Forgot your password?
Svetoslav Nikolow, Bulgaria (in cooperation with WELISA)
Document Actions
Nicolas Le Novère, UK
| What | Invited talk |
|---|---|
| When |
2010-02-01 from 13:00 to 14:00 |
| Where | Ulmenstrasse 69, Haus 1, room 118 |
| Contact Name | Dagmar Waltemath |
| Contact Email | dagmar.waltemath@uni-rostock.de |
| Contact Phone | 4987440 |
| Add event to calendar |
vCal
iCal
|
Toward a consistent set of interoperable standards to represent models and simulations
A decade ago, the creation of the Systems Biology Markup Language
(SBML)
changed the way people exchanged, verified and re-used models in systems
biology. The robustness and versatility of this standard format, coupled
to
a wide software support fostered the emergence of a whole area of
research
centred on model processing such as encoding, annotation, merging,
comparison and integration with other datasets.
Other community standards of representation were created in
computational
systems biology, and a vertical organisation is emerging, with different
layers of descriptions. While the model structure is covered by SBML and
similar efforts, the biological semantics can be described using BioPAX
while models and pathways can be graphically represented using the
languages of the Systems Biology Graphical Notation (SBGN). Computing
glues
permit to relate the components of the different layers. For instance
one
can generate SBGN maps from SBML using the Systems Biology Ontology
(SBO)
and convert SBML into BioPAX using the controlled MIRIAM annotations.
Independently to the systems biology community, other scientists
developed
their own standards of representations, such as CellML (physiology),
NeuroML (neurophysiology), SimileXML (ecology), with more on the way.
More
recently, new languages appeared that complement the model description,
such as SED-ML to describe the simulation experiments or SBRML to encode
the numerical results. The developers of all those initiatives are now
in
contact, and try to improve the interoperability of the languages.
One can hope to see, in a not too elusive future, the creation of a
coherent set of non-overlapping standards, similar to the W3C standards
for
the World Wide Web, that will cover the various modeling approaches and
scales, but also the different levels of discourse and representation in
Systems Biology.
First Prize at the Second International Biomodellling Competition Dagstuhl 2011