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SBML-NeuroML interfaces mini-workshop 2010

Contents

EBI, Hinxton, UK, 17–18 May 2010

The purpose of this meeting was to discuss technical aspects of possible interfaces between NeuroML and SBML.

Meeting organization

Michael Hucka, Padraig Gleeson and Robert Cannon were the primary organizers. Local hosting was provided by Nicolas Le Novère's computational systems neurobiology group at the EBI. The first day took place in the "Hall-View room", located at the upper level of the "East-wing" of the EBI. The second day took place in room "A3-01", at the upper level of the "old building".

Participants

In alphabetical order, the participants in the end were the following people:

  • Robert Cannon
  • Sharon Crook (remotely)
  • Padraig Gleeson
  • Michael Hucka
  • Sarah Keating
  • Nicolas Le Novère
  • Michele Mattioni

Agenda

The following is a general list of the meeting goals, though not necessarily in this order:

  • Give people an update on the draft NeuroML v.2 examples first discussed at the NeuroML meeting in Arizona in March.
  • Get feedback from SBML people on overall style of the new version, specification methods (Schema or UML), libNeuroML (C++ & Swig or Java...), and related aspects.
  • To discuss with SBML people the process towards a more formalised specification of v.2 (e.g., drafts of individual parts such as morphologies and channels sent to the NeuroML mailing list, feedback, a wider draft specification to the comp neuro community, feedback including demo implementations, appointing editors, production of a new specification).
  • Technical discussion on SBML support (hooks/pointers to model elements in SBML from NeuroML in CellML/NineML).
  • Discussion of possible common metadata schemes, such as controlled annotations/ontologies etc. (MIRIAM URNs, extension of SBO to cover electrophysiology ...)
  • Discussion of units: what should be done.

Day 1 (Monday, May 17)

Recordings are available in audio-only MP3 format as well as EVO audio-visual session recordings. Most modern browsers will start an MP3 player when you simply double-click on the MP3 file links. To view the EVO recordings, you will first need to download the EVO recording archive (a zip file) to your local hard disk, then use the free EVO Player to open the .evo file within the zip archive.

Time Lead person(s) Topic Files Audio only EVO
A/V
09:35–11:50 Padraig Review of general NeuroML v.2 status, followed by discussion none MP3 zip
14:00–15:15 Mike Summary of some key points of the SBML-BioModels.net hackathon held May 1–4 none MP3 zip
15:30–18:10 Padraig Further review & discussion of neuroml proposals from earlier today NeuroML file MP3 zip

Day 2 (Tuesday, May 18)

Recordings are available in audio-only MP3 format as well as EVO audio-visual session recordings. Most modern browsers will start an MP3 player when you simply double-click on the MP3 file links. To view the EVO recordings, you will first need to download the EVO recording archive (a zip file) to your local hard disk, then use the free EVO Player to open the .evo file within the zip archive.

Time Lead person(s) Topic Files Audio only EVO
A/V
09:30–11:10 Padraig & Nicolas Some recap of yesterday, then discussion of annotations, then general SBML/libSBML discussions none MP3 zip
11:30–12:30 Everyone Units Image MP3 zip
13:30–14:00 TDB TBD none none zip
15:30–17:30 Padraig General topics & re-discussing some XML from yesterday none MP3 zip

Remote connection information

We used EVO to make the session available to others who wanted to listen in or participate. See the separate page of instructions for information about how to get started with EVO. The session password was "SBML" (without the double quotes).

Background materials

For NeuroML, there is the NeuroML website and the workshop report from the 2010 meeting in Arizona. Padraig also put together the following useful NeuroML v.2 draft example models as background materials:

For NineML, there is the NineML website, in particular the NineML abstracts.

For SBML, there is of course this website, and particularly the Level 3 specification.

For SED-ML, there is the SED-ML website, and the draft specification

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