MASTER version 5.0.0

This release incorporates the internal changes necessary to make MASTER compatible with version 4.0 of BEAST 2.

As always, download MASTER-5.0.0.zip if you're interested in the stand-alone version. Otherwise, install using BEAUti's package manager.

MASER version 4.1.3

This release addresses a subtle issue (#42) specific to network simulation which was causing edges in the extended Newick network representation to sometimes be associated with the wrong population.

The file MASTER-4.1.3.zip contains the stand-alone release, while MASTER.package.v4.1.3.zip is the BEAST package release installable via BEAUti's package manager.

MASTER version 4.1.2

This release modifies the lineage postprocessors LineageSampler and LineageFilter to ensure they preserve tree/network orientation. Note that the orientation of the network depends on the order in which reactants and products appear in reaction strings. This has not previously been made clear as I've personally never before assigned significance to this ordering. However, I'm aware that many people do use this ordering to convey information - hence this update.

The file MASTER-4.1.2.zip contains the stand-alone release, while MASTER.package.v4.1.2.zip is the BEAST package release installable via BEAUti's package manager.

MASTER version 4.1.1

This release fixes a bug in an example script. It also provides better and hopefully more informative handling of errors encountered parsing reaction strings and expression strings.

The file MASTER-4.1.1.zip contains the stand-alone release, while MASTER.package.v4.1.1.zip is the BEAST package release installable via BEAUti's package manager.

MASTER version 4.1.0

This release improves the expression handling introduced in v4.0.0 in a couple of ways:

1. A critical bug in the array subscripting mechanism has been fixed.
2. Function expressions are now allowed to include functions (either another function or the same).
3. Functions are now actually "closures" in the sense that they may refer to variables from their calling scope.

The file MASTER-4.1.0.zip contains the standalone release, while MASTER.package.v4.1.0.zip is the BEAST package release installable via BEAUti's package manager.

MASTER version 4.0.0

This release removes support for <iteration> and <range> elements, replacing them both with a much more powerful system for specifying reaction networks. A tutorial is in the works, but for now refer to the Reaction page of the MASTER wiki.

In addition, the Diffusion*.xml scripts in the examples/ folder demonstrate some possible use cases.

As usual, the MASTER-4.0.0.zip archive contains the stand-alone release while MASTER.package.v4.0.0.zip is the BEAST 2 package installable via BEAUti's package manager.

MASTER version 3.0.0

This release simply reflects a change in the versions of software MASTER depends on.

• The standalone release of MASTER 3 (MASTER-3.0.0.zip) requires Java 8 to be installed.
• The MASTER 3 BEAST package (MASTER.package.v3.0.0.zip) requires BEAST version 2.2 and Java 8 to be installed.

MASTER version 2.0.0

This release includes a fix for a bug introduced by the changes to LineageSampler in the last version. This release also changes the way that <range> elements are used. Previously, you would have used something like this:

<reaction spec='Reaction' reactionName='Birth' rate="1.0">
    <range spec='Range' variableName="i" from="0" to="3"/>
    ...
</reaction>

Now, you embed the <range> element(s) inside an <iteration> element like this:

<reaction spec='Reaction' reactionName='Birth' rate="1.0">
    <iteration spec='Iteration'>
        <range spec='Range' variableName="i" from="0" to="3"/>
    </iteration>
    ...
</reaction>

While more verbose, this allows us to abstract the iteration code out of the reaction code, and will allow us to implement much more interesting iterations in future.

Because this update is not backwards-compatible with previous releases, semantic versioning requires we call this what it is: a major release.

MASTER version 1.10

This release includes @alexeid's improved LineageSampler that allows for probabilistic sampling of lineages.

MASTER-1.10.0.zip is the stand-alone release, MASTER.package.v1.10.0.zip is the BEAST 2 package installable via BEAUti.

MASTER version 1.9

This release adds the ability to record the probability density of simulated trajectories via the recordTrajLogP attribute. This attribute is available for all simulation types besides EnsembleSummary. For example, see the description on the trajectory specification wiki page.

As usual, the MASTER-1.9.0.zip archive contains the stand-alone release while MASTER.package.v1.9.0.zip is the BEAST 2 package installable via BEAUti's package manager.