PeakLab v1 Documentation Contents AIST Software Home AIST Software Support
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PeakLab v2
Copyright
PeakLab includes the C++ parallel processing libraries from Intel, OpenBLAS, and NVIDIA. PeakLab also
includes an embedded distribution of the Python programming language for handling advanced numerical
and scientific algorithms.
High-Performance C++ Math & Parallelism
Intel® oneAPI Math Kernel Library (MKL)
Functionality: Provides the core industrial-strength linear algebra, FFTs, and vector math
routines. This includes the OpenMP threading technology used for multi-core parallelization across PeakLab’s
fitting engines.
License: Intel Simplified Software License (ISS)
URL: https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html
Copyright © 2024, Intel Corporation. All rights reserved.
OpenBLAS
Functionality: An optimized Basic Linear Algebra Subprograms (BLAS) library based on GotoBLAS2,
used as a high-performance alternative for matrix multiplications and linear equation solvers.
License: BSD 3-Clause "New" or "Revised" License
Source Code: https://github.com/OpenMathLib/OpenBLAS
Copyright (c) 2011-2024, The OpenBLAS Project.
NVIDIA Management Library (NVML)
Functionality: Used specifically for hardware detection to determine the presence of NVIDIA
GPUs and their compatibility with PeakLab’s CUDA-accelerated processing features.
License: NVIDIA NVML License
URL: https://developer.nvidia.com/management-library-nvml
Copyright: Copyright © 2024, NVIDIA Corporation. All rights reserved.
Specific: only the DLL for identifying an NVidia card and CUDA capability is included
with Peaklab. Users with GPU NVidia hardware must independently install the NVML.
Python Programming Language
Python Interpreter
PeakLab includes an embedded distribution of the Python programming language to handle advanced numerical
optimizations and specialized scientific baseline algorithms.
Software Name: Python
Version: 3.12.4
License: Python Software Foundation (PSF) License Agreement
Source Code: https://www.python.org/
Copyright © 2001-2026 Python Software Foundation. All rights reserved.
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.
Scientific Computation and Optimization
NumPy
License: BSD 3-Clause "New" or "Revised" License
Source Code: https://github.com/numpy/numpy
Copyright (c) 2005-2024, NumPy Developers. All rights reserved.
SciPy
Functionality: PeakLab utilizes SciPy's Differential Evolution (DE) genetic algorithm to find
the optimal lambda, p, and BEADS values required to replicate a human-engineered baseline.
License: BSD 3-Clause "New" or "Revised"
Source Code: https:/github.com/scipy/scipy
Copyright (c) 2001-2002 Enthought, Inc. 2003-2024, SciPy Developers. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided
that the following conditions are met:
Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation and/or other materials provided
with the distribution.
Neither the name of the copyright holder nor the names of its
contributors may be used to endorse the names of its contributors to promote products derived from this
software without specific prior written permission.
llvmlite
Functionality: Provides the low-level LLVM-based code generation required by Numba for Just-In-Time
compilation.
License: BSD 3-Clause "New" or "Revised" License
Source Code: https://github.com/numba/llvmlite
Copyright: Copyright (c) 2014-2024, Numba Developers.
Baseline Algorithms
pybaselines
Author: Donald J. Erb
License: BSD 3-Clause "New" or "Revised" License
Primary Functionality: This library provides highly optimized Python implementations of
modern baseline correction routines, which PeakLab embeds for high-performance scientific data analysis.
Source Code: https://github.com/derb12/pybaselines
Copyright (c) 2019-2024, Donald J. Erb. All rights reserved. Redistribution and use in
source and binary forms, with or without modification, are permitted provided that the following conditions
are met:
Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation and/or other materials provided
with the distribution.
Neither the name of the copyright holder nor the names of its contributors
may be used to endorse the names of its contributors to promote products derived from this software without
specific prior written permission.
pentapy
Functionality: The pentapy library is used as the high-performance engine for PeakLab’s reweighted
Whittaker-based baseline algorithms (such as drpls and aspls). It provides a highly optimized solver for
pentadiagonal matrix systems, ensuring that even the most complex baseline fits are completed in milliseconds.
License: MIT License
Source Code: https://github.com/GeoStat-Framework/pentapy
Copyright (c) 2023 Sebastian Müller. All rights reserved.
numba
Functionality: PeakLab utilizes numba to perform Just-In-Time (JIT) compilation of performance-critical
Python code. This allows mathematical routines to run at near-native C++ speeds by translating Python
functions into optimized machine code at runtime.
License: BSD 2-Clause "Simplified" License
Source Code: https://github.com/numba/numba
Copyright (c) 2017, Numba Developers / Anaconda, Inc. All rights reserved.
Machine Learning & Data Mining
scikit-learn (DBSCAN, Density-Based Spatial Clustering of Applications with Noise)
Module: sklearn.cluster.DBSCAN
License: BSD 3-Clause "New" or "Revised" License
Source Code: https://github.com/scikit-learn/scikit-learn
Copyright (c) 2007-2024 The scikit-learn developers. All rights reserved.
joblib
Functionality: Used for lightweight pipelining and efficient parallel processing of analytical
tasks.
License: BSD 3-Clause "New" or "Revised" License
Source Code: https://github.com/joblib/joblib
Copyright: Copyright (c) 2008-2024, Joblib Developers.
threadpoolctl
Functionality: Provides control over the number of threads used by BLAS and OpenMP libraries
during numerical computations.
License: BSD 3-Clause "New" or "Revised" License
Source Code: https://github.com/joblib/threadpoolctl
Copyright: Copyright (c) 2019-2024, threadpoolctl Developers.
Mass Spectrometry
OpenMS
Library Name: pyopenms (Python bindings for OpenMS)
Functionality: PeakLab utilizes OpenMS for MSExperiment management, MzMLFile input/output,
and PeakPickerHiRes for sophisticated isotopic and centroid data extraction.
License: Three-clause BSD License (compatible with PeakLab’s other scientific libraries).
Source Code: https://github.com/OpenMS/OpenMS
Copyright (c) 2002-2026, The OpenMS Team. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted
provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation and/or other materials provided
with the distribution.
Neither the name of the copyright holder nor the names of its contributors
may be used to endorse the names of its contributors to promote products derived from this software without
specific prior written permission.
Chemometrics
pyMCR
Functionality: PeakLab utilizes the McrAR engine, NNLS (Non-Negative Least Squares) regressors,
and ConstraintNonneg to perform constrained alternating least squares decomposition.
License: MIT License
Source Code: https://github.com/usnistgov/pymcr
Copyright (c) 2017-2024, Charles H. Camp Jr., National Institute of Standards and Technology
(NIST).
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.
Data Management & Databases
Pandas
Functionality: used for high-performance data manipulation and analysis, specifically for
handling the complex metadata and result tables generated during peak fitting.
License: BSD 3-Clause "New" or "Revised" License.
Source: https://github.com/pandas-dev/pandas
Copyright (c) 2008-2024, AQR Capital Management, LLC, Lambda Foundry, Inc. and PyData
Development Team.
Rainbow
Library Name: rainbow (rainbow-api)
Functionality: PeakLab utilizes the rainbow library for high-speed binary data I/O and
indexed storage of large-scale analytical datasets.
License: It is licensed under the GNU Lesser General Public License v3 (LGPLv3).
Source: https://github.com/evanyeyeye/rainbow
Copyright: © Copyright 2022, Evan Shi and Eugene Kwan
SQLAlchemy
Functionality: Provides the Object Relational Mapper (ORM) for PeakLab's SQL-based database
interactions, allowing for robust data persistence across different SQL dialects.
License: MIT License.
Source: https://github.com/sqlalchemy/sqlalchemy
Copyright (c) 2005-2024 SQLAlchemy authors and contributors.
DuckDB
Functionality: An in-process SQL OLAP database management system used for fast analytical
queries on large datasets without the overhead of a separate server process.
License: MIT License.
Source: https://github.com/duckdb/duckdb
Copyright (c) 2018-2024 DuckDB Labs.
TileDB
Functionality: Used for managing large-scale, multi-dimensional dense and sparse arrays, particularly
useful for high-resolution mass spectrometry imaging or complex spectral libraries.
License: MIT License.
Source: https://github.com/TileDB-Inc/TileDB
Copyright (c) 2017-2024 TileDB, Inc.
Zarr
Functionality: A format for the storage of chunked, compressed, binary arrays, providing an
efficient way to store and read massive chromatographic data files.
License: MIT License.
Source: https://github.com/zarr-developers/zarr-python
Copyright (c) 2015-2024 Zarr Developers.
pyodbc
Functionality: Provides Open Database Connectivity (ODBC) for PeakLab, allowing it to interface
with legacy and enterprise database systems.
License: MIT License
Source Code: https://github.com/mkleehammer/pyodbc
Copyright: Copyright (c) 2008-2024, Michael Kleehammer.
PyMySQL
Functionality: A pure-Python MySQL client used for connecting to MySQL and MariaDB databases.
License: MIT License
Source Code: https://github.com/PyMySQL/PyMySQL
Copyright: Copyright (c) 2010-2024, PyMySQL contributors.
psycopg2-binary
Functionality: The primary PostgreSQL database adapter for Python.
License: LGPL v3 License
Source Code: https://github.com/psycopg/psycopg2
Copyright: Copyright (c) 2001-2024, Federico Di Gregorio and Daniele Varrazzo.
pyarrow
Functionality: Provides a cross-language development platform for in-memory data, used by
PeakLab to accelerate the reading and writing of columnar data formats used in large-scale analytics.
License: Apache License 2.0
Source Code: https://github.com/apache/arrow
Copyright: Copyright (c) 2016-2024, The Apache Software Foundation.
Data Visualization
Matplotlib
Functionality: PeakLab utilizes Matplotlib for specialized Python-based scientific data visualization,
including complex 3D contour plots and Mass Spectrometry XICs
License: PSF-compatible (Matplotlib) License
Source Code: https://github.com/matplotlib/matplotlib
Copyright (c) 2012-2024 Matplotlib Development Team; All Rights Reserved.
Pillow
Functionality: The "friendly" PIL fork used by PeakLab’s visualization engine for
opening, manipulating, and saving many different image file formats.
License: HPND (Historical Permission Notice and Disclaimer) License
Source Code: https://github.com/python-pillow/Pillow
Copyright: Copyright (c) 2010-2024 by Jeffrey A. Clark and contributors; Copyright (c)
1885-2011 by Secret Labs AB.
Note: PeakLab utilizes several standard Python utility libraries for internal operations such as packaging, python-dateutil, pytz, six, and typing_extensions. These components are provided under their respective PSF, BSD, and MIT licenses.