User:Vincent Rouilly

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<div style="padding: 10px; width: 75%; color: #FFFFFF; background-color: #2171B7">
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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''', PhD Candidate</font size>
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email: vincent.rouilly [-at-] gmail [-dot-] com
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<font size="2">Department of Bioengineering<br>
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Paris, France.
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Imperial College London<br>
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South Kensington
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SW7 2AZ<br>
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London, UK<br>
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email: vincent.rouilly03 (at) imperial.ac.uk
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[http://www.linkedin.com/in/vincentrouilly join my LinkedIn Network]
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== Work Experiences ==
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* Bioinformatician, LabEx Milieu Interieur, Institut Pasteur, Paris France (Current).
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* Data Analyst & Scientific Software Programmer, ResearchIT, University of Basel, Switzerland.
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* Research Associate, Institute of Systems and Synthetic Biology, Imperial College London
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* GE Medical Systems, Paris, Software R&D Engineer, Image Processing on digital mammography systems.
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* Visiospace, Paris, Software R&D Engineer.
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== Register to [http://conferences.theiet.org/biosysbio/ BioSysBio-2008@ImperialCollege (20-22 April 2008)] ==
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== Education ==
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* PhD, Computational Biology, Department of Bioengineering, Imperial College London.
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* M.Sc, ENST Paris and ERASMUS exchange at ETSIT Madrid (Signal and Image Processing Major).
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BioSysBio 2008 is primarily aimed at graduate students, post-docs and junior faculty working in biology and biotechnology.
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== Affiliations ==
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* [http://www.synbiostandards.co.uk/index.php SynBioStandard Network (member)]
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* [http://kn.theiet.org/communities/biology/index.cfm IET Systems and Synthetic Biology Network (executive member)]
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* [http://openwetware.org/ OpenWetWare (steering committee member)]
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* [http://bbf.openwetware.org/ BioBrick Foundation (member)]
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* [http://conferences.theiet.org/biosysbio/ BioSysBio (program committee)]
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* [http://www.rsc.org/ Royal Society of Chemistry (member)]
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The IET BioSysBio Organising Committee welcomes contributions in the fields of Synthetic Biology, Systems Biology and Bioinformatics. These may range from research concepts and ideas to technical issues and industrial applications. You can submit your paper '''[http://conferences.theiet.org/biosysbio/abstract/abstract.html here]'''.
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==Synthetic Biology in the making==
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(or how to keep track of what is happening in the Synthetic Biology community)
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== Education and Past Work Experiences==
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<!--* '''TATAvox Blog''': [http://tatavox.wordpress.com link] -->
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* PhD candidate at Imperial College London
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* '''Personal Tweeter Feed''' : [http://twitter.com/vrouilly link]
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* GE Medical Systems, Paris, Software R&D Engineer.
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* '''Tweeter Feed on SynBioNews''' : [http://twitter.com/SynBioNews link]
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* Visiospace, Paris, Software R&D Engineer.
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* '''Facebook group on synthetic biology''': [http://www.facebook.com/#!/group.php?gid=2204701004&ref=mf link]
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* M.Sc, ENST Paris and ERASMUS exchange at ETSIT Madrid (Signal and Image Processing Major).
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* '''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]
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* '''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 ==
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* Contributing to build a Synthetic Biology framework (establishing standards, design for modularity and re-usability, parts characterization) + societal impact of Synthetic Biology.
* 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 Information System.
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* Lab Automation
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* Laboratory Automation
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== My Open Source Hardware/Software Projects to support Synthetic Biology==
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* [[Citizen_Science/Open_Fluorometer_Project | Open Fluorometer]]
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* [[Citizen_Science/Open_Colony_Counter_Project | Open Colony Counter]]
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* [[Citizen_Science/Open_Spectrophotometer_Project | Open Spectrophotomoter]]
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* [[User:Vincent Rouilly/XYZ_Table_Project | XYZ Table Project]] from [http://www.garagefab.cc/contraptor Contraptor] DIY Plotter Kit.
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* [[User:Vincent Rouilly/Distributed Annotation System (DAS) for DNA Part Registries | DAS server on Google App Engine for DNA parts]]
