Permissions

General Permissions and Copyright Statement for Gerstein Lab Website

The manuscripts available on our site are provided for your personal use only and may not be retransmitted or redistributed without written permissions from the paper’s publisher and author. You may not upload any of this site’s material to any public server, on-line service, network, or bulletin board without prior written permission from the publisher and author. You may not make copies for any commercial purpose. Reproduction or storage of materials retrieved from this website is subject to the U.S. Copyright Act of 1976, Title 17 U.S.C.

UNLESS OTHERWISE NOTATED, all the material on this site — including lectures, motions database, genome analysis system, and computer code — is produced by the Gerstein Lab at Yale University and is copyright Mark Gerstein, 1997-2014.

Free Academic Use with Proper Acknowledgement

You may freely use this material, in research, papers, and talks as long as you properly acknowledge us. It is preferred to refer to an actual journal article where possible — e.g. users of motions database movies should refer to NAR paper. Where this is not possible, e.g. for lectures, a statement like the following is sufficient: “This material is adapted from the Mark Gerstein’s Lab website (gersteinlab.org). Please consult the website regarding reuse.” Where appropriate, we’d, of course, appreciate a link to the appropriate resource.

Commercial Use

If you want to use the website material in a commercial context, please contact Mark Gerstein (see contact info).

Electronic preprints and E-prints

The e-print and other directories contain paper in various stages of the publication process. For all the unpublished papers and preprints, the free academic use section above applies. For reprints from commercial journals, the policies vary. The largest number of papers from the lab are from the Journal of Molecular Biology, which has a clear statement regarding the posting of material on servers. The following is abstracted from JMB’s copyright statement:

3. Personal Servers
3.1. Upon submitting an article to an Academic Press journal for review and possible publication, authors are requested to add the following notice to the first screen of any posted electronic preprint versions of the paper: This work has been submitted to Academic Press for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible. Authors should note that posting the entire work may be regarded as prior publication by some journal editors (see Information for Authors of the specific journal).
3.2. When an Academic Press journal accepts the work for publication, the authors may post it, in its final accepted form, on their personal servers (but not on any organized preprint server) with a notice Accepted for publication in <name of journal> as of <date>, until it is published by Academic Press in print or electronic form.
3.3. After publication, authors may post their Academic Press copyrighted material on their own servers without permission, provided that the server displays as the first line of the HTML page the following notice alerting readers to their obligations with respect to copyrighted material: This material has been published in <name of journal, issue number and date, page numbers>, the only definitive repository of the content that has been certified and accepted after peer review. Copyright and all rights therein are retained by Academic Press. This material may not be copied or reposted without explicit permission. The posted work must also include the Academic Press copyright notice (Copyright © 199x by Academic Press) and a link to IDEAL (International Digital Electronic Access Library) at <http://www.idealibrary.com> or <http://www.europe.idealibrary.com>.

We try to make our redistribution of preprints and e-prints consistent the variety of regulations summarized at http://www.sherpa.ac.uk/romeo.php. We’re also trying to incorporate the license addendums at Scholar’s Copyright Project into our publishing.

Movies

Movies generated by the Morph server may be freely used in teaching contexts and recorded on videotape as long as clear attribution is given.

Course Material

If you want to use the overheads from the Bioinformatics Course in your own course, feel free, as long as you give proper attribution. (In fact, a number of the overheads were derived from related courses at Stanford, particularly those given by M Levitt, and are so acknowledged.) In particular, for slides prepared by the course instructors, it is sufficient to simply say something like “Slide derived from Yale Bioinformatics Course (CBB752b)” and then give the course web link (gersteinlab.org/courses/452). For slides, originally created by instructors outside of the course, you should acknowledge them directly and contact them as appropriate.

Most of the course reading material is copyright and can NOT be freely distributed. It should not be accessible outside of Yale.

Software

Unless noted otherwise on a lab software’s GitHub repository, the default license to copyright lab software is the MIT License. For more details, please check each software’s repository on GitHub.

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. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.