Standard Formats

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SED-ML L1 V2


Simulation Experiment Description Markup Language Level 1 Version 2

Synopsis

SED-ML aims at describing simulation protocols for computational experiments.

Description

The Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. [ ... ] It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions.*

SED-ML is a format describing how a simulation experiment is carried out. The simulation itself is described in the interfaced format. Biological application is therefore viewed as a property of the interfaced standard.

*(Waltemath D et al.. BMC Systems Biology. 2011; 5:198.)

Publication Date

12/2013

Authors

Le Novère, Nicolas
T. Bergmann, Frank
P. Nickerson, David
Cooper, Jonathan
Waltemathr, Dagmar

Organizations


Biological Scales

Scale molecular cellular tissue organ organism ecosystem
Support potential potential potential potential potential potential

Spatial Representation

Spatial Representation Level Compartment Dimensions Gradients Spatial Structures
Support unknown unknown unknown unknown

Modeling Formalisms for this format

Software support for this format

Examples for this format


Modularity: yes


Components Relation
Flat Network: no


Supported Math

MathML Support: yes

Full MathML Support: no

Description

Subset of MathML 2.0 elements.

Unit Support

Unit Required: no

Support: undefined

Description

Units is a feature of the underling model, not of the simulation protocol.

Annotation Support

Miriram Support: yes

identifiers.org Support: yes


There are no biological applications available!
There are no transformations available!

jlibsedml


Programming language

Java

Links

API

libsedml


Programming language

.NET

Links

Webpage

jlibsedml


SEDML


Validation Portal

Simulation Experiment Description Markup Language (SED-ML)


Description

SBGN describes the procedures and conditions under which a particular model is used in a unambiguous way.

Derived from

XML

Publication date

03/2011

Organizations

Links

All formats for this class

Free and Open


Description

Not closely defiened license allowing for free use and open participation. The product is viewed as community effort.