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<center><font face="trebuchet ms" style="color:#FFFFFF" size="5">'''Vincent Rouilly's Profile'''</font><br>
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<font size="4">Vincent Rouilly</font size>
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<font size="2">Department of Bioengineering<br>
<font size="2">
Imperial College London<br>
email: vincent.rouilly [-at-] gmail [-dot-] com
South Kensington, SW7<br>
London, UK<br>


email: vincent.rouilly (at) ic.ac.uk
Paris, France.


[http://www.linkedin.com/in/vincentrouilly join my LinkedIn Network]
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My name is Vincent, I am a Phd student at Imperial College London. I am under the supervision of Prof Kitney.
== Work Experiences ==
The research project I am involved in deals with modelling Synthetic Biology systems.
* Bioinformatician, LabEx Milieu Interieur, Institut Pasteur, Paris France (Current).
We are implementing a framework allowing to model from gene circuits to population behaviour.
* Data Analyst & Scientific Software Programmer, ResearchIT, University of Basel, Switzerland.
* Research Associate, Institute of Systems and Synthetic Biology, Imperial College London
* GE Medical Systems, Paris, Software R&D Engineer, Image Processing on digital mammography systems.
* Visiospace, Paris, Software R&D Engineer.
 
== Education ==
* PhD, Computational Biology, Department of Bioengineering, Imperial College London.
* M.Sc, ENST Paris and ERASMUS exchange at ETSIT Madrid (Signal and Image Processing Major).
 
== Affiliations ==
* [http://www.synbiostandards.co.uk/index.php SynBioStandard Network (member)]
* [http://kn.theiet.org/communities/biology/index.cfm IET Systems and Synthetic Biology Network (executive member)]
* [http://openwetware.org/ OpenWetWare (steering committee member)]
* [http://bbf.openwetware.org/ BioBrick Foundation (member)]
* [http://conferences.theiet.org/biosysbio/ BioSysBio (program committee)]
* [http://www.rsc.org/ 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''': [http://tatavox.wordpress.com link] -->
* '''Personal Tweeter Feed''' : [http://twitter.com/vrouilly link]
* '''Tweeter Feed on SynBioNews''' : [http://twitter.com/SynBioNews link]
* '''Facebook group on synthetic biology''': [http://www.facebook.com/#!/group.php?gid=2204701004&ref=mf link]
* '''SynBio Blog Aggregator''':[http://feeds.feedburner.com/WhatAboutSyntheticBiology RSS Feed], [http://www.feedburner.com/fb/a/emailverifySubmit?feedId=2712861&amp;loc=en_US Email Subscription]
* '''CiteULike SynBio Literature''':[http://feeds.feedburner.com/Synthetic_biology_literature RSS Feed], [http://www.feedburner.com/fb/a/emailverifySubmit?feedId=2717166&amp;loc=en_US Email Subscription].


== Research Interests ==
== Research Interests ==
<blockquote>
* Computational Biology: stochastic processes, Generalized Petri Nets, Agent Based modelling, Design of Experiments.
* Computational Biology: stochastic processes, Petri Nets, Agent Based modelling
* Contributing to build a Synthetic Biology framework (establishing standards, design for modularity and re-usability, parts characterization) + societal impact of Synthetic Biology.
* Synthetic Biology
* Laboratory Information System.
* Laboratory Information System
* Laboratory Automation
</blockquote>
 
== My Open Source Hardware/Software Projects to support Synthetic Biology==
* [[Citizen_Science/Open_Fluorometer_Project | Open Fluorometer]]
* [[Citizen_Science/Open_Colony_Counter_Project | Open Colony Counter]]
* [[Citizen_Science/Open_Spectrophotometer_Project | Open Spectrophotomoter]]
* [[User:Vincent Rouilly/XYZ_Table_Project | XYZ Table Project]] from [http://www.garagefab.cc/contraptor Contraptor] DIY Plotter Kit.
* [[User:Vincent Rouilly/Distributed Annotation System (DAS) for DNA Part Registries | DAS server on Google App Engine for DNA parts]]
 
==Past 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==
* [http://www.connotea.org/wiki/User:vincentrouilly my Connotea bookmark]
* [http://delicious.com/Manosquin my delicious bookmark]
* [http://tataaavox.wordpress.com/ blog]
 
