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![build](https://github.com/hicops/hicops/workflows/build/badge.svg) [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/hicops/hicops/blob/develop/README.md#contributing) [![pages yes](https://img.shields.io/badge/pages-yes-blue.svg)](https://hicops.github.io) [![GitHub forks](https://img.shields.io/github/forks/hicops/hicops.svg?style=social&label=Fork&maxAge=2592000)](https://GitHub.com/hicops/hicops/network/) [![GitHub stars](https://img.shields.io/github/stars/hicops/hicops.svg?style=social&label=Star&maxAge=2592000)](https://GitHub.com/hicops/hicops/stargazers/) [![GitHub contributors](https://img.shields.io/github/contributors/hicops/hicops.svg)](https://GitHub.com/hicops/hicops/graphs/contributors/) [![GitHub issues](https://img.shields.io/github/issues/hicops/hicops.svg)](https://GitHub.com/hicops/hicops/issues/) [![Github all releases](https://img.shields.io/github/downloads/hicops/hicops/total.svg)](https://GitHub.com/hicops/hicops/releases/) <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-nc-sa/4.0/80x15.png" /></a> | ||
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# <img src="https://user-images.githubusercontent.com/14217455/97767279-84a86100-1af1-11eb-92db-52edf709cb1f.png" width="100" valign="middle" alt="HiCOPS"/> HiCOPS | ||
# <img src="https://user-images.githubusercontent.com/14217455/97767279-84a86100-1af1-11eb-92db-52edf709cb1f.png" width="100" valign="middle" alt="HiCOPS"/> HiCOPS & GiCOPS | ||
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*HiCOPS*: Computational framework for accelerating database peptide search workloads on supercomputing systems. | ||
***HiCOPS***: Computational framework for accelerating database peptide search workloads on supercomputing systems. | ||
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## Citation | ||
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Read our work in the following research paper. You can access the paper via [SharedIt](https://rdcu.be/cvFan). Please cite our paper if you use our work. | ||
***GiCOPS***: CPU-GPU-based super-accelerated HiCOPS framework. | ||
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> <span style="color:black">Muhammad Haseeb, and Fahad Saeed. ***"High performance computing framework for tera-scale database search of mass spectrometry data."*** Nature Computational Science, Volume no. 1, Issue no. 8 (2021): pp no. 550-561.</span> [https://doi.org/10.1038/s43588-021-00113-z](https://doi.org/10.1038/s43588-021-00113-z) | ||
## Homepage & Gateway | ||
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Visit the HiCOPS/GiCOPS homepage [here](https://hicops.github.io) and its ACCESS SGCI Gateway [here](https://hicops.cs.fiu.edu). | ||
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## License | ||
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This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>. All contributions are welcome including new features, documentation and bug fixes through standard GitHub pull request method. | ||
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## Documentation | ||
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Full HiCOPS documentation can be found [here](https://hicops.github.io). | ||
Complete documentation on HiCOPS installation and usage can be found [here](https://hicops.github.io). | ||
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## License | ||
## Installation Tutorials | ||
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Tutorials and automated scripts for installing and setting up HiCOPS on a desktop or cluster computer can be found [here](https://github.com/hicops/tutorials#-hicops-tutorials). | ||
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## Research Works | ||
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Read more about HiCOPS and GiCOPS in the following research works. Please ***CITE*** our work if you use it. Thank you. | ||
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> <span style="color:black">Muhammad Haseeb, and Fahad Saeed. ***"High performance computing framework for tera-scale database search of mass spectrometry data."*** Nature Computational Science, Volume no. 1, Issue no. 8 (2021): pp no. 550-561.</span> [https://doi.org/10.1038/s43588-021-00113-z](https://doi.org/10.1038/s43588-021-00113-z) (Read at [SharedIt](https://rdcu.be/cvFan)) | ||
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> <span style="color:black">Muhammad Haseeb, and Fahad Saeed. ***"GPU-Acceleration of the Distributed-Memory Database Peptide Search on Supercomputers."*** In 2022 ASMS Conference on Mass Spectrometry and Allied Topics, ASMS 2022.</span> | ||
This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>. All contributions are welcome including new features, documentation and bug fixes through standard GitHub pull request method. | ||
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## Issues and Feature Requests | ||
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Open an issue [here](https://github.com/hicops/hicops/issues). Please include any logs, screenshots and/or helpful observations. Also, do not forget to describe the dataset(s), database, steps performed etc. so that the issue can be reproduced. | ||
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## Credits | ||
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1. [Muhammad Haseeb](https://sites.google.com/fiu.edu/muhammadhaseeb) [![Twitter](https://flat.badgen.net/twitter/follow/iHaseebM?icon=twitter)](https://twitter.com/iHaseebM) | ||
2. [Fahad Saeed](https://prof-s.github.io) [![Twitter](https://flat.badgen.net/twitter/follow/Prof_FahadSaeed?icon=twitter)](https://twitter.com/Prof_FahadSaeed) | ||
HiCOPS and GiCOPS are under active development at the [Parallel Computing and Data Science Laboratory](https://saeedlab.cs.fiu.edu) at the [Florida International University](https://www.cis.fiu.edu) in Miami, Florida, USA. | ||
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Primary researchers: | ||
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1. [Muhammad Haseeb](https://www.haseebm.com) [![Twitter](https://flat.badgen.net/twitter/follow/iHaseebM?icon=twitter)](https://twitter.com/iHaseebM) | ||
2. [Fahad Saeed](https://prof-s.github.io) [![Twitter](https://flat.badgen.net/twitter/follow/Prof_FahadSaeed?icon=twitter)](https://twitter.com/Prof_FahadSaeed) | ||
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