User:Vincent Rouilly
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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:
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