The People Xiaomo Xiaomo Y Yao ao Freshman Wei P ei Pan an Yuw uwei ei Cui Cui Geophysics 1 st Master Junior Biomedical Designer of the GUI part from Engineering Condensed an awesome ‘ab‐ini.o’ design Ma6er Physics Overall construc.on and director of the project, wiki Core algorithm – PSO, SA and writer, our captain all related Iden.fica.on Bo Ding Bo Ding Ph.D Candidate Jiahao Jiahao Li Li Computa@onal Sophermore Yu He u He Biology Electronic Junior Engineering Core algorithm – GA Condensed Instruc.ons on biological Ma6er Physics All about SBML and the related technical issues I/O issues Raw construc.on of database, I/O issues, logo and wiki‐pages
USTC _ S oftware P resents
US USTC_Sof C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China At the sunny beach…… Prof X: Hey, Doc. I don’t want do experiment. Can you give me some ideas? Dr Ding: I’m here, Professor. �
US USTC_Sof C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China Dr Ding: What do you want, professor? Prof X: I want ……
USTC_Sof US C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China Dr Ding: What do you have in your lab, professor? Prof X: I have all BioBricks in partsregistry. Dr Ding: Do you have any special restric.ons? Prof X: I have……
US USTC_Sof C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China Our soTware is running at full speed: Topologies…… Parameters…… BioBricks……
USTC_Sof US C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China AGer the vaca@on…… Prof X: Hey, Dr. Ding. Dr Ding: Nice to meet you. Here is your solu.on. Prof X: Only one solu.on? Dr Ding: No, several to choose.
US USTC_Sof C_Softw twar are, Univ , Univer ersity of Science and T sity of Science and Tec echnology of China hnology of China In Prof. X’s lab…… Prof X: Wow, it works. � Dr Ding: Do you have any dissa.sfac.on?
Why ABCD? Confronted with dazzling Biobricks, ABCD helps you What has Sir Isaac Newton get down to focus brought to modern physics? QUANTIFICATION. Get a control! Dynamics can help make predic@on, device manipula@on and real‐ life applica@on. Last pic from 中国会计网
1. Simula@on and Iden@fica@on – an alterna@ve approach to DEFINE parameters
Runge‐ Ku6a Original ODE Raw Desired Model Array Behavior Behavior G eneral P erformance A verage PSO/SA Gene@c Algorithm Op@mized Parameters Experimental Op@mized Scheme Topology Database LSA Robustness Quan@fica@on Analysis And GSA New Standard
Prerequisite, Standard and Flow Chart 2. Prototype of two intertwined databases Reac@on Substance
Graphical User Interface Source code, soGware and demo available at: h6p://ustcabcd.sourceforge.net For further interests, see our wiki: h6p://2009.igem.org/Team:USTC_SoGware
Demo decompose and dilute BBa_K176026
Demo Parameters BBa_F2620 Iden@fied: K 3 3 = 0.8 rA1 rA1 = 0.001 rmG rmG = 0.0144 a a = 0.108 pG = 24 pG d = 0.00847 C 1 = 1.5*10 -10 C 2 = 10 10 C 3 = 8*10 -7 C 4 = 5.8*10 11 Barry Canton et al. Nature Biotechnology 26, 787 ‐ 793 (2008)
Application – Bistable Toggle Switch SA works for parameter iden.fica.on successfully! Realize iden.fica.on for nonlinear systems with MIMO. Timothy S.Gardner. Ph. D Thesis (2000) �
Application – Tunable Oscillator Target: Tunable Amplitude! Realiza@on of Par@al Design! What about frequency? Method: Par@cle Swarm Op@miza@on � Michael B. Elowitz & Stanislas Leibler Nature 403, 335‐338 (2000) �
Application – Tunable Oscillator Tunable Frequency ! Michael B. Elowitz & Stanislas Leibler Nature 403, 335‐338 (2000) �
Application – Adaptation Nega@ve Incoherent Target: Feedback Feed Forward Realiza.on of ab‐ini@o Design ! Iden.fica.on of both Topology & Parameters! Global Sensi@vity Topology Feed Back Feed Forward Method: Two days and two nights calcula.on …… � Gene.c Algorithm & PSO Wenzhe Ma, et al. Cell, 138, 760‐773 (2009) �
Summary In our project, we successfully achieve: Parameter Iden@fica@on for Specific Topology （ PSO/ SA) Topology Iden@fica@on & ab‐ini@o Design for Black Box (GA) New Standard for Quan@ta@ve Characteriza@on of Biobricks Friendly Graphic User Interface �
Future Plan - Algorithms • Fourier transforma@on • Logarithmic space (wavelet) • Parallel compu@ng Evolu@on Linear Regime Exponen@al Regime Subs Subs Variables X i Variables X i = exp( Y i ) Target behavior Experimental behavior X i : Lnx min to Ln x max Y i : Lnx min to Ln x max Score Func@on Variables Y i Func@on/ODE Array F i (exp Y i ) = F i (X i ) F i (X i ), F ix (X i ) = dF i (X i )/dX i dF i (X i )/dY i = e yi F ix (y i ) T T Fourier Fourier Trans. Trans. Sampling Step Sampling Step L x L y = Ln L x Subs Subs Experimental behavior Target behavior Score Calcula@on Func@on Variables X i Variables X i = exp( Y i ) Frequency Frequency X i : Lnx min to Ln x max Y i : Lnx min to Ln x max Evolu@on move the score func.on into frequency move all sampling and ini.aliza.on space aTer Fourier Transforma.on � in logarithmic space �
Future Plan – Miscellaneous • Restric@on input standard & concision • Output SBML, SBGN, SBW easy‐drag interface � • Database data requirement output of .me course plot �
Acknowledgements We thank Prof. Lingchong You, Duke and Prof. Pablo Iglesias, JHU for illumina@ve discussions! We specially thank our wet team for incarna@on of our Danqian Liu, we owe you DRYasdust idea twenty seven cups of tasty milk tea Also we’d like to express gra@tude to our sponsors – USTC Teaching Affair Office, USTC Foreign Affair Office, USTC School of Life Sciences, USTC School for the GiGed Young, USTC School of Informa@on Sciences and Technology
In Memory of Our Great Masters � Tsien Hsue‐shen ( 钱学森 ) Bei Shi‐zhang ( 贝时璋 ) 1911.12.11‐2009.10.31 � 1903.10.10‐2009.10.29 �
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