Licenses

BioExcel is committed to business-friendly open source licensing for all code developed in the project, but to ensure impact for the most widely used application codes we also need to ensure the code can be used with existing code bases and their licenses. This is handled by making all BioExcel code available as independent libraries or scripts, which can easily be adapted to other codes too when more liberal licenses are available. The licenses used in BioExcel are all OSI-approved and well-recognized Open Source licenses that grant the right to run the code for any purpose, to link it into closed commercial applications, as well as to modify and/or redistribute the code. The licenses differ mainly in minor details such as restrictions on derived works or protections against software patent infringements.

Although most of the source code is maintained and distributed in upstream repositories, BioExcel also provide project releases with semi-regular source snapshots. New source code and workflows developed within BioExcel is maintained in GitHub.

GROMACS

GROMACS is Free Software, available under the GNU Lesser General Public License 2.1 (LGPL-2.1+) or later. You can redistribute GROMACS and/or modify it under the terms of the LGPL as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. It is our understanding that this license permits unrestricted (including commercial) linking to the library as well as free or commercial modification or redistribution.

The pmx toolkit is licensed under the GNU Lesser General Public License version 3.0 (LGPL-3.0+) or later.

HADDOCK

HADDOCK software consists of a collection of python and CNS scripts, as well as other scripts and programs (csh, awk, perl, c++). The HADDOCK distribution can be obtained free of charge for non commercial users by completing and returning (via email) the license agreement form to a.m.j.j.bonvin@uu.nl. You can find more details on the HADDOCK licensing page.

(HADDOCK has a critical dependency upon the third-party software CNS for the core computational work, which effectively restricts HADDOCK to those licensed to use CNS (Academic, non-profit). BioExcel has explored the feasibility of working towards relaxing this restriction; the required modularization will be part of future BioExcel-2 work.

HADDOCK web server access is free for non-profit users upon registration.

The HADDOCK open source tools are released under the Apache License, version 2.0 (Apache-2.0), it is our understanding that this license permits unrestricted use, redistribution, modification for private, public and commercial users, as long as attribution and original license text is retained.

CPMD and MiMiC

The current version of CPMD, 4.1, is copyrighted jointly by IBM Corp and by Max Planck Institute, Stuttgart, and is distributed free of charge to non-profit organisations and non-commercial users by accepting the license terms and registering on the CPMD website. Profit organizations interested at the code should contact the CPMD consortium at cpmd@cpmd.org.

In order to run CPMD in the fully hamiltonian hybrid QM/MM mode, additional routines are needed that are not included in the standard CPMD release. To use these routines a Gromos96 license is required and can be obtained by contacting the CPMD developers at cpmd@cpmd.org.

The MiMic communication library that works with CPMD is licensed under the GNU Lesser General Public License 3.0 (LGPL-3.0+) or later. This library facilitates communication betweeen CPMD and GROMACS and can be linked separately with both GROMACS (using the option to upgrade to LGPL 3.0) and CPMD (using a patch).

Workflow building blocks

The BioExcel workflow blocks biobb as well as workflow examples are licensed under the Apache License, version 2.0; it is our understanding that this license permits unrestricted use, redistribution, modification for private, public and commercial users, as long as attribution and original license text is retained.

Note that many of these workflow blocks effectively call command line tools, which may be distributed under a different license, e.g. GROMACS.

The workflow systems facilitated by BioExcel have their own licenses:

Runtime licenses

GROMACS, HADDOCK, PyCOMPSs, biobb building blocks and several of the workflow systems, may use Python which is distributed under the Python License 2.0 (Python-2.0). COMPSs, Apache Taverna and KNIME need a Java/JDK runtime, which are either available commercially from vendors like Oracle or IBM, or open source OpenJDK under the General Public License 2.0 with Classpath exception (GPL-2.0-with-classpath-exception).