Re: [galaxy-dev] Licensing Galaxy workflows; are they software or documents?
On Tue, Aug 20, 2013 at 2:57 PM, John Chilton wrote: > I don't have time to argue about this especially because I agree that > cc is likely better than OSS licenses, but I am just too passionate > about this point not too. Workflows are 100% software!!! I think we agree here - although I want workflows in Galaxy to be a bit broader than just the scripted actions and include help text and sample data as well (which should also happen with software in general): http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016132.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016133.html > A python script is just a protocol or a cookbook that tells a Python > interpreter (runtime) how to behave. Even assembly is just a set of > bits without a machine to run it on. > > You would never tell a biologist this, but Galaxy is a high-level > graphical programming environment, histories are an interactive > console for testing and debugging, workflows are finished programs > that can be rerun using the same runtime on different inputs. > > -John So yes, we could indeed use traditional software licenses (open source or otherwise) for workflows. I've been using the MIT license on most of my recent Galaxy Tools, which is extremely liberal - so if I used that on workflows it would of course allow editing etc, and should be OK for combining with other workflows too. I don't want to accidentally block reuse of my workflows due to a too narrow license. Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Licensing Galaxy workflows; are they software or documents?
I don't have time to argue about this especially because I agree that cc is likely better than OSS licenses, but I am just too passionate about this point not too. Workflows are 100% software!!! A python script is just a protocol or a cookbook that tells a Python interpreter (runtime) how to behave. Even assembly is just a set of bits without a machine to run it on. You would never tell a biologist this, but Galaxy is a high-level graphical programming environment, histories are an interactive console for testing and debugging, workflows are finished programs that can be rerun using the same runtime on different inputs. -John On Tue, Aug 20, 2013 at 8:26 AM, Bjoern Gruening wrote: > Hi Peter, > > http://www.myexperiment.org seems to favor Creative Commons licenses: > > 1500 by-sa > 342 by-nd > 318 by > 25 BSD > 13 GPL > 10 Apache > 9 LGPL > 6 by-nc-sa > 4 CC0 > 1 MIT > > For me a plain workflow in XML is not a software, its a protocol, like a > cookbook. Sure its written in a really high level computing language, > but the reason is mainly because computer need to read it. > > I would vote for CC. > > Cheers, > Bjoern > > > >> Hello all, >> >> A philosophical question - for my Galaxy tools and wrappers, >> I have been using open source software (OSS) licences, e.g. >> the MIT license, or GPL. >> >> For licensing my Galaxy workflows, should I also treat them as >> software and do the same, or as a protocol document and go >> for something like one of the Creative Commons licenses? >> e.g. CC BY, or CC BY-SA >> >> Thanks, >> >> Peter >> ___ >> 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: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > > > ___ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Licensing Galaxy workflows; are they software or documents?
On Tue, Aug 20, 2013 at 2:26 PM, Bjoern Gruening wrote: > Hi Peter, > > http://www.myexperiment.org seems to favor Creative Commons licenses: > > 1500 by-sa > 342 by-nd > 318 by > 25 BSD > 13 GPL > 10 Apache > 9 LGPL > 6 by-nc-sa > 4 CC0 > 1 MIT > > For me a plain workflow in XML is not a software, its a protocol, like a > cookbook. Sure its written in a really high level computing language, > but the reason is mainly because computer need to read it. > > I would vote for CC. > > Cheers, > Bjoern That is a pretty clear margin too - adding up the software licenses I make that count just 58, versus 2170 using one form or another of the CC license family. Good idea to check myexperiment.org :) Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Licensing Galaxy workflows; are they software or documents?
Hi Peter, http://www.myexperiment.org seems to favor Creative Commons licenses: 1500 by-sa 342 by-nd 318 by 25 BSD 13 GPL 10 Apache 9 LGPL 6 by-nc-sa 4 CC0 1 MIT For me a plain workflow in XML is not a software, its a protocol, like a cookbook. Sure its written in a really high level computing language, but the reason is mainly because computer need to read it. I would vote for CC. Cheers, Bjoern > Hello all, > > A philosophical question - for my Galaxy tools and wrappers, > I have been using open source software (OSS) licences, e.g. > the MIT license, or GPL. > > For licensing my Galaxy workflows, should I also treat them as > software and do the same, or as a protocol document and go > for something like one of the Creative Commons licenses? > e.g. CC BY, or CC BY-SA > > Thanks, > > Peter > ___ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Licensing Galaxy workflows; are they software or documents?
