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Statistical models workshop 2011


20–22 June 2011

The purpose of this meeting is to work on defining a package (or several packages) for supporting statistical models in SBML Level 3. Those include models where the variables are not single values but ranges, distributions or lists of values. Such models are used for instance in population pharmacokinetics.

Some pre-existing work is available about the distrib package.

Photo album

Logistical information

EVO usage information


Times are UK Summer times.

The audiovisual recordings are done using the EVO teleconferencing system; see the EVO information page for help on playing the recordings. Also available are audio-only recordings in mp3 format—these usually have higher quality than the audio recorded as part of the EVO session.

Monday 20th June

EVO Audio
Time Title Presenter Materials Rec. only
morning Arrivals
14:00 Aims of the meeting, context & organisation Nicolas Le Novère Slides EVO MP3
14:30 SBML Mike Hucka Slides EVO MP3
15:00 Encoding non linear mixed effects model Marc Lavielle Slides EVO MP3
15:30 BUGS David Lunn Slides EVO MP3
16:00 Coffee
16:30 GNU MCSim Frederic Bois Slides EVO MP3
17:00 CaliBayes Conor Lawless Slides EVO MP3
17:30 SBML distrib package Darren Wilkinson Slides EVO MP3
18:00 UncertML2, an overview Dan Cornford Slides EVO MP3
Time What Where Notes
19:30 Dinner Red Lion, Hinxton Google map

Tuesday 21st June

EVO Audio
Time Title Presenter Materials Rec. only
09:20–10:25 What do-we need to encode? What are the existing tools? Everyone pic1, pic2 EVO MP3
10:25–11:05 Brief presentation on COMBINE and SED-ML Nicolas Le Novère Slides EVO MP3
11:05–12:00 Discussion Everyone (None) EVO MP3
12:00 Lunch
14:00 What are the L3 packages needed? Everyone pic3,
Marc's slides
15:00 Definition of required SBML structures Everyone pic4, pic5, pic6,
Nicolas' notes
16:30 Continuing discussions Everyone xml1, xml2, xml3, xml4, xml5 EVO MP3
Time What Where Notes
19:30 Taxi for Cambridge EBI Taxi Bay
20:00 Dinner Cambridge chop house Google map
22:00 Taxi for Hinxton

Wednesday 22th June

EVO Audio
Time Title Presenter Materials Rec. only
10:00-12:30 Further work Everyone pic1, PKModel.xml N/A MP3
12:30–13:15 Lunch
13:15-15:00 Continuing work & wrap-up Everyone truncated.xml, range.xml MP3

Pre and post meeting Background Information


Some participants attended physically; others attended remotely. The following table lists the attendees.

Name Affiliation Relevant projects Physical location
Frank Bergmann University of Washington, Seattle, USA SBML remote
Frederic Bois Technology University of Compiegne, Compiegne, FR MCSim EBI
Dan Cornford Aston University, Birmingham, UK UncertML EBI
Colin Gillespie Newcastle University, Newcastle, UK BASIS remote
Martin Golebiewski HITS, Heidelberg, DE SABIO-RK remote
Mike Hucka Caltech, Pasadena, USA SBML EBI
Sarah Keating EMBL-EBI, Hinxton, UK SBML EBI
Marc Lavielle University Paris-sud, Orsay, FR Monolix EBI
Conor Lawless Newcastle University, Newcastle, UK CaliBayes, BASIS EBI
Nicolas Le Novère EMBL-EBI, Hinxton, UK SBML, BioModels Database EBI
David Lunn MRC Biostatistics Unit, Cambridge, UK BUGS EBI
Chris Myers University of Utah, Salt Lake City, USA SBML, iBioSim Remote
Nicolas Rodriguez EMBL-EBI, Hinxton, UK JSBML, SBMLeditor EBI
Sven Sahle BioQUANT, Heidelberg, DE SBML, COPASI Remote
Lucian Smith University of Washington, Seattle, USA SBML, antimony Remote
Maciej Swat University of Amsterdam, NL SBPKPD EBI
Darren Wilkinson Newcastle University, Newcastle, UK Darren's software EBI

Funding Acknowledgements

We gratefully acknowledge funding for this workshop from the following agencies:





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