User:Vincent Rouilly



Vincent Rouilly's Profile


 * Research interests:
 * Synthetic Biology: Part Characterisation and Standardisation
 * Computational Biology: Stochastic Gene Expression, Rational Nucleic Acid Probe design.
 * Laboratory Automation and High Content Screening Analysis

Education and Past Work Experiences

 * Research Associate, Institute of Systems and Synthetic Biology, Imperial College London
 * PhD,Department of Bioengineering, Imperial College London.
 * GE Medical Systems, Paris, Software R&D Engineer.
 * Visiospace, Paris, Software R&D Engineer.
 * M.Sc, ENST Paris and ERASMUS exchange at ETSIT Madrid (Signal and Image Processing Major).

Affiliations

 * SynBioStandard Network (member)
 * IET Systems and Synthetic Biology Network (executive member)
 * OpenWetWare (steering committee member)
 * BioBrick Foundation (member)
 * BioSysBio (program committee)
 * Royal Society of Chemistry (member)

Synthetic Biology in the making
(or how to keep track of what is happening in the Synthetic Biology community)


 * TATAvox Blog: link
 * Tweeter Feed on SynBioNews : link
 * Facebook group on synthetic biology: link
 * SynBio Blog Aggregator:RSS Feed, Email Subscription
 * CiteULike SynBio Literature:RSS Feed, Email Subscription.

Research Interests

 * Computational Biology: stochastic processes, Generalized Petri Nets, Agent Based modelling, Design of Experiments.
 * Contributing to build a Synthetic Biology framework (establishing standards, design for modularity and re-usability, parts characterization) + societal impact of Synthetic Biology.
 * Laboratory Information System.
 * Laboratory Automation

My Open Source Hardware/Software Projects to support Synthetic Biology

 * Open Fluorometer
 * Open Colony Counter
 * Open Spectrophotomoter
 * XYZ Table Project from Contraptor DIY Plotter Kit.
 * DAS server on Google App Engine for DNA parts

Current Projects

 * Recombineering for Synthetic Biology
 * Homology recombination-based promoter screening construct.
 * Homology recombination-based rolling device integration.
 * Droplet-based Microfluidics for Synthetic Biology
 * Open Source Hardware for Synthetic Biology
 * Arduino-based Peltier controller
 * Colony counting / picking system

Online shared resources

 * my Connotea bookmark
 * my delicious bookmark

Teaching Experience

 * Synthetic Biology Course (Fall 2009, MRes): Lecturer @ Imperial College
 * Synthetic Biology Course (Fall 2008, MRes): Lecturer @ Imperial College
 * Synthetic Biology Course (Spring 2008): Lecturer @ Imperial College
 * Synthetic Biology Computer Modelling Practicals (Spring 2008): Lecturer @ Imperial College.
 * iGEM instructor:
 * iGEM 2006: "Engineering a Molecular Predation Oscillator", 1st Runner-Up, Best Documentation, Best Characterisation.
 * iGEM 2007: "Cell-Free Infection Detector", Gold Medal.
 * iGEM 2008: "BioFabricator".
 * Co-Supervisor master project (summer 2007): "Sensitivity analysis applied to genetic circuit induction protocols".
 * Co-Supervisor UROP project (summer 2007): "Building modular biobricks models implemented with CellML"

OWW Contributions

 * Data_Exchange_Standards_For_Synthetic_Biology
 * Computational Biology with R
 * SynBio Community Pointers
 * Open Spectrophotometer Project
 * Steering committee member and outreach co-chair.
 * minicells
 * Digital Microfluidics
 * Open_Source_Standard_Biological_Part_Registry
 * Minimum_Information_for_Biological_and_Biomedical_Investigations
 * Cell-Free Systems
 * Hands on BioBrick Activity for a science fair
 * Lab Automation Review
 * Computational Biology
 * Stochastic Gene Expression
 * Registry of Standard Models
 * Registry of Standard Models/Architecture
 * Catalog of standard models in CellML
 * Basic Components in CellML
 * iGEM@imperial project framework
 * iGEM@imperial Instructor
 * iGEM@imperial template to document a part
 * IGEM WetLab Planning Tool
 * OWW Image Annotation Tool

Other:
 * IGEM:IMPERIAL/2006/Created_Pages

Interesting links found on OWW

 * Who Is Online ?
 * F2620 Part Characterization (Labno/Canton)
 * GFP calibration and measurements
 * Titratable control of pBAD and lac promoters

Useful Open Source Softwares

 * Inkscape: SVG editor
 * FreeMind: Mind map editor
 * GanttProject: Gantt chart editor.
 * OpenProj: Project management software. Equivalent to Microsoft project.
 * OSALT site lists Open Source softwares with their commercial equivalents.

