APPAGATO

an APproximate PArallel and stochastic GrAph querying TOol for biological networks.

APPAGATO

May, 2017
License Contacts Downloads References

APPAGATO APPAGATO is a stochastic and parallel algorithm to find approximate occurrences of a query network in biological networks. APPAGATO allows nodes and edges mismatches. To speed-up the querying process, APPAGATO has been also implemented in parallel to run on graphics processing units (GPUs).


APPAGATO is developed in C++ for CUDA under GNU\Linux. It requires NVIDIA GPU devices with compute capability 3.0 and above (Kepler and Maxwell architectures).


See the related scientific article for more details.

License

APPAGATO is distributed under the MIT license. This means that it is free for both academic and commercial use.
Note however that some third party components in APPAGATO require that you reference certain works in scientific publications.
You are free to link or use APPAGATO inside source code of your own program. If do so, please reference (cite) APPAGATO and this website. We appreciate bug fixes and would be happy to collaborate for improvements.

Copyright © 2015 by Nicola Bombieri

APPAGATO is provided under the terms of The MIT License (MIT):

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Contacts

For helps and bugs please send an email to Nicola Bombieri (nicola [dot] bombieri [at] univr [dot] it) and Federico Busato (fedebusato [at] gmail [dot] com).


APPAGATO
is developed by

Vincenzo Bonnici¹, Federico Busato¹, Giovanni Micale², Nicola Bombieri¹, Alfredo Pulvirenti², Rosalba Giugno²
¹University of Verona, Italy; ²University of Catania, Italy

Downloads

Software Sources

download grapes Appagato Repository

GNU\Linux C++ source code of APPAGATO.
APPAGATO is distributed under the MIT license.

download grapes Download Documentation

Appagato installation guide and usage.

Graph Datasets

RI Datasets

References

If you have used any of the APPAGATO project software or dataset, please cite the following article: 

@article{,
  title={APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks},
  author={Bonnici, Vincenzo; Busato, Federico; Micale, Giovanni; Bombieri, Nicola; Pulvirenti, Alfredo; Giugno, Rosalba},
  journal={Bioinformatics},
  volume={32},
  number={14},
  pages={2159--2166},
  year={2016},
  publisher={Oxford Univ Press}
}

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