User:Vincent Rouilly: Difference between revisions
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<center><font face="trebuchet ms" style="color:#FFFFFF" size="5">'''Vincent Rouilly's Profile'''</font><br> | |||
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email: vincent.rouilly [-at-] gmail [-dot-] com | |||
Paris, France. | |||
[http://www.linkedin.com/in/vincentrouilly join my LinkedIn Network] | |||
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== 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 == | |||
* [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&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&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. | ||
* | * Laboratory Automation | ||
== 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 | ||
* iGEM | * [[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 == | == 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. | * 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]] | ||
* [[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== | ||
*[[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]] | ||
*[[ 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== | ==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] | ||
* [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=== | ===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)] | ||
* [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.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://www.tincantools.com TinCanTools: embedded ARM boards for engineers, programmers, and enthusiasts] | * [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] | * [http://www.phidgets.com/ Phidgets: Sensing/Control building blocks from your PC] | ||
<!-- | |||
== 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 ...) | ||
--> | |||
== 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?== | ==Who is visiting my page?== |
Latest revision as of 10:36, 18 November 2012
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email: vincent.rouilly [-at-] gmail [-dot-] com Paris, France. |
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
- 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)
- Personal Tweeter Feed : 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
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
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:
- 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:
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.
- Laser Cutter 2.x
- from KickStarter:
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)
Do-It-Yourself / Developing World Technologies for Biological Engineering
General
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
Project
Here is an overview of the modelling framework I am working on:
Delicio.us Tags
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Who is visiting my page?
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