Hi Sebastian, Thanks for your thoughts. As to the details, I guess most people agree that Galaxy Tool wrappers are software, although they range from trivial XML markup files, to complex XML with embedded scripting, to some with a second script file working with the XML. Galaxy Workflows are recorded (currently) as plain text JSON files, which can be edited by hand but are best created and edited via the Galaxy interface. In both cases there can or should be test and sample data, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016133.html John Chilton replied via twitter, "Workflows are software (written in a high-level language), but somehow OS licenses feel incorrect - paper citations seem the goal." https://twitter.com/jmchilton/status/369643138911961088 I guess we as a community could go down either route for licensing Galaxy workflows - but it might make sense to have a consensus as that would simplify combining workflows together and redistributing the resulting super workflow. Perhaps if we'll be able to use Galaxy Workflows like Galaxy Tools within the interface one day it would be better to treat them all under software licenses? Peter On Mon, Aug 19, 2013 at 11:21 PM, Sebastian Schaaf wrote: > Hello Peter, > > First of all, interesting question :). Generally, I would suppose both > approaches are correct: on the one hand those workflows are a defined set > of processing rules in an explicit format, like software is the > implementation of algorithms. More detailed, it is a script, processed by > an interpreter (= Galaxy). On the other hand, those rules are on a more or > less abstract level (does that matter?) and carry somewhat creativity > (well, just the uplink to *Creative* Commons...). > > I would redirect your question to the counter question "How similar is the > saved workflow to software code?". Means: is there a file or a database > entry, which is comparable to an (interpreted) programming language (-> > software)? Or is it more similar to a markup language like XML, which is > indeed the case for some other basic elements in Galaxy (-> document)? > > Hope that helps... > > Looking forward to some more replies, > Cheers, > > Sebastian > > > Peter Cock schrieb: >> Hello all, >> >> A philosophical question - for my Galaxy tools and wrappers, >> I have been using open source software (OSS) licences, e.g. >> the MIT license, or GPL. >> >> For licensing my Galaxy workflows, should I also treat them as >> software and do the same, or as a protocol document and go >> for something like one of the Creative Commons licenses? >> e.g. CC BY, or CC BY-SA >> >> Thanks, >> >> Peter >> ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Licensing Galaxy workflows; are they software or documents?
Hello Peter, First of all, interesting question :). Generally, I would suppose both approaches are correct: on the one hand those workflows are a defined set of processing rules in an explicit format, like software is the implementation of algorithms. More detailed, it is a script, processed by an interpreter (= Galaxy). On the other hand, those rules are on a more or less abstract level (does that matter?) and carry somewhat creativity (well, just the uplink to *Creative* Commons...). I would redirect your question to the counter question "How similar is the saved workflow to software code?". Means: is there a file or a database entry, which is comparable to an (interpreted) programming language (-> software)? Or is it more similar to a markup language like XML, which is indeed the case for some other basic elements in Galaxy (-> document)? Hope that helps... Looking forward to some more replies, Cheers, Sebastian Peter Cock schrieb: > Hello all, > > A philosophical question - for my Galaxy tools and wrappers, > I have been using open source software (OSS) licences, e.g. > the MIT license, or GPL. > > For licensing my Galaxy workflows, should I also treat them as > software and do the same, or as a protocol document and go > for something like one of the Creative Commons licenses? > e.g. CC BY, or CC BY-SA > > Thanks, > > Peter > ___ > 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: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich Marchioninistr. 15, K U1 (postal) Marchioninistr. 17, U 006 (office) D-81377 Munich (Germany) Tel: +49 89 2180-78178 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Licensing Galaxy workflows; are they software or documents?
Hello all, A philosophical question - for my Galaxy tools and wrappers, I have been using open source software (OSS) licences, e.g. the MIT license, or GPL. For licensing my Galaxy workflows, should I also treat them as software and do the same, or as a protocol document and go for something like one of the Creative Commons licenses? e.g. CC BY, or CC BY-SA Thanks, Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