Cool Open Source Hardware Projects

 * Arduino, microcontroller.
 * Contraptor, DIY cartesian robot (XY plotter, CNC router).
 * RepRap, 3D printer.
 * BugLabs, modular linux computer.
 * OpenMoko, mobile phone.
 * OpenServo, servo motor.
 * Linksys WRT54GL, router.

Recommended Books

 * 'An Introduction to Systems Biology', Uri Alon
 * 'System Modeling in Cellular Biology: From Concepts to Nuts and Bolts', Szallasi, Stelling and Periwal
 * 'Stochastic Modelling for Systems Biology', D. Wilkinson
 * 'Design And Analysis of Experiments', D.C. Montgomery
 * 'Sensitivity Analysis', A. Saltelli
 * Calculations for Molecular Biology and Biotechnology, FH Stephenson
 * Fundamentals of Enzyme Kinetics, Cornish-Bowden (2004)

General

 * Dr. Shawn's Molecular Biology Science Fair Projects
 * BioHackery
 * experimental DIY

DNA manipulation

 * THE MACGYVER PROJECT: GENOMIC DNA EXTRACTION AND GEL ELECTROPHORESIS EXPERIMENTS USING EVERYDAY MATERIALS
 * MAKE zine
 * WIRED: DNA Sequence Kit
 * DIY PCR cycler (New Scientist)
 * A Programmable $25 Thermal Cycler for PCR
 * DIY A Pocket-Sized Convective PCR Thermocycler
 * DIY DNA extraction
 * Do it yourself magnetic stirrers
 * Egg Incubator
 * Disposable pipettes

Measuremements and Characterization

 * DIY lab scanner (New Scientist)
 * DIY microarrays
 * An Inexpensive LED-Based Fluorometer Used to Study a Hairpin-Based DNA Machines, Hanwen Yan
 * Improvements in LED-based fluorescence analysis systems
 * Enhanced fluorescence emission using a programmable
 * Prizmatix
 * Do-it-yourself microelectrophoresis chips with integrated sample recovery
 * On-line measurement of green fluorescent protein (GFP) fluorescence for the monitoring of recombinant adenovirus production
 * Low-cost microbioreactor for high-throughput bioprocessing
 * LED GFP sensor
 * On-line LED GFP sensor
 * LED-based Cheaposcope from Haseloff's lab
 * PC controlled digital camera
 * Cheap DIY USB Digital Microscope

Data Acquisition, Control and Lab Automation

 * Java Distributed Data Acquisition and Control
 * EPICS Open Source project
 * Lego Mindstorm
 * Liberlab: Open Source Scientific Experimentation Kit
 * Arduino project, Make article on Arduino
 * Gainer: Another Open-Source microcontroller platform
 * Make: Open Source Hardware Projects
 * TinCanTools: embedded ARM boards for engineers, programmers, and enthusiasts
 * Phidgets: Sensing/Control building blocks from your PC

building a stronger community

 * get people to define on their User page their area(s) of interest using 'wiki-categories' (could help to find collaborators).
 * if people defines their area of interest using references, would be interesting to use that information to match people's profiles.

support to find relevant info

 * 'contextual' browsing ('hacking' google-ads-type-of-service to show other relevant wiki-pages or wiki-users on the side of a wiki page ... instead of ads).
 * set essential keywords pages. 'Experts', in a given field, would recommend a set of keywords to help new comers to google more efficiently.
 * setting-up a calendar with info about conferences, workshops, submission deadlines ...

adding features

 * implementing java applets which are enable to read/write an xml-like format into the wiki:
 * image annotation (microscope images, gel analysis, colonies plate ..) see iNote, SVG.
 * graph editor/viewer to build/view/run kinetic models (SBML, CellML ...)

Project
Here is an overview of the modelling framework I am working on:

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