FRAGPIPE-THIRD-PARTY-LICENSES.txt

FragPipe is a comprehensive computational platform designed for the analysis of mass spectrometry-based proteomics data. It includes a Graphical User Interface and pipeline wrapper code (FragPipe-GUI), distributed alongside various independent software tools and workflow files. Each component of FragPipe is available under its own license, as detailed in the THIRD-PART-LICENSES.txt file. Users must review and comply with the licenses of each component when using FragPipe. FragPipe and its contributors disclaim any liability for damages or issues resulting from the use, misuse, or inability to use the software. Users are responsible for ensuring that FragPipe and its components are suitable for their intended purposes and adhere to all relevant legal and regulatory requirements.

Major external tools included in the distribution:
- DIA-Umpire: open source (GPL 3.0) https://github.com/nesvilab/DIA-Umpire
- Crystal-C: open source (Apache 2.0) https://github.com/Nesvilab/Crystal-C
- MSBooster: open source (LGPL 3.0) https://github.com/Nesvilab/MSBooster
- Percolator: open source (Apache 2.0) https://github.com/percolator/percolator
- PeptideProphet (Philosopher version): open source (LGPL 2.0, GPL 2.0) https://github.com/nesvilab/philosopher, based on https://sourceforge.net/projects/sashimi/
- ProteinProphet (Philosopher version): open source (LGPL 2.0, GPL 2.0) https://github.com/nesvilab/philosopher, based on https://sourceforge.net/projects/sashimi/
- PTMProphet: open source (LGPL 2.0, GPL 2.0) https://sourceforge.net/projects/sashimi/
- Philosopher: open source (GPL 3.0) https://github.com/nesvilab/philosopher
- PTM-Shepherd: open source (Apache 2.0) https://github.com/nesvilab/PTM-Shepherd
- EasyPQP: open source (BSD 3-Clause) https://github.com/grosenberger/easypqp
- Skyline: open source (Apache 2.0) https://skyline.ms/wiki/home/software/Skyline/page.view?name=source
- FragPipe-PDV: open source (GPL 3.0) https://github.com/nesvilab/FragPipe-PDV
- SAINTexpress: open source https://saint-apms.sourceforge.net/Main.html
- TMT-Integrator: open source (Apache 2.0) https://github.com/Nesvilab/TMT-Integrator
- DIA-NN 1.8.1: closed source. Available for both academic and commercial use within FragPipe, as outlined in the included DIA-NN license file located in the tools/diann folder.
- FP-PDV: open source (GPL 3.0) https://github.com/Nesvilab/FragPipe-PDV
- OPair: open source (MIT license) https://github.com/Nesvilab/OPair_FragPipe
- Skyline runner: open source (Apache 2.0) https://skyline.ms/project/home/software/Skyline/begin.view
- generate_reports_pdf.py: open source (Apache 2.0)
- LFQ-SiteReporter: closed source, both academic and commercial use is permitted.
- FragPipe-Meta: closed source, both academic and commercial use is permitted.
- Batmass-IO: closed source tool, both academic and commercial use is permitted.

Utility tools included in the distribution:
- FragPipe_FPOP_Analysis.py: open source (Apache 2.0)
- Grppr: open source (GPL 2.0) https://github.com/chhh/Grppr
- hipparchus: open source (Apache 2.0) https://github.com/Hipparchus-Math/hipparchus
- jfreechart: open source (LGPL 2.1) https://www.jfree.org/jfreechart/
- msfragger_pep_split.py: open source (Apache 2.0)
- speclib: open source (Apache 2.0)
- OpenJDK: open source (GPL 2.0) https://openjdk.org/
- Python: open source (Python Software Foundation License) https://www.python.org/

Python packages:
- biopython: open source (Biopython License,) https://biopython.org/
- click: open source (BSD 3-Clause) https://github.com/pallets/click/
- colorama: open source (BSD 3-Clause) https://github.com/tartley/colorama
- contourpy: open source (BSD 3-Clause) https://github.com/contourpy/contourpy
- cycler: open source (BSD 3-Clause) https://github.com/matplotlib/cycler
- easypqp: open source (BSD 3-Clause) https://github.com/grosenberger/easypqp
- fonttools: open source (MIT License) https://github.com/fonttools/fonttools
- joblib: open source (BSD 3-Clause) https://joblib.readthedocs.io/en/stable/
- kiwisolver: open source (BSD 3-Clause) https://github.com/nucleic/kiwi
- llvmlite: open source (BSD 2-Clause) https://github.com/numba/llvmlite
- lxml: open source (BSD 3-Clause) https://lxml.de/
- matplotlib: open source (Python Software Foundation License) https://github.com/matplotlib/matplotlib
- numba: open source (BSD 2-Clause) https://numba.pydata.org/
- numpy: open source (BSD 3-Clause) https://numpy.org/
- packaging: open source (BSD 2-Clause, Apache 2.0) https://github.com/pypa/packaging
- pandas: open source (BSD 3-Clause) https://pandas.pydata.org/
- patsy: open source (BSD 2-Clause, Python Software Foundation License) https://github.com/pydata/patsy
- pillow: open source (MIT-CMU) https://python-pillow.github.io/
- pyopenms: open source (BSD 3-Clause) https://github.com/OpenMS/OpenMS/tree/develop/src/pyOpenMS
- pyparsing: open source (MIT License) https://github.com/pyparsing/pyparsing/
- python-deteutil: open source (Apache 2.0, BSD 3-Clause) https://github.com/dateutil/dateutil
- pytz: open source (MIT License) https://pythonhosted.org/pytz/
- scikit-learn: open source (BSD 3-Clause) https://scikit-learn.org/
- scipy: open source (BSD 3-Clause) https://scipy.org/
- seaborn: open source (BSD 3-Clause) https://github.com/mwaskom/seaborn
- setuptools: open source (MIT License) https://github.com/pypa/setuptools
- six: open source (MIT License) https://github.com/benjaminp/six
- statsmodels: open source (BSD 3-Clause) https://www.statsmodels.org/
- threadpoolctl: open source (BSD 3-Clause) https://github.com/joblib/threadpoolctl
- tqdm: open source (MIT License) https://github.com/tqdm/tqdm
- tzdata: open source (Apache 2.0) https://github.com/python/tzdata
- uv: open source (MIT License, Apache 2.0) https://github.com/astral-sh/uv
- narwhals: open source (MIT License) https://github.com/narwhals-dev/narwhals
- plotly: open source (MIT License) https://github.com/plotly/plotly.py
- PyPDF2: open source (BSD 3-Clause) https://github.com/py-pdf/pypdf
- kaleido: open source (MIT License) https://github.com/plotly/Kaleido
- pyarrow: open source (Apache 2.0) https://arrow.apache.org/


