Alice Villeger

Dr Alice C. Villéger
Research Associate
Bioanalytical Sciences Group

School of Chemistry/School of Computer Science
Faculty of Engineering and Physical Sciences
The University of Manchester

Contact information

Kilburn Building (room 2.92)
Oxford Road
Manchester M13 9PL
United Kingdom

alice.villeger@manchester.ac.uk

Main current project

Arcadia: a visualisation tool for metabolic pathways

Other projects of interest

These are projects I am more or less closely involved in.

UTOPIA: User-friendly Tools for OPerating Informatics Applications

UTOPIA is a collection of interactive tools for analysing protein sequence and structure. Up front are user-friendly and responsive visualisation applications, behind the scenes a sophisticated model that allows these to work together and hides much of the tedious work of dealing with file formats and web services.

Arcadia is to become a component of the Utopia suite.

REFINE: Representing Evidence For Interacting Network Elements

Project goal

to adapt and develop text mining tools to evaluate the basis in the literature for the structure of biochemical and signalling models in systems biology
to integrate text mining techniques with visualisation technologies for better understanding of the evidence for biochemical and signalling pathways
to enrich models encoded in the Systems Biology Markup Language (SBML) with information derived from text mining
to evaluate in conjunction with domain experts the effectiveness of using models of pathways augmented with evidence derived from text mining

Arcadia will be used to visualise the result of text-mining queries onto the graphic representation of the pathway.

SBGN: A Visual Notation for Network Diagrams in Biology

The Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in diagrams of biochemical and cellular processes studied in systems biology.

I have been involved in the development of the Process Description notation Level 1, which Arcadia supports

SBML: The Systems Biology Markup Language

The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks in software. It's applicable to models of metabolism, cell-signaling, and many others. SBML has been evolving since mid-2000 thanks to an international community of software developers and users. This website is the portal for the global SBML development effort; here you can find information about all aspects of SBML.

Arcadia supports the SBML format through LibSBML, and I have implemented specific annotations for storing dynamic layout information.