Our project Biosystem’s function I. Introduction Increase the level of & requirements abstraction II. Background oof Context Elec VS Bio Our Goals Designing your best biosystem’s Global project diagram This year Idea Finding III. Software the best IV. Demo BioBricks Simulate V. Future your best VI. Thank you Biosystem System’s specifications iGEM 2011 World Jamboree 11/6/2011 8/19 ENSPS Strasbourg
Biobricks model generator for electronics simulator Our project Biosystem’s function I. Introduction & requirements II. Background oof Context Elec VS Bio One function = several Our Goals Designing your biobricks best biosystem’s Global project diagram You have to find the most This year Idea Finding suitable BioBrick assembly III. Software the best for your application IV. Demo BioBricks Simulate V. Future your best VI. Thank you Biosystem System’s specifications iGEM 2011 World Jamboree 11/6/2011 9/19 ENSPS Strasbourg
Biobricks model generator for electronics simulator Our project Biosystem’s function I. Introduction To validate the proof & requirements of concept of your II. Background system, you need a Context qualitative and a Elec VS Bio quantitative Our Goals simulation Designing your best biosystem’s Global project diagram This year Powerfull electronic Idea Finding III. Software tools can help you the best IV. Demo BioBricks Simulate V. Future your best VI. Thank you Biosystem System’s specifications iGEM 2011 World Jamboree 11/6/2011 10/19 ENSPS Strasbourg
Biobricks model generator for BIOBRICK electronics simulator Biosystem’s function FINDER & requirements BioBrick parts registry DESIGNER Block diagram of BioBricks System Automatic elementary Compiler Analyzer Synthesizer function BioBrick Idea Assembly Model Synthetizer Validation SIMULATOR BIOLOGY Proof of concept ELECTRONICS Behavioral Simulator Simulation Results ‘0’ -or- ’1’ (Qualitative) Behavioral Model Continuous – time Conservative simulator Simulation System’s specifications Model Results (Quantitative)
Biobricks model generator for Behavioral model BIOBRICK - Based on boolean algebra ( electronics simulator Biosystem’s function Biosystem’s function FINDER logic description) & requirements & requirements BioBrick parts registry - Written in VHDL (electronic [A ] DESIGNER DESIGNER [AB] description language) [B] [OUT] - Each block is linking to each Block diagram of Block diagram of BioBricks System System Automatic Automatic elementary elementary Compiler Analyzer Analyzer Synthesizer Synthesizer other by the names of the [E] [C] function function BioBrick species Idea Assembly - Quantitative information only Model Synthetizer Validation SIMULATOR BIOLOGY Proof of concept ELECTRONICS Behavioral Simulator Simulation Results ‘0’ -or- ’1’ (Qualitative) Behavioral Model Continuous – time Conservative simulator Simulation System’s specifications Model Results (Quantitative)
Biobricks model generator for BIOBRICK electronics simulator Biosystem’s function FINDER & requirements BioBrick parts registry DESIGNER Conservative model - Based on ODE and analogy SYNTH SYNTHETIC BIO ELEC Block diagram of BioBricks System Automatic elementary Compiler Analyzer Synthesizer function d mX k tr BioBrick d mX mX n Idea dt K Assembly R 1 A - Written in VHDL-AMS (electronic Model description language) Synthetizer Validation SIMULATOR BIOLOGY Proof of concept - Qualitative information ELECTRONICS Behavioral (concentrations) Simulator Simulation Results ‘0’ -or- ’1’ (Qualitative) Behavioral Model Continuous – time Conservative simulator Simulation System’s specifications Model Results (Quantitative)
Biobricks model generator for electronics simulator Our first year • Convincing the biologist’s community I. Introduction II. Background that electronics and biology can be Context combined to improve biosystem’s Elec VS Bio design Our Goals Global project This year III. Software • Creating a software which simulates a IV. Demo biosystem as an electrical circuit V. Future VI. Thank you iGEM 2011 World Jamboree 11/6/2011 14/19 ENSPS Strasbourg
Biobricks model generator for Graphical User Interface electronics simulator Input species Output species Mechanisms Model Block diagram of elementary - Inhibition Synthetizer - Association function - Synthesis Reactions BIOLOGY parameters ELECTRONICS Using of an Behavioral electronic Simulator Simulation Results description ‘0’ -or- ’1’ (Qualitative) Behavioral Model language in the automatic code Continuous- Simulation generator time Simulator Results Conservative (Quantitative) Model iGEM 2011 World Jamboree 11/6/2011 15/19 ENSPS Strasbourg
Biobricks model generator for Biobricks model generator for electronics simulator electronics simulator Software Software core written in C++ I. Introduction II. Background Qt framework for the Graphic User III. Software Interface Tools Two BioSystem models ’ generator with one IV. Demo architecture V. Future VI. Thank you iGEM 2011 World Jamboree 11/6/2011 16/19 ENSPS Strasbourg
Biobricks model generator for electronics simulator iGEM 2011 World Jamboree 11/6/2011 17/19 ENSPS Strasbourg
Biobricks ’ model generator usable by a Biobricks model generator for electronics simulator electronic simulator Software Graphical User Interface Engine SYSTEM Syst.vhd MECH. Entities.vhd Main Manager Window TestBench.vhd SPECIES Simulation file Pattern files iGEM 2011 World Jamboree 11/6/2011 18/19 ENSPS Strasbourg
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