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Licenses

Instructional Material

All Carpentries (Software Carpentry, Data Carpentry, and Library Carpentry) instructional material is made available under the Creative Commons Attribution license. The following is a human-readable summary of (and not a substitute for) the full legal text of the CC BY 4.0 license.

You are free:

  • to Share---copy and redistribute the material in any medium or format
  • to Adapt---remix, transform, and build upon the material

for any purpose, even commercially.

The licensor cannot revoke these freedoms as long as you follow the license terms.

Under the following terms:

  • Attribution---You must give appropriate credit (mentioning that your work is derived from work that is Copyright (c) The Carpentries and, where practical, linking to https://carpentries.org/), provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.

  • No additional restrictions---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:

Notices:

  • You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation.
  • No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material.

Software

Except where otherwise noted, the example programs and other software provided by The Carpentries are made available under the OSI-approved 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.

Sample Dataset

This information specifically applies to the contents of the data‑for‑snakemake‑novice‑bioinformatics.tar.xz file which you will need to download as part of the standard setup for this course. This info is also included within the tar file itself.

Short read data

These originate from a dataset lodged in [ArrayExpress at EBI][aa]:

https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-4044

As per the [BioStudies terms of use][bs] "New datasets in BioStudies are released into the public domain under the terms of a Creative Commons Zero (CC0) waiver". This means you may legally use the files for any purpose without attribution. However, if you do re-use the dataset it is basic academic courtesy to state the accession E-MTAB-4044, and cite the paper:

Lahtvee PJ, Kumar R, Hallström BM, Nielsen J. Adaptation to different types of stress converge on mitochondrial metabolism. Mol Biol Cell. 2016;27(15):2505-2514. doi: 10.1091/mbc.E16-03-0187.

The subset of the dataset included here was selected by the authors of the Snakemake lesson.

Yeast transcriptome

This was downloaded from the [Ensembl yeast database][eyd], specifically this location:

https://ftp.ensembl.org/pub/release-100/fasta/saccharomyces_cerevisiae/cdna/

The description provided by Ensembl states that:

The data on this site is a direct import of the Saccharomyces Genome Database (SGD) dataset for the Saccharomyces cerevisiae S288C genome. The assembly provided is R64-1-1, supplemented with additional cross-references and annotations. The protein-coding and non-coding gene model annotation was imported from SGD in April 2018. This gene set is based on Liachko et al. 2013

The [SGD website][sgd] provides full information on appropriate citation of their genome builds, but the appropriate papers to cite regarding this reference sequence are:

Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM. (2013) The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now. G3 (Bethesda). 2013 Dec 27. pii: g3.113.008995v1. doi: 10.1534/g3.113.008995. [PMID: 24374639]

Liachko I, Youngblood RA, Keich U, Dunham MJ. High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast. Genome Res. 2013;23(4):698-704. doi: 10.1101/gr.144659.112.

Trademark

"The Carpentries", "Software Carpentry", "Data Carpentry", and "Library Carpentry" and their respective logos are registered trademarks of Community Initiatives.