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<h1 class="page-header"><i class="fa fa-fw fa-home"></i> What is SED-ML?</h1>
<p>
Welcome to the home page of the <b>Simulation Experiment
Description Markup Language</b> (SED-ML). SED-ML is an XML-based format
for encoding simulation setups, to ensure exchangeability and
reproducibility of simulation experiments.
</p>
<p>
The current version is <a href="documents/sed-ml-L1V5.pdf" target="_blank"><b>SED-ML Level 1 Version 5</b></a>.
For additional specification documents and proposals see the <a href="specifications.html" title="Specifications">Specifications</a> page.
</p>
<a href="documents/sed-ml-L1V5.pdf" target="_blank">
<span class="btn btn-default" style="font-weight: bold;">
<img alt="logo" src="images/logoSEDML_w90_t.png"/>
L1V5 (official specification document)
<img alt="pdf" src="images/pdf.png"/>
</span>
</a>
<h2>Introduction</h2>
<p>
The increasing use of computational simulation experiments to inform modern biological
research creates new challenges to annotate, archive, share and reproduce such experiments.
The recently published <a href="http://biomodels.net/miase">Minimum Information About a Simulation
Experiment (MIASE)</a>
proposes a minimal set of information that should be provided to allow the reproduction of simulation
experiments
among users and software tools.
</p>
<p>
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.
</p>
<p>
SED-ML covers the description of the most frequent type of simulation experiments in the area,
namely time course simulations. SED-ML documents specify
</p>
<ul>
<li>which experimental data to use in an experiment,</li>
<li>which models to use in an experiment,</li>
<li>modifications to apply on the models before using them,</li>
<li>which simulation procedures to run on each model,</li>
<li>what analysis results to output,</li>
<li>and how the results should be presented.</li>
</ul>
<p>
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.
</p>
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<h3 class="panel-title"><i class="fa fa-clock-o fa-fw"></i> News</h3>
</div>
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<div class="list-group">
<a href="about.html" class="list-group-item">
<span class="badge">2021-02-10</span>
<i class="fa fa-fw fa-user"></i> <b>Jonathan Karr and Tomas Helikar elected as SED-ML editors</b><br/>
Jonathan Karr and Tomas Helikar replace Herbert Sauro and Alan Garny.
</a>
<a href="http://co.mbine.org/events/HARMONY_2021" class="list-group-item">
<span class="badge">2020-03-09</span>
<i class="fa fa-fw fa-group"></i> <b>HARMONY 2021, Online (virtual) meeting, March 22-26</b><br/>
HARMONY2021 will take place on March 22-26, 2021, as an online hackathon.
</a>
<a href="about.html" class="list-group-item">
<span class="badge">2020-01-01</span>
<i class="fa fa-fw fa-user"></i> <b>Matthias König and Frank Bergmann elected as SED-ML editors</b><br/>
Frank Bergmann has been elected to replace Dagmar Waltemath; Matthias König serves a second term.
</a>
<a href="about.html" class="list-group-item">
<span class="badge">2018-01-16</span>
<i class="fa fa-fw fa-user"></i> <b>Herbert Sauro and Alan Garny elected as SED-ML editors</b><br/>
Herbert Sauro and Alan Garny have been elected to replace David Nickerson and Brett Olivier.
</a>
<a href="https://github.com/SED-ML/sed-ml/releases/tag/L1V3" class="list-group-item">
<span class="badge">2017-10-09</span>
<i class="fa fa-fw fa-github"></i> <b>Release of L1V3</b><br/>
SED-ML Level 1 Version 3 has been released.
</a>
</div>
</div>
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</div>
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<div class="row">
<div class="col-lg-12">
<h2>Overview</h2>
<p>
SED-ML is build of the following main objects: the <code>DataDescription</code>, the <code>Model</code>,
the <code>Simulation</code>, the <code>Task</code>, the <code>DataGenerator</code>, and
the <code>Output</code>.
</p>
<img src="images/sedml/main.svg" width="600"/>
<h3>DataDescription</h3>
<p>The <code>DataDescription</code> class allows to specify datasets for a simulation experiment. Such data can be used
for instance for parametrization of model simulations or to plot data together with simulation results.
</p>
<h3>Model</h3>
<p>
The <code>Model</code> class is used to reference the models
used in the simulation experiment. SED-ML itself is
independent of the model encoding underlying the models.
The only requirement is that the model needs to be
referenced by using an unambiguous identifier which allows
for finding it, for example using a <a
href="http://biomodels.net/miriam/#miriam_uris"
title="MIRIAM URI">MIRIAM URI</a>. To specify the
language in which the model is encoded, a set of
predefined <a href="#sedmlLanguage">language URNs</a> is
provided.
</p>
<p>
The SED-ML <code>Change</code> class allows the application
of changes to the referenced models, including changes on
the attributes, e.g. changing the value of an
observable, computing the change of a value using
mathematics, or general changes on any element of the
model representation that is addressable, such as by XPath
expressions, e.g. substituting a piece of XML by an
updated one.
