Open Source Software
AbLead is built using a variety of high-quality open source software components. We are grateful to the maintainers and contributors of these projects for their work in advancing the fields of bioinformatics, web development, and scientific computing.
Below is a list of the primary open source packages utilized by AbLead, including links to their repositories, documentation, and licensing information.
Core Framework & Infrastructure
| Package | Description | License | Website / Repository |
|---|---|---|---|
| Python | Primary programming language | PSF License | python.org |
| Flask | Core web application framework | BSD 3-Clause | Website |
| Jinja2 | Template engine | BSD 3-Clause | Website |
| SQLAlchemy | Database abstraction and ORM | MIT | Website |
| Flask-SQLAlchemy | Flask integration for SQLAlchemy | BSD 3-Clause | Repository |
| Werkzeug | WSGI utility library | BSD 3-Clause | Repository |
| flup-py3 | FastCGI bridge for web server hosting | BSD 2-Clause | Repository |
Bioinformatics & Scientific Computing
| Package | Description | License | Website / Repository |
|---|---|---|---|
| AntPack v0.3.8.6.2 | Antibody numbering and region assignments | GPLv3 | Repository |
| ANARCI | VJ gene assignment | BSD 3-Clause | Repository |
| BioPhi | Antibody Sapiens humanization method | MIT | Repository |
| AbLang / AbLang2 | Antibody-specific language models | BSD 3-Clause | AbLang / AbLang2 |
| IgBert | Antibody language model | MIT | Repository |
| PLAbDab | Patent and Literature sequence database and search | BSD 3-Clause | Repository |
| ImmuneBuilder | 3D structural modeling (ABodyBuilder2) | MIT | Repository |
| Biopython | Biological sequence processing | Biopython License | biopython.org |
| PyTorch | Deep learning framework for model inference | BSD | pytorch.org |
| OpenMM | Molecular simulation and structural refinement | MIT / LGPL | openmm.org |
| PDBFixer | Tool for fixing structural issues in PDB files | MIT | Repository |
| Einops | Tensor operations for deep learning models | MIT | Repository |
| Pandas | Data analysis and manipulation | BSD 3-Clause | pandas.pydata.org |
| NumPy | Numerical computing for arrays | BSD 3-Clause | numpy.org |
| SciPy | Scientific and technical computing | BSD 3-Clause | scipy.org |
Licensing Note: Usage of components like AntPack v0.3.8.6.2 (GPLv3) within the AbLead SaaS model is commercially compliant. Because AbLead is a web-based service and the software is not distributed to end-users, the GPLv3 "copyleft" requirement for source code disclosure is not triggered, allowing the platform to remain proprietary while utilizing these open-source tools.
Reporting & Exports
| Package | Description | License | Website / Repository |
|---|---|---|---|
| PyMuPDF (fitz) | High-performance PDF/SVG rendering | AGPLv3 | Documentation |
| Openpyxl | Excel file manipulation (.xlsx) | MIT | Repository |
| Python-docx | Word document generation (.docx) | MIT | Repository |
| LXML | XML and HTML processing | BSD 3-Clause | lxml.de |
Security & Utilities
| Package | Description | License | Website / Repository |
|---|---|---|---|
| zxcvbn | Password strength estimation | MIT | Repository |
| pyotp | Two-factor authentication (TOTP) | MIT | Repository |
| qrcode | QR code generation for 2FA setup | BSD 3-Clause | Repository |
| Pillow (PIL) | Image processing for QR codes | MIT-CMU | Repository |
| Pytz | Timezone database for Python | MIT | Repository |
| webauthn | Passkey/WebAuthn authentication support | BSD 3-Clause | Repository |
Documentation
| Package | Description | License | Website / Repository |
|---|---|---|---|
| MkDocs | Static site generator for docs | BSD 2-Clause | mkdocs.org |
| MkDocs Material | Material theme for MkDocs | MIT | Repository |
License Attribution & Copyright Notices
The following libraries are included under licenses (such as BSD and MIT) that require the reproduction of their copyright notices and license text in this documentation.
Core Scientific & Bioinformatics Libraries
- NumPy: Copyright (c) 2005-2024, NumPy Developers.
- Pandas: Copyright (c) 2008-2011, AQR Capital Management, LLC, Lambda Foundry, Inc. and PyData Development Team. 2011-2024, Pandas Development Team.
- SciPy: Copyright (c) 2001-2002 Enthought, Inc. 2003-2024, SciPy Developers.
- Biopython: Copyright 1999-2024 by Jeffrey Chang and the Biopython Contributors.
- LXML: Copyright (c) 2004-2024 by Stefan Behnel, Martijn Faassen and members of the lxml team.
- ANARCI: Copyright (c) 2015-2024, James Dunbar & University of Oxford.
- AbLang / AbLang2: Copyright (c) 2021-2024, Tobias H. Olsen & University of Oxford.
- IgBert: Copyright (c) 2024 Exscientia.
- PLAbDab: Copyright (c) 2024, University of Oxford.
- ImmuneBuilder: Copyright (c) 2023, Brennan Abanades & University of Oxford.
- BioPhi (Sapiens): Copyright (c) 2021 Merck & Co., Inc., Kenilworth, NJ, USA.
- PyTorch: Copyright (c) 2016-present PyTorch Contributors.
- OpenMM: Copyright (c) 2008-2024 Stanford University and contributors.
- PDBFixer: Copyright (c) 2012-2024 Stanford University and contributors.
- Einops: Copyright (c) 2018-2024 Alex Rogozhnikov.
Web & Documentation Infrastructure
- Flask / Werkzeug / Jinja2: Copyright 2010 Pallets.
- Flask-SQLAlchemy: Copyright 2010 Pallets.
- flup-py3: Copyright (c) 2013, Allan L. Saddi.
- MkDocs: Copyright (c) 2012-2024, Tom Christie.
- MkDocs Material: Copyright (c) 2016-2024, Martin Donath.
- PyMuPDF: Copyright (c) 2013-2024, Artifex Software, Inc.
Security, Reporting, & Utility Libraries
- webauthn: Copyright (c) 2017-2021 Duo Security, Inc. All rights reserved.
- zxcvbn: Copyright (c) 2013 Dropbox, Inc. / Python port Copyright (c) 2016-2023 David Wolsky.
- pyotp: Copyright (c) 2011-2024 PyOTP contributors.
- qrcode: Copyright (c) 2011 Lincoln Loop.
- Pillow (PIL): Copyright (c) 2010-2024 by Jeffrey A. Clark and contributors.
- Pytz: Copyright (c) 2003-2024 Stuart Bishop.
- openpyxl: Copyright (c) 2010 openpyxl.
- python-docx: Copyright (c) 2013 Steve Canny.
W3C Software and Document License Notice
Applied to WebAuthn / FIDO2 browser API standards compatibility.
Although the backend webauthn library is implemented via Duo Security's pythonic wrapper (licensed under BSD 3-Clause), the client-side integration interacts with browser-native WebAuthn APIs developed in accordance with the World Wide Web Consortium (W3C) Web Authentication specifications.
Copyright © 2017-2026 World Wide Web Consortium, (Massachusetts Institute of Technology, European Research Consortium for Informatics and Mathematics, Keio University, Beihang). All Rights Reserved. This work is distributed under the W3C® Software and Document License in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Standard BSD 3-Clause License Text
Applied to NumPy, Pandas, SciPy, LXML, AbLang, Flask, Werkzeug, Flask-SQLAlchemy, qrcode, webauthn, and others.
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 or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Note: This list is maintained for compliance and transparency. For detailed licensing questions, please refer to the respective package authors and the linked license texts.