BiVeS (Biomodel Version Control System) is a library based on the XyDiff algorithm. It is able to detect differences between two versions of a computational model and to communicate these changes.
Read more about BiVeS in our preprint An algorithm to detect and communicate the differences in computational models describing biological systems and consult our tracs for more details on BiVeS.
The algorithm implemented in BiVeS maps the entities of the model documents onto each other and identifies inserted, deleted, moved, and updated element.
BiVeS is able to export identified differences in both machine- and human-readable formats.
- The XML encoded delta contains all differences for a subsequent processing by machines
- The highlighted reaction network displays the differences graphically, which makes is easy to grasp the changes. The graph is encoded in GraphML, DOT, or JSON.
- The text-based report lists all differences between both versions. It is encoded in either MarkDown, reStructuredText, or HTML.
BiVeS is intended to be used as a library in other software projects. It provides an Java API (more information on the API) to compare models directly from within your Java projects. Tools not developed in Java may use the BiVeS web service (more information on the web service and a client library) or call BiVeS directly from command line.
The most current binaries of BiVeS can be downloaded from our bin-repository at bin.sems.uni-rostock.de.
git clone https://github.com/SemsProject/BiVeS-Core.git
git clone https://github.com/SemsProject/BiVeS-SBML.git
git clone https://github.com/SemsProject/BiVeS-CellML.git
git clone https://github.com/SemsProject/BiVeS.git
git clone https://github.com/SemsProject/BiVeS-WS.git
- BiVeS-WebApp Client:
git clone https://github.com/SemsProject/BiVeS-WS-Client.git
Besides the sources you’ll find an ant build file and a maven
To build the project using ant create a directory
lib and copy the binaries of the dependencies to it. Then, just call
ant dist to build the library.
To build the project using maven just call
mvn package to let maven download dependencies and compile the project. Don’t forget to include our maven repository to your list of repositories.
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