</p>
<h3>Simulation</h3>
<p>
The <code>Simulation</code> class defines the simulation
settings and the steps taken during simulation. These
include the particular type of simulation and the
algorithm used for the execution of the simulation;
preferably an unambiguous reference to such an algorithm
should be given, using a controlled vocabulary, or
ontologies. One example for an ontology of simulation
algorithms is the <em>Kinetic Simulation Algorithm
Ontology</em> <a href="http://biomodels.net/kisao/">KiSAO</a>.
Further information encodable in the Simulation class
includes the step size, simulation duration, and other
simulation-type dependent information.
</p>
<h3>Task</h3>
<p>
SED-ML makes use of the notion of a <code>Task</code> class
to combine a defined model (from the Model class) and a
defined simulation setting (from the Simulation class). A
task always holds one reference each. To refer to a
specific model and to a specific simulation, the
corresponding IDs are used.
</p>
<h3>DataGenerator</h3>
<p>
The raw simulation result sometimes does not correspond
to the desired output of the simulation, e.g. one might
want to normalise a plot before output, or apply
post-processing like mean-value calculation. The <code>DataGenerator</code>
class allows for the encoding of such post-processings
which need to be applied to the simulation result before
output. To define data generators, any addressable
variable or parameter of any defined model (from instances
of the Model class) may be referenced, and new entities
might be specified using MathML definitions.
</p>
<h3>Output</h3>
<p>
The <code>Output</code> class defines the output of the
simulation, in the sense that it specifies <em>what</em>
shall be plotted in the output. To do so, an output type
is defined, e.g. 2D-plot, 3D-plot or data table, and the
according axes or columns are all assigned to one of the
formerly specified instances of the DataGenerator class.
</p>
</div>
</div>
<div class="row">
<div class="col-lg-12">
<h2>L1V3 UML diagrams</h2>
<h3>Legend</h3>
<img src="images/sedml/uml/00_Legend.svg" style="width: 800px;"/>
<h3>Base class (<code>SedBase</code>)</h3>
<img src="images/sedml/uml/sedBase.svg" style="width: 400px;"/>
<h3>Tasks (<code>AbstractTask</code>, <code>Task</code>, <code>RepeatedTask</code>)</h3>
<img src="images/sedml/uml/abstractTask.svg" style="width: 400px;"/>
<h3>Repeated tasks (<code>RepeatedTask</code>, <code>Range</code>, <code>SetValue</code>)</h3>
<img src="images/sedml/uml/repeatedTask.svg" style="width: 600px;"/>
<h3>Ranges of a repeated task (<code>Range</code>, <code>FunctionalRange</code>, <code>UniformRange</code>, <code>VectorRange</code>)</h3>
<img src="images/sedml/uml/range.svg" style="width: 800px;"/>
<h3>Model and changes to models (<code>Model</code>, <code>Change</code>)</h3>
<img src="images/sedml/uml/model.svg" style="width: 500px;"/>
<h3>Model change (<code>Change</code>, <code>ChangeAttribute</code>, <code>ComputeChange</code>, <code>AddXML</code>, <code>RemoveXML</code>, <code>ChangeXML</code>)</h3>
<img src="images/sedml/uml/change.svg" style="width: 600px;"/>
<h3>Simulation, algorithm, and changes to algorithm parameters (<code>Simulation</code>, <code>OneStep</code>, <code>SteadyState</code>, <code>UniformTimeCourse</code>, <code>Algorithm</code>, <code>AlgorithmParameter</code>)</h3>
<img src="images/sedml/uml/simulation.svg" style="width: 600px;"/>
<h3>Reports and plots (<code>Output</code>, <code>Report</code>, <code>Plot2D</code>, <code>Plot3D</code>, <code>DataSet</code>, <code>Curve</code>, <code>Surface</code>)</h3>
<img src="images/sedml/uml/output.svg" style="width: 600px;"/>
<h3>Recording simulation outputs for reports and plots (<code>DataGenerator</code>, <code>Variable</code>, <code>Parameter</code>)</h3>
<img src="images/sedml/uml/dataGenerator.svg" style="width: 400px;"/>
<h3>Input data (<code>DataDescription</code>, <code>DimensionDescription</code>, <code>DataSource</code>, <code>Slice</code>)</h3>
<img src="images/sedml/uml/dataDescription.svg" style="width: 800px;"/>
<h3>Model and simulation variables for calculating model changes and recording simulation outputs (<code>Variable</code>)</h3>
<img src="images/sedml/uml/variable.svg" style="width: 300px;"/>
<h3>Parameters of mathematical expressions for calculating model changes and recording simulation outputs (<code>Parameter</code>)</h3>
<img src="images/sedml/uml/parameter.svg" style="width: 200px;"/>
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