Legal

Open Source Licenses

Ampliova is built on open source software and published scientific algorithms. We are grateful to all authors and contributors. This page lists all third-party components used, their licences, and attribution requirements.

Scientific algorithms

rdmlpython / LinRegPCR1.7.2MITgithub.com/RDML-consortium/rdmlpython

Cite: Untergasser A., Ruijter J.M., Benes V. and Van Den Hoff M.J.B. (2021). Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data. BMC Bioinformatics 22(1), 398.

Used for per-well PCR efficiency estimation via LinRegPCR sliding-window regression on amplification curves. The MIT licence requires this copyright notice to be retained in all derivative works.

The MIT License

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.

RefSeeker1.0.4GPL >= 2github.com/Hannibal83dk/RefSeeker

Copyright: Copyright (c) Patrick H.D. Petersen

Cite: Asmussen M.H. and Dalgaard L. (2024). RefSeeker: Identification of Suitable Reference Genes in RT-qPCR Experiments Using the R Package RefSeeker. Bio-Protocol 14(17), e5081.

Used server-side via subprocess for reference gene stability analysis (rs_reffinder). RefSeeker is licensed under GPL >= 2. Ampliova calls this package as a system tool and does not distribute it to end-users; no GPL obligations are imposed on Ampliova's own source code under the GPL v2 distribution clause. The full GPL v2 licence is available at https://www.gnu.org/licenses/old-licenses/gpl-2.0.html

ctrlGene1.0.1GPL >= 2CRAN.R-project.org/package=ctrlGene

Copyright: Copyright (c) Shanliang Zhong

Cite: Vandesompele J. et al. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3(7), research0034.1.

Provides the geNorm2 function implementing the stepwise geNorm M algorithm. Dependency of RefSeeker. Licensed under GPL >= 2. Same distribution clause analysis applies as for RefSeeker above.

NormFinder (r.NormOldStab5.txt)Distributed within RefSeeker (GPL >= 2)moma.dk

Copyright: Copyright (c) Claus Lindbjerg Andersen, Molecular Medicine group, Odense University Hospital

Cite: Andersen C.L., Jensen J.L. and Orntoft T.F. (2004). Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets. Cancer Res. 64(15), 5245-5250.

The NormFinder R implementation (r.NormOldStab5.txt) is downloaded at runtime by RefSeeker from moma.dk and distributed as part of the RefSeeker package under GPL >= 2. Used for reference gene stability evaluation with optional group-based analysis.

geNorm algorithmScientific method (see ctrlGene for R implementation)doi.org/10.1186/gb-2002-3-7-research0034

Copyright: Vandesompele et al. 2002

Cite: Vandesompele J. et al. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3(7), research0034.1.

The geNorm M stability metric and stepwise exclusion algorithm are implemented via the ctrlGene R package (geNorm2 function).

BestKeeper algorithmScientific method (implemented in RefSeeker)doi.org/10.1023/B:BILE.0000019559.84305.62

Copyright: Pfaffl et al. 2004

Cite: Pfaffl M.W., Tichopad A., Prgomet C. and Neuvians T.P. (2004). Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper, Excel-based tool using pair-wise correlations. Biotechnol. Lett. 26(6), 509-515.

MAD (mean absolute deviation) of Cq values as stability criterion, implemented via RefSeeker's rs_bestkeeper function.

RefFinder comprehensive rankingScientific method (implemented in RefSeeker)doi.org/10.1007/s11103-012-9971-9

Copyright: Xie et al. 2012

Cite: Xie F. et al. (2012). miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs. Plant Mol. Biol. (RefFinder comprehensive ranking algorithm).

Geometric mean of per-method ranks to produce a combined stability ranking across geNorm, BestKeeper, NormFinder, and delta-Ct.

Python backend

FastAPI0.115MITgithub.com/tiangolo/fastapi

Used in the Ampliova analysis engine. Full licence text available in the package repository.

NumPy>=1.24BSD 3-Clausenumpy.org

Used in the Ampliova analysis engine. Full licence text available in the package repository.

SciPy>=1.10BSD 3-Clausescipy.org

Used in the Ampliova analysis engine. Full licence text available in the package repository.

Pydantic1.10MITdocs.pydantic.dev

Used in the Ampliova analysis engine. Full licence text available in the package repository.

Uvicorn0.30BSD 3-Clausewww.uvicorn.org

Used in the Ampliova analysis engine. Full licence text available in the package repository.