search

debbiemarkslab / EVcouplings

Evolutionary couplings from protein and RNA sequence alignments
http://evcouplings.org
Other
232 stars 75 forks source link

Dependencies licences #83

Closed sacdallago closed 6 years ago

sacdallago commented 6 years ago

Check licenses for tools and report here

As from #74

For this purpose, I propose listing all external dependencies here and slowly commenting with their licenses.

Dependencies:

sacdallago commented 6 years ago

PSIPRED

http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/LICENSE

PLEASE READ THE FOLLOWING LICENSE AGREEMENT. BY USING THE PROGRAM YOU ARE ACKNOWLEDGING THE FACT THAT YOU AGREE TO THE TERMS OUTLINED IN THIS AGREEMENT. USERS WISHING TO USE THE SOFTWARE FOR COMMERCIAL ACTIVITIES NOT COVERED BY THIS AGREEMENT SHOULD SEND E-MAIL TO: dtj@cs.ucl.ac.uk

In regard to the protein structure prediction program (PSIPRED3) herewith (the Software) the copyright and other intellectual property rights to which belong to the Author(s).

Any user (the User) of the program undertakes to the Copyright holder that he or she shall be bound by the following terms and conditions:-

  1. The User will receive the Software and any related documentation in confidence and will not use the same except for the purpose of their own research. The Software will be used only by such of the User's officers or employees to whom it must reasonably be communicated to enable them to undertake their research and who agree to be bound by the same confidence. The User shall procure and enforce such agreement from his or her staff for the benefit of the Copyright holder.

  2. The publication of research using the Software must include an appropriate citation to the method:

Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202.

  1. All forms of the Software will be kept in a reasonably secure place to prevent unauthorised access.

  2. Each copy of the Software or, if not practicable then, any package associated therewith shall be suitably marked (and such marking maintained) with the following copyright notice: "Copyright 2000 D.T.Jones. All Rights Reserved.".

  3. The Software may be modified, but any changes made shall be communicated to the Author(s) and made freely available.

  4. The Software may not be sold as a standalone package, or incorporated into a commercial software package without the written permission of the Copyright holder. The Software may be used freely for individual academic or commercial research. The Software may also be made freely available for training or teaching purposes.

  5. The results produced by the Software may not be incorporated into any data banks or databases which are subject to the payment of access or license fees without the written permission of the Copyright holder.

  6. The Software may be made available to users over a local network or wide area network (including the Internet), but only if access is granted free of charge to all authorised users. Incorporation of the Software into a commercial Web site or other fee paying service is not allowed without the written permission of the Copyright holder. If PSIPRED results are returned to the user via such a network service, then a suitable acknowledgement of the PSIPRED method must be returned somewhere in the output text.

  7. The confidentiality obligation in paragraph one shall not apply:

    (i) to information and data known to the User at the time of receipt hereunder (as evidenced by its written records);

    (ii) to information and data which was at the time of receipt in the public domain or thereafter becomes so through no wrongful act of the User;

    (iii) to information and data which the User receives from a third party not in breach of any obligation of confidentiality owed to the Author(s).

  8. The User understands that the Software is supplied "as is". No warranty as to its fitness or suitability for any purpose whatsoever is made or implied. In no event shall the Author(s) or Copyright holder be held responsible for any direct or indirect damages arising through the use of the Software.

thomashopf commented 6 years ago

With CNS I think it would be the simplest solution if Debbie and Chris ask Axel Brunger if it would be okay to include it in the container

sacdallago commented 6 years ago

CNS

http://cns-online.org/v1.21 (license button on bottom right)

LICENSE FOR ACADEMIC (NON-PROFIT) INSTITUTIONS TO USE CNSSOLVE GENERAL-RELEASE 1.2

TERMS OF AGREEMENT

BY DOWNLOADING OR USING THE CRYSTALLOGRAPHY & NMR SYSTEM SOLVE (CNSSOLVE) GENERAL-RELEASE 1.2 SOFTWARE YOU AGREE TO THE FOLLOWING TERMS:

sacdallago commented 6 years ago

Bottom line: both can be used for non-commercial purposes (so, we are good to go) but we should cite them in the Readme (which we do, if I'm not mistaken).

Please let me know if there are other licenses to be checked ( pinging @kpgbrock && @b-schubert )

thomashopf commented 6 years ago

YOU SHALL NOT DISCLOSE IN ANY FORM EITHER THE DELIVERED SOFTWARE OR DOCUMENTATION OR ANY MODIFICATIONS OR DERIVATIVE WORKS BASED ON THE SOFTWARE OR DOCUMENTATION TO THIRD PARTIES WITHOUT PRIOR WRITTEN AUTHORIZATION.

This is the much bigger problem unfortunately - hence why I suggest Debbie and Chris reach out to them to ask for permission

sacdallago commented 6 years ago

I'll ping them

aggreen commented 6 years ago

Update: Debbie will email Axel (the creator of CNS)

sacdallago commented 6 years ago

Update: this discussion is only relevant if the dependencies are shipped with the package itself, so for now we won't do that. In terms of docker container, we can make a container which expects the dependencies on a certain volume (e.g. a path on the local computer, or container-to-container volumes sharing, but the container with the dependencies will be maintained by whoever needs it, whereas the container for evcouplings will build on this repo)