==Teaching Experience ==
* [[Imperial_College/Courses/Fall2009/Synthetic_Biology_(MRes_class)| Synthetic Biology Course (Fall 2009, MRes)]]: Lecturer @ Imperial College
* [[Imperial_College/Courses/Fall2008/Synthetic_Biology_(MRes_class)| Synthetic Biology Course (Fall 2008, MRes)]]: Lecturer @ Imperial College
* [[Imperial_College/Courses/Spring2008/Synthetic Biology| Synthetic Biology Course (Spring 2008)]]: Lecturer @ Imperial College
* [[ Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals| Synthetic Biology Computer Modelling Practicals (Spring 2008)]]: Lecturer @ Imperial College.
* '''[http://www.igem.org iGEM] instructor''':
** [[IGEM:IMPERIAL/2006|iGEM 2006]]: "Engineering a Molecular Predation Oscillator", 1st Runner-Up, Best Documentation, Best Characterisation.
** [[IGEM:IMPERIAL/2007|iGEM 2007]]: "Cell-Free Infection Detector", Gold Medal.
** [[IGEM:IMPERIAL/2008|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 ==
* [[User:Vincent_Rouilly/Data_Exchange_Standards_For_Synthetic_Biology | Data_Exchange_Standards_For_Synthetic_Biology]]
* [[User:Vincent_Rouilly/Computational_Biology_With_R | Computational Biology with R]]
* [[User:Vincent_Rouilly/Synthetic_Biology_Community_Pointers | SynBio Community Pointers]]
* [[Citizen Science/Open Spectrophotometer Project | Open Spectrophotometer Project]]
* Steering committee member and outreach co-chair.
* [[Minicells | minicells]]
* [[Digital_Microfluidics | Digital Microfluidics]]
* [[User:Vincent_Rouilly/Open_Source_Standard_Biological_Part_Registry | Open_Source_Standard_Biological_Part_Registry]]
* [[Minimum_Information_for_Biological_and_Biomedical_Investigations_%28MIBBI%29 | Minimum_Information_for_Biological_and_Biomedical_Investigations]]
* [[User:Vincent Rouilly/Cell-Free Systems | Cell-Free Systems]]
* [[User:Vincent_Rouilly/Hands_On_BioBrick_Activity | Hands on BioBrick Activity for a science fair]]
* [[OpenWetWare:Equipment/Laboratory_Automation | Lab Automation Review]]
* [[Computational_Biology | Computational Biology]]
* [[Computational_Biology/Gene_Expression_modeling/Stochastic_Approach | Stochastic Gene Expression]]
* [[Registry of Standard Biological Models| Registry of Standard Models]]
* [[Registry of Standard Biological Models/General_Architecture_Discussion| Registry of Standard Models/Architecture]]
* [[Registry of Standard Biological Models/Model Catalog| Catalog of standard models in CellML]]
* [[Registry of Standard Biological Models/Basic_Component_Models| Basic Components in CellML]]
* [[IGEM:IMPERIAL/Methodology|  iGEM@imperial project framework ]]
* [[IGEM:IMPERIAL/2006| iGEM@imperial Instructor]]
* [[IGEM:IMPERIAL/Methodology/Part_documentation_template | iGEM@imperial template to document a part]]
* [[IGEM:IMPERIAL/Methodology/IGEM_WetLab_Planning_Tool | IGEM WetLab Planning Tool]]
* [[OWW_Image_Editor | OWW Image Annotation Tool]]
 
Other:
* [[IGEM:IMPERIAL/2006/Created_Pages]]
 
== Interesting links found on OWW==
*[[OpenWetWare:Whosonline | Who Is Online ?]]
*[[Endy:F2620 | F2620 Part Characterization (Labno/Canton)]]
*[[Endy:Victor3_plate_reader/Calibrating_the_GFP-separated_label | GFP calibration and measurements]]
*[[ Titratable control of pBAD and lac promoters in individual E. coli cells | Titratable control of pBAD and lac promoters]]
 
==Useful Open Source Softwares==
* [http://www.inkscape.org/ Inkscape]: SVG editor
* [http://freemind.sourceforge.net/wiki/index.php/Main_Page FreeMind]: Mind map editor
* [http://ganttproject.biz/ GanttProject]: Gantt chart editor.
* [http://openproj.org/openproj OpenProj]: Project management software. Equivalent to Microsoft project.
* [http://www.osalt.com/ OSALT site] lists Open Source softwares with their commercial equivalents.
 
==Cool [http://en.wikipedia.org/wiki/Open_hardware Open Source Hardware] Projects==
* [http://www.arduino.cc/ Arduino], microcontroller.
* [http://www.garagefab.cc/contraptor Contraptor], DIY cartesian robot (XY plotter, CNC router).
* [http://reprap.org/bin/view/Main/WebHome RepRap], 3D printer.
* [http://www.buglabs.net/ BugLabs], modular linux computer.
* [http://www.openmoko.com/ OpenMoko], mobile phone.
* [http://www.openservo.com/ OpenServo], servo motor.
* [http://www.linuxelectrons.com/features/howto/consolidated-hacking-guide-linksys-wrt54gl Linksys WRT54GL], router.
* [http://www.buildlog.net/blog/2011/02/buildlog-net-2-x-laser/ Laser Cutter 2.x]
* from KickStarter:
** [http://www.kickstarter.com/projects/93832939/makerslide-open-source-linear-bearing-system MakerSlide Open Source Linear Bearing System]
** [http://www.kickstarter.com/projects/nortd/lasersaur-open-source-laser-cutter-0?ref=category Laseraur open source laser cutter]
** [http://www.kickstarter.com/projects/701662757/makerbeam-an-open-source-building-kit MakerBeam an Open Source building kit]
** [http://www.kickstarter.com/projects/nicholasclewis/inkshield-an-open-source-inkjet-shield-for-arduino?ref=category inkshield for Arduino]
 
==Recommended Books==
* [http://www.amazon.com/Introduction-Systems-Biology-Mathematical-Computational/dp/1584886420 'An Introduction to Systems Biology', Uri Alon]
* [http://www.amazon.com/System-Modeling-Cellular-Biology-Concepts/dp/0262195488 'System Modeling in Cellular Biology: From Concepts to Nuts and Bolts', Szallasi, Stelling and Periwal]
* [http://www.amazon.com/Stochastic-Modelling-Systems-Mathematical-Computational/dp/1584885408 'Stochastic Modelling for Systems Biology', D. Wilkinson]
* [http://www.amazon.com/Design-Analysis-Experiments-Douglas-Montgomery/dp/0471316490 'Design And Analysis of Experiments', D.C. Montgomery]
* [http://www.amazon.com/Sensitivity-Analysis-Andrea-Saltelli/dp/0471998923 'Sensitivity Analysis', A. Saltelli]
* [http://www.amazon.com/Calculations-Molecular-Biology-Biotechnology-Mathematics/dp/0126657513 Calculations for Molecular Biology and Biotechnology, FH Stephenson]
* [http://www.amazon.co.uk/Fundamentals-Enzyme-Kinetics-Athel-Cornish-Bowden/dp/1855781581 Fundamentals of Enzyme Kinetics, Cornish-Bowden (2004)]
 
==Do-It-Yourself / Developing World Technologies for Biological Engineering==
 
===General===
* [http://www.scifair.org/kid-science-project-molbio.html Dr. Shawn's Molecular Biology Science Fair Projects]
* [http://biohackery.com/ BioHackery]
* [http://www.sciencemadness.org/ experimental DIY]
 
===DNA manipulation===
* [http://www.scq.ubc.ca/?p=40 THE MACGYVER PROJECT: GENOMIC DNA EXTRACTION AND GEL ELECTROPHORESIS EXPERIMENTS USING EVERYDAY MATERIALS]
* [http://www.makezine.com/blog/archive/2006/12/extracting_dna.html MAKE zine]
* [http://www.wired.com/wired/archive/11.12/tools.html?pg=3 WIRED: DNA Sequence Kit]
* [http://www.newscientist.com/article.ns?id=dn11763 DIY PCR cycler (New Scientist)]
* [http://digitalcommons.bryant.edu/sci_jou/6/ A Programmable $25 Thermal Cycler for PCR]
* [http://www3.interscience.wiley.com/cgi-bin/abstract/114229381/ABSTRACT DIY A Pocket-Sized Convective PCR Thermocycler]
* [http://www.york.ac.uk/res/sots/activities/diydna.htm DIY DNA extraction]
* [http://www.shroomery.org/68/Do-it-yourself-magnetic-stirrers Do it yourself magnetic stirrers]
* [http://www.motherearthnews.com/DIY/1982-03-01/Build-Your-Own-Incubator.aspx Egg Incubator]
* [http://www.marketlabinc.com/products/details/375 Disposable pipettes]
 
===Measuremements and Characterization===
* [http://technology.newscientist.com/article/dn12688-diy-lab-scanner-made-from-standard-cd-drive.html DIY lab scanner (New Scientist)]
* [http://cmgm.stanford.edu/pbrown/mguide/ DIY microarrays]
* [http://www.springerlink.com/content/gmtnx79g8gfd5qhu/ An Inexpensive LED-Based Fluorometer Used to Study a Hairpin-Based DNA Machines, Hanwen Yan]
* [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6THH-4G1V68J-2&_user=217827&_coverDate=11%2F11%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000011279&_version=1&_urlVersion=0&_userid=217827&md5=c06e6c717614cd6361a0989ef4b238f9 Improvements in LED-based fluorescence analysis systems]
* [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1403614 Enhanced fluorescence emission using a programmable]
* [http://www.prizmatix.com/docs/app_notes_fluorometer.cfm Prizmatix]
* [http://www3.interscience.wiley.com/cgi-bin/abstract/112781514/ABSTRACT Do-it-yourself microelectrophoresis chips with integrated sample recovery]
* [http://www.springerlink.com/content/n6w58205753hxj71/ On-line measurement of green fluorescent protein (GFP) fluorescence for the monitoring of recombinant adenovirus production]
* [http://www3.interscience.wiley.com/cgi-bin/abstract/76504044/ABSTRACT Low-cost microbioreactor for high-throughput bioprocessing]
* [http://userpages.umbc.edu/~jili/ench772/sensor.html LED GFP sensor]
* [http://dx.doi.org/10.1016/j.jbiotec.2003.10.039 On-line LED GFP sensor]
* [http://www.plantsci.cam.ac.uk/Haseloff/imaging/cheaposcope/cheaposcope.htm LED-based Cheaposcope from Haseloff's lab]
* [http://www.math.ualberta.ca/imaging/ PC controlled digital camera]
* [http://www.instructables.com/id/Build-a-USB-Digital-Microscope-in-60min-and-15/ Cheap DIY USB Digital Microscope]
 
===Data Acquisition, Control and Lab Automation===


== Education==
* [https://jddac.dev.java.net/ Java Distributed Data Acquisition and Control]
<blockquote>M.Sc, ENST Paris <br>
* [http://www.aps.anl.gov/epics/ EPICS Open Source project]
My undergrad degree was in computer science with a major in image processing.  
* [http://mindstorms.lego.com/ Lego Mindstorm]
<br>
* [http://www.liberlab.net/ Liberlab: Open Source Scientific Experimentation Kit]
</blockquote>
* [http://www.arduino.cc/ Arduino project], [http://www.makezine.com/blog/archive/2007/04/diecimila_ten_thousand_ha.html Make article on Arduino]
* [http://gainer.cc/ Gainer: Another Open-Source microcontroller platform]
* [http://blog.makezine.com/archive/2006/11/the_open_source_1.html Make: Open Source Hardware Projects]
* [http://www.tincantools.com TinCanTools: embedded ARM boards for engineers, programmers, and enthusiasts]
* [http://www.phidgets.com/ Phidgets: Sensing/Control building blocks from your PC]
<!--
== OWW ideas (random) ==
=== 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 ==
== Project ==
Here is an overview of the modelling framework I am working on:
Here is an overview of the modelling framework I am working on:
[[Image:MSMrouilly2.png]]
[[Image:MSMrouilly2.png]]
== Delicio.us Tags ==
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==Who is visiting my page?==
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== [[User:Vincent/sandbox| Sandbox]] ==
[[Category:User_United_Kingdom]][[Category:User_London]][[Category:User_Imperial_College]]

Latest revision as of 10:36, 18 November 2012

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Vincent Rouilly's Profile


email: vincent.rouilly [-at-] gmail [-dot-] com

Paris, France.

join my LinkedIn Network

Work Experiences

  • Bioinformatician, LabEx Milieu Interieur, Institut Pasteur, Paris France (Current).
  • Data Analyst & Scientific Software Programmer, ResearchIT, University of Basel, Switzerland.
  • Research Associate, Institute of Systems and Synthetic Biology, Imperial College London
  • GE Medical Systems, Paris, Software R&D Engineer, Image Processing on digital mammography systems.
  • Visiospace, Paris, Software R&D Engineer.

Education

  • PhD, Computational Biology, Department of Bioengineering, Imperial College London.
  • M.Sc, ENST Paris and ERASMUS exchange at ETSIT Madrid (Signal and Image Processing Major).

Affiliations

Synthetic Biology in the making

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

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

Past 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

Teaching Experience

OWW Contributions

Other:

Interesting links found on OWW

Useful Open Source Softwares

Cool Open Source Hardware Projects

Recommended Books

Do-It-Yourself / Developing World Technologies for Biological Engineering

General

DNA manipulation

Measuremements and Characterization

Data Acquisition, Control and Lab Automation

Project

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

Delicio.us Tags

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