Reusability: Software Publication

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Title
Reusability: Software Publication
Title of Series
Part Number
8
Number of Parts
9
Author
Hammitzsch, Martin
License
CC Attribution 3.0 Germany:
You are free to use, adapt and copy, distribute and transmit the work or content in adapted or unchanged form for any legal purpose as long as the work is attributed to the author in the manner specified by the author or licensor.
DOI
Publisher
Technische Informationsbibliothek (TIB)
Release Date
2018
Language
English

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does anyone know what a softer publication is you
make it publicly available for others you can name this publication you open to soften some way if you look at research system at publication is a bit different we can see how we can improve it so that you are your interest as the researchers are meant so is there anyone was published suffered before to be what of the last days perfect and OK so on detailed by a conductor ok if and by OK yes OK so why do suffer publications matter while we're researches
it's part of its research product we should Hamlet-like publications like a paper or like the data itself is a research product and we should make sure that it's open enough so that others can reproduce our findings and modify it and create new findings with that and who benefits from soft the publications the users parent
in future you in future you there's a lot of change right now in Europe and in the world it's