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Welcome to Pactolus !

The goal of Pactolus is to enable the large-scale application of database searching for metabolite identification by overcoming core computational challenge and improving accuracy as well as to provide a foundation for the community to develop new scoring approached in an efficient manner.

Origins of the name Pactolus

The original development of Pactolus was inspired by MIDAS (see http://midas-omicsbio.ornl.gov/, a database searching approach for metabolite identification in metabolomics based on the matching of measured tandem mass spectra against the predicted fragments of metabolites in a database. In Greek mythology, King Midas is popularly remembered for his ability to turn everything he touched into gold. According to legend, King Midas divested himself of the golden touch by washing himself in the river Pactolus. After King Midas washed himself in the river Pactolus, the power of the golden touch flowed into the river, and the sands of the river turned into gold.

How do I get set up?

Pactolus is written in pure python. The main dependencies of Pactolus are h5py, numpy, scipy, and optionally mpi4py.

Contribution guidelines

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Who do I talk to?

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Third-party Copyrights/Licences

To avoid the need for external dependencies, Pactolus includes several third-party codes as part of the pactolus/third_party package. Third-party code (e.g., codes extracted from BASTet) may include their own copyright and license restrictions.

Copyright

Pactolus Copyright (c) 2016, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.

If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Innovation and Partnerships department at IPO@lbl.gov referring to " Pactolus (2016-036),."

NOTICE. This software was developed under funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.

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