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==Past Projects==
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* '''Recombineering for Synthetic Biology'''
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** Homology recombination-based promoter screening construct.
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** Homology recombination-based rolling device integration.
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* '''Droplet-based Microfluidics for Synthetic Biology'''
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* '''Open Source Hardware for Synthetic Biology'''
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** Arduino-based Peltier controller
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** Colony counting / picking system
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==Online shared resources==
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* [http://www.connotea.org/wiki/User:vincentrouilly my Connotea bookmark]
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* [http://delicious.com/Manosquin my delicious bookmark]
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* [http://tataaavox.wordpress.com/ blog]
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== Current Research Projects==
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==Teaching Experience ==
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* Writing-up PhD thesis: "An Engineering Approach To The Modeling Of Genetic Circuits"
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* [[Imperial_College/Courses/Fall2009/Synthetic_Biology_(MRes_class)| Synthetic Biology Course (Fall 2009, MRes)]]: Lecturer @ Imperial College
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* iGEM instructor (2006, 2007)
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* [[Imperial_College/Courses/Fall2008/Synthetic_Biology_(MRes_class)| Synthetic Biology Course (Fall 2008, MRes)]]: Lecturer @ Imperial College
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* Supervising master project: "Sensitivity analysis applied to genetic circuit induction protocols".
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* [[Imperial_College/Courses/Spring2008/Synthetic Biology| Synthetic Biology Course (Spring 2008)]]: Lecturer @ Imperial College
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* Supervising UROP project: "Building modular biobricks models implemented with CellML"
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* [[ Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals| Synthetic Biology Computer Modelling Practicals (Spring 2008)]]: Lecturer @ Imperial College.
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* '''[http://www.igem.org iGEM] instructor''':
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** [[IGEM:IMPERIAL/2006|iGEM 2006]]: "Engineering a Molecular Predation Oscillator", 1st Runner-Up, Best Documentation, Best Characterisation.
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** [[IGEM:IMPERIAL/2007|iGEM 2007]]: "Cell-Free Infection Detector", Gold Medal.
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** [[IGEM:IMPERIAL/2008|iGEM 2008]]: "BioFabricator".
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* Co-Supervisor master project (summer 2007): "Sensitivity analysis applied to genetic circuit induction protocols".
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* Co-Supervisor UROP project (summer 2007): "Building modular biobricks models implemented with CellML"
== OWW Contributions ==
== OWW Contributions ==
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* [[User:Vincent_Rouilly/Data_Exchange_Standards_For_Synthetic_Biology | Data_Exchange_Standards_For_Synthetic_Biology]]
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* [[User:Vincent_Rouilly/Computational_Biology_With_R | Computational Biology with R]]
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* [[User:Vincent_Rouilly/Synthetic_Biology_Community_Pointers | SynBio Community Pointers]]
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* [[Citizen Science/Open Spectrophotometer Project | Open Spectrophotometer Project]]
* Steering committee member and outreach co-chair.
* Steering committee member and outreach co-chair.
* [[Minicells | minicells]]
* [[Minicells | minicells]]
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* [[User:Vincent_Rouilly/Hands_On_BioBrick_Activity | Hands on BioBrick Activity for a science fair]]
* [[User:Vincent_Rouilly/Hands_On_BioBrick_Activity | Hands on BioBrick Activity for a science fair]]
* [[OpenWetWare:Equipment/Laboratory_Automation | Lab Automation Review]]
* [[OpenWetWare:Equipment/Laboratory_Automation | Lab Automation Review]]
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* [[Computational_Biology | Computational Biology]]
* [[Computational_Biology/Gene_Expression_modeling/Stochastic_Approach | Stochastic Gene Expression]]
* [[Computational_Biology/Gene_Expression_modeling/Stochastic_Approach | Stochastic Gene Expression]]
* [[Registry of Standard Biological Models| Registry of Standard Models]]
* [[Registry of Standard Biological Models| Registry of Standard Models]]
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== Interesting links found on OWW==
== Interesting links found on OWW==
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*[[OpenWetWare:Whosonline | Who Is Online ?]]
*[[Endy:F2620 | F2620 Part Characterization (Labno/Canton)]]
*[[Endy:F2620 | F2620 Part Characterization (Labno/Canton)]]
*[[Endy:Victor3_plate_reader/Calibrating_the_GFP-separated_label | GFP calibration and measurements]]
*[[Endy:Victor3_plate_reader/Calibrating_the_GFP-separated_label | GFP calibration and measurements]]
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*[[ Titratable control of pBAD and lac promoters in individual E. coli cells | Titratable control of pBAD and lac promoters]]
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==Useful Open Source Softwares==
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* [http://www.inkscape.org/ Inkscape]: SVG editor
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* [http://freemind.sourceforge.net/wiki/index.php/Main_Page FreeMind]: Mind map editor
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* [http://ganttproject.biz/ GanttProject]: Gantt chart editor.
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* [http://openproj.org/openproj OpenProj]: Project management software. Equivalent to Microsoft project.
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* [http://www.osalt.com/ OSALT site] lists Open Source softwares with their commercial equivalents.
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==Cool [http://en.wikipedia.org/wiki/Open_hardware Open Source Hardware] Projects==
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* [http://www.arduino.cc/ Arduino], microcontroller.
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* [http://www.garagefab.cc/contraptor Contraptor], DIY cartesian robot (XY plotter, CNC router).
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* [http://reprap.org/bin/view/Main/WebHome RepRap], 3D printer.
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* [http://www.buglabs.net/ BugLabs], modular linux computer.
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* [http://www.openmoko.com/ OpenMoko], mobile phone.
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* [http://www.openservo.com/ OpenServo], servo motor.
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* [http://www.linuxelectrons.com/features/howto/consolidated-hacking-guide-linksys-wrt54gl Linksys WRT54GL], router.
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* [http://www.buildlog.net/blog/2011/02/buildlog-net-2-x-laser/ Laser Cutter 2.x]
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* from KickStarter:
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** [http://www.kickstarter.com/projects/93832939/makerslide-open-source-linear-bearing-system MakerSlide Open Source Linear Bearing System]
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** [http://www.kickstarter.com/projects/nortd/lasersaur-open-source-laser-cutter-0?ref=category Laseraur open source laser cutter]
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** [http://www.kickstarter.com/projects/701662757/makerbeam-an-open-source-building-kit MakerBeam an Open Source building kit]
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** [http://www.kickstarter.com/projects/nicholasclewis/inkshield-an-open-source-inkjet-shield-for-arduino?ref=category inkshield for Arduino]
==Recommended Books==
==Recommended Books==
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* [http://www.amazon.com/Design-Analysis-Experiments-Douglas-Montgomery/dp/0471316490 'Design And Analysis of Experiments', D.C. Montgomery]
* [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/Sensitivity-Analysis-Andrea-Saltelli/dp/0471998923 'Sensitivity Analysis', A. Saltelli]
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* [http://www.amazon.com/Calculations-Molecular-Biology-Biotechnology-Mathematics/dp/0126657513 Calculations for Molecular Biology and Biotechnology, FH Stephenson]
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* [http://www.amazon.co.uk/Fundamentals-Enzyme-Kinetics-Athel-Cornish-Bowden/dp/1855781581 Fundamentals of Enzyme Kinetics, Cornish-Bowden (2004)]
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==Do-It-Yourself / Developing World Technologies for Biological Engineering==
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=='Do It Yourself' or Developing World Technologies for Biological Engineering==
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===General===
===General===
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* [http://www.wired.com/wired/archive/11.12/tools.html?pg=3 WIRED: DNA Sequence Kit]
* [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://www.newscientist.com/article.ns?id=dn11763 DIY PCR cycler (New Scientist)]
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* [http://digitalcommons.bryant.edu/sci_jou/6/ A Programmable $25 Thermal Cycler for PCR]
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* [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.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.shroomery.org/68/Do-it-yourself-magnetic-stirrers Do it yourself magnetic stirrers]
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* [http://dx.doi.org/10.1016/j.jbiotec.2003.10.039 On-line 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.plantsci.cam.ac.uk/Haseloff/imaging/cheaposcope/cheaposcope.htm LED-based Cheaposcope from Haseloff's lab]
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* [http://www.math.ualberta.ca/imaging/ PC controlled digital camera]
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* [http://www.instructables.com/id/Build-a-USB-Digital-Microscope-in-60min-and-15/ Cheap DIY USB Digital Microscope]
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===Data Acquisition, Control and Lab Automation===
===Data Acquisition, Control and Lab Automation===
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* [http://www.arduino.cc/ Arduino project], [http://www.makezine.com/blog/archive/2007/04/diecimila_ten_thousand_ha.html Make article on Arduino]
* [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://gainer.cc/ Gainer: Another Open-Source microcontroller platform]
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* [http://blog.makezine.com/archive/2006/11/the_open_source_1.html Make: Open Source Hardware Projects]
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* [http://www.tincantools.com TinCanTools: embedded ARM boards for engineers, programmers, and enthusiasts]
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* [http://www.phidgets.com/ Phidgets: Sensing/Control building blocks from your PC]
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<!--
== OWW ideas (random) ==
== OWW ideas (random) ==
=== building a stronger community ===
=== building a stronger community ===
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**image annotation (microscope images, gel analysis, colonies plate ..) see iNote, SVG.
**image annotation (microscope images, gel analysis, colonies plate ..) see iNote, SVG.
**graph editor/viewer to build/view/run kinetic models (SBML, CellML ...)
**graph editor/viewer to build/view/run kinetic models (SBML, CellML ...)
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-->
== 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]]
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== Delicio.us Tags ==
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==Who is visiting my page?==
==Who is visiting my page?==

Current revision


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: Image:MSMrouilly2.png

Delicio.us Tags

Who is visiting my page?

Locations of visitors to this page

Sandbox

Personal tools