Java libraries used by FragPipe-GUI
- juniversalchardet: open source (Mozilla Public License 1.1) https://github.com/albfernandez/juniversalchardet
- gson: open source (Apache 2.0) https://github.com/google/gson
- streamex: open source (Apache 2.0) https://github.com/amaembo/streamex
- jool: open source (Apache 2.0) https://github.com/jOOQ/jOOL
- maven-artifact: open source (Apache 2.0) https://maven.apache.org/repositories/artifacts.html
- jgrapht-core: open source (LGPL 2.1) https://github.com/jgrapht/jgrapht
- jgraphx: open source (BSD 3-Clause) https://github.com/jgraph/jgraphx
- commons-math3: open source (Apache 2.0) https://commons.apache.org/proper/commons-math/
- commons-compress: open source (Apache 2.0) https://commons.apache.org/proper/commons-compress/
- commons-lang3: open source (Apache 2.0) https://commons.apache.org/proper/commons-lang/
- miglayout-swing: open source (BSD, GPL) http://www.miglayout.com/
- commons-text: open source (Apache 2.0) https://commons.apache.org/proper/commons-text/
- rxjava: open source (Apache 2.0) https://github.com/ReactiveX/RxJava
- eventbus-java: open source (Apache 2.0) https://github.com/greenrobot/EventBus
- jsoup: open source (MIT License) https://jsoup.org/
- okio: open source (Apache 2.0) https://square.github.io/okio/
- okhttp: open source (Apache 2.0) https://square.github.io/okhttp/
- balloontip: open source (BSD 3-Clause) https://mvnrepository.com/artifact/net.java.balloontip/balloontip
- org-netbeans-swing-outline: open source (LGPL 2.1) https://github.com/apache/netbeans
- commons-io: open source (Apache 2.0) https://commons.apache.org/proper/commons-io/
- logback-classic: open source (EPL 1.0, LGPL 2.1) https://logback.qos.ch/
- logback-core: open source (EPL 1.0, LGPL 2.1) https://logback.qos.ch/
- parquet-hadoop: open source (Apache 2.0) https://parquet.apache.org/
- hadoop-common: open source (Apache 2.0) https://hadoop.apache.org/
- hadoop-mapreduce-client-core: open source (Apache 2.0) https://hadoop.apache.org/
- junit: open source (EPL 1.0) https://junit.org/junit4/


Java libraries used by Batmass-IO
- jaxb-stream: open source (Apache 2.0) https://github.com/chavaillaz/jaxb-stream
- commons-csv: open source (Apache 2.0) https://commons.apache.org/proper/commons-csv/
- slf4j-api: open source (MIT License) https://www.slf4j.org/
- jna: open source (Apache 2.0, LGPL 2.1) https://github.com/java-native-access/jna
- sqlite-jdbc: open source (Apache 2.0, BSD 2-Clause) https://github.com/xerial/sqlite-jdbc
- grpc-protobuf: open source (Apache 2.0) https://grpc.io/
- grpc-stub: open source (Apache 2.0) https://grpc.io/
- javax.annotation-api: open source (CDDL 1.0, GPL 2.0) https://github.com/javaee/javax.annotation
- javacl: open source (BSD 3-Clause) https://github.com/nativelibs4java/JavaCL
- org.osgi.core: open source (Apache 2.0) https://github.com/osgi/osgi
- org.osgi.compendium: open source (Apache 2.0) https://github.com/osgi/osgi
- guava: open source (Apache 2.0) https://github.com/google/guava
- commons-pool2: open source (Apache 2.0) https://commons.apache.org/proper/commons-pool/
- biojava-ontology: open source (LGPL 2.1) https://biojava.org/
- jaxb-runtime: open source (EDL 1.0) https://eclipse-ee4j.github.io/jaxb-ri/
- maven-model: open source (Apache 2.0) https://maven.apache.org/ref/3.9.9/maven-model/index.html
- mockito-core: open source (MIT License) https://github.com/mockito/mockito
- junit-jupiter-api: open source (EPL 2.0) https://junit.org/junit5/
- junit-jupiter-engine: open source (EPL 2.0) https://junit.org/junit5/