1 I. BaSysBio European project 1. Research themes 2. Partners II. - - PowerPoint PPT Presentation

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1 I. BaSysBio European project 1. Research themes 2. Partners II. - - PowerPoint PPT Presentation

Jun 29, 2023 225 likes •495 views

1 I. BaSysBio European project 1. Research themes 2. Partners II. Live Cell Array 1. Data recovery 2. Curves processing III. Interface 1. Tool structure 2. Demo IV. Perspectives 2 3 Towards an understanding of dynamic transcriptional

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  • I. BaSysBio European project
  • 1. Research themes
  • 2. Partners
  • II. Live Cell Array
  • 1. Data recovery
  • 2. Curves processing
  • III. Interface
  • 1. Tool structure
  • 2. Demo
  • IV. Perspectives

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  • Objective: Understand genetic regulations in bacteria across the cell:
  • linkages between genetic and metabolic networks.
  • responses of bacteria in terms of pathogenicity.
  • 15 European partners including modelers and biologists.
  • Data production at all levels of the cell: transcriptome, proteome,

Fluxome, metabolome, live cell arrays, Chip-Chip, prot-prot interactions, etc.

  • Models and tools developments to understand and integrate biological

complexity.

  • MIG (Mathématique, Informatique et Génome):

1. Genome structural annotation (A. Leduc, P . Nicolas, P . Bessières). 2. Formalization and analysis of biological systems (A. Goelzer, V. Fromion). 3. Data processing/analysis (L. Aïchaoui, V. Fromion).

Towards an understanding of dynamic transcriptional regulation at global scale in bacteria: a systems biology approach

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Tony Wilkinson Mark Fogg Rachel Adamson Jan Maarten van Dijl Emma Denham Sjouke Piersma Gröningen - Netherlands Kevin Devine Eric Botella Annette Hansen Sebastian Hübner Dublin - Ireland Philippe Bessières Pierre Nicolas Aurélie Leduc Vincent Fromion Anne Goelzer Leslie Aichaoui Jouy-en-Josas (MIG)- France Stephane Aymerich Matthieu Jules Ludovic Le Chat Dominique Le Coq Grignon - France York - England LCA Technology Data treatments

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Development of a new technology for B. subtilis, the LCA High-throughput : Real-time monitoring of promoter activities in living cells

96-well plate Promoter GFP mut3 spec R ColE1 Promoter gene X RBS* RBS High-thoughput reading Library of Px-gfp strains Data storage and analysis

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OD GFP

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  • A useR!-friendly interface to entering data

into the database

  • A database to store data from LCA
  • A useR!-friendly interface to process data

and retrieve results and graphs

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  • LCA Objectives:
  • High-throughput
  • Real-time monitoring of promoter activities in living cells
  • Organizing regulations in a temporal hierarchy
  • In order to test perturbations on a coherent subset of fusions:
  • Mutants
  • Growth conditions

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Ak

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k k k

Bu x A x  

  1

ˆ ˆ

Q A AP P

T k k

 

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(1) Project the state ahead (2) Project the error covariance ahead

1

) (

  

  R H HP H P K

T k T k k

) ˆ ( ˆ ˆ

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k K k k k

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(1) Compute the Kalman gain (2) Update estimate with measurement zk

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k k k

P H K I P ) (

(3) Update the error covariance

Time Update (“Predict”) Measurement Update (“Correct”)

Initial estimates for and

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k

x

1  k

P

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RMySQL Database Statistical processing Interface

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system("C:/.../R/R-2.10.0/bin/Rcmd" BATCH C:/.../.../script.R)

R call in PHP

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library(RMySQL) m=dbDriver("MySQL") chaCurv=dbConnect(m,dbname=dsnc,user=uidc,password=pwdc) reqbg=paste("SELECT well_pk FROM well WHERE backgd='yes' AND platew_pk='",nplate,"'",sep="") wbg=dbGetQuery(chaCurv,reqbg) dbDisconnect(chaCurv) Connexion to MySQL database

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Very smoothed Less smoothed

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  • Development of an installer
  • Automatic classification of promoter activity curves
  • Tool distribution to the LCA community
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  • The BaSysBio Consortium
  • Vincent Fromion and Anne Goelzer for their assistance
  • Matthieu Jules and Ludovic Le Chat for their help in

biology

  • Hugo Devillers for his advices in R
  • Thibault De Maillard for his help in javascript
  • Pascal Neveu and Anne Tireau for their help on the first

version of the interface

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  • Zaslaver A, Mayo AE, Rosenberg R, Bashkin P

, Sberro H, Tsalyuk M, Surette MG, Alon U. (2004). Just-in-time transcription program in metabolic

  • pathways. Nat Genet. 36, 486-91.
  • G. Welch and G. Bishop An Introduction to the Kalman Filter, University of

North Carolina at Chapel Hill, Department of Computer Science

  • David A. James and Saikat DebRoy (2009). RMySQL: R interface to the

MySQL database, http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL.

  • Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W,

Surette MG, Alon U. (2006), A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods. 3, 623-8.

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http://ciam.inra.fr/r4ciam/

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