Papers that cite Galaxy workflows
Hi all, I’m writing a paper that will include some evangelism for Galaxy in language sciences and I’d like to be able to cite examples of papers in the Bio field that cite Galaxy workflows. Even better would be the re-use of a Galaxy workflow cited in another paper. Does anyone have any good example papers they could refer me to. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy
Hi Steve, This isn't a very strong example, as it is self-reuse and self-citing, but anyway - we described some workflows in this book chapter: Cock and Pritchard (2014) Galaxy as a Platform for Identifying Candidate Pathogen Effectors. http://dx.doi.org/10.1007/978-1-62703-986-4_1 We re-used a workflow and cited the chapter in this paper where I was a co-author: Espada et al (2015) Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy http://dx.doi.org/10.1111/mpp.12280 (It was also cited by our associated tools paper, and a third-party review paper, but those were not re-using the workflows) Peter On Fri, Jul 22, 2016 at 3:21 AM, Steve Cassidy <steve.cassidy@mq.edu.au> wrote:
Hi all, I’m writing a paper that will include some evangelism for Galaxy in language sciences and I’d like to be able to cite examples of papers in the Bio field that cite Galaxy workflows. Even better would be the re-use of a Galaxy workflow cited in another paper. Does anyone have any good example papers they could refer me to.
Thanks,
Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy
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Hi Steve, I don't have a precise answer to your question, but the Galaxy CiteULike archive might be helpful here. Any paper that uses, extends, or references Galaxy gets put in that library. Papers are tagged with one or more of 17 tags <https://wiki.galaxyproject.org/CiteULike>. There aren't specific tags for "defines and publishes a workflow" or "reuses a previously published workflow" but I'm pretty sure I've come across many papers that do this. A good place to start though would be papers with the shared tag <http://www.citeulike.org/group/16008/tag/shared>: Papers that have published/shared workflows, histories, datasets, pages, visualizations in a Galaxy instance. Also, not sure if CloudMap <http://www.citeulike.org/group/16008/article/11450604> qualifies here, but if it does, many papers that reference it are reusing the pipeline defined in it. Hope this helps, Dave C On Thu, Jul 21, 2016 at 7:21 PM, Steve Cassidy <steve.cassidy@mq.edu.au> wrote:
Hi all, I’m writing a paper that will include some evangelism for Galaxy in language sciences and I’d like to be able to cite examples of papers in the Bio field that cite Galaxy workflows. Even better would be the re-use of a Galaxy workflow cited in another paper. Does anyone have any good example papers they could refer me to.
Thanks,
Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy
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Thanks Dave, that’s just what I’m looking for, I found a few good examples of workflow citations. Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy On 27 Jul 2016, at 6:29 AM, Dave Clements <clements@galaxyproject.org<mailto:clements@galaxyproject.org>> wrote: Hi Steve, I don't have a precise answer to your question, but the Galaxy CiteULike archive might be helpful here. Any paper that uses, extends, or references Galaxy gets put in that library. Papers are tagged with one or more of 17 tags<https://wiki.galaxyproject.org/CiteULike>. There aren't specific tags for "defines and publishes a workflow" or "reuses a previously published workflow" but I'm pretty sure I've come across many papers that do this. A good place to start though would be papers with the shared tag<http://www.citeulike.org/group/16008/tag/shared>: Papers that have published/shared workflows, histories, datasets, pages, visualizations in a Galaxy instance. Also, not sure if CloudMap<http://www.citeulike.org/group/16008/article/11450604> qualifies here, but if it does, many papers that reference it are reusing the pipeline defined in it. Hope this helps, Dave C On Thu, Jul 21, 2016 at 7:21 PM, Steve Cassidy <steve.cassidy@mq.edu.au<mailto:steve.cassidy@mq.edu.au>> wrote: Hi all, I’m writing a paper that will include some evangelism for Galaxy in language sciences and I’d like to be able to cite examples of papers in the Bio field that cite Galaxy workflows. Even better would be the re-use of a Galaxy workflow cited in another paper. Does anyone have any good example papers they could refer me to. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/
participants (3)
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Dave Clements -
Peter Cock -
Steve Cassidy