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README.md

BiVeS Framework

bives logo BiVeS 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.

The Algorithm implemented in BiVeS was published as

Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath: An algorithm to detect and communicate the differences in computational models describing biological systems. Bioinformatics 32 (4): 563-570;

More documentation on the BiVeS framework can be found and the GitHub pages of the SEMS project.

BiVeS consists of several modules

bives modules

BiVeS itself consists of a number of modules:

  • xmlutils is a library for advanced XML handling
  • jCOMODI provides programmatic access to the COMODI ontology
  • BiVeS-Core is the core library for comparison of computational models
  • BiVeS-SBML is a module providing special strategies for models encoded in SBML
  • BiVeS-CellML is a module providing special strategies for models encoded in CellML
  • BiVeS ties all modules together and provides command line access
  • BiVeS-WebApp is a web interface to access BiVeS through the network
  • BiVeS-WebApp-Client provides a Java library for comparing models using the BiVeS-WebApp

Usage of BiVeS

BiVeS currently supports different flavours of XML documents. It supports special comparison strategies for computational models encoded in SBML (though BiVeS-SBML) or CellML (through BiVeS-CellML).

To just compare two documents A.xml and B.xml just call it as:

java -jar BiVeS.jar A.xml B.xml

The output will be an XML patch listing all operations necessary to convert A.xml into B.xml. An XSD schema for the XML can be found in res/bives-diff-schema.xsd.

BiVeS supports other output formats and flags to activate special merge strategies, just call it with --help to get a full list of available options.

There is also a Web Application that happily accepts thrown models and returns comparison results. Just have a look at BiVeS-WebApp and its demo instance at bives.bio.informatik.uni-rostock.de.

LICENSE

Artwork and text etc is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License Creative Commons License

The code is licensed under an Apache 2.0 license:

Copyright martin scharm <https://binfalse.de/contact/>

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

   http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

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