Vincent Rouilly, PhD Candidate
Department of Bioengineering
email: vincent.rouilly (at) imperial (dot) ac (dot) uk
BioSysBio 2008 is primarily aimed at graduate students, post-docs and junior faculty working in biology and biotechnology.
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 here.
Education and Past Work Experiences
- PhD candidate at Imperial College London
- Writing-up PhD thesis: "An Engineering Approach To The Modeling Of Genetic Circuits"
- 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).
- 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.
- Lab Automation
- Synthetic Biology Course (Spring 2008): Instructor @ Imperial College
- Synthetic Biology Computer Modelling Practicals (Spring 2008): Instructor @ 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"
- Steering committee member and outreach co-chair.
- Digital Microfluidics
- 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
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.
- '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
- 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
- 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
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 ...
- 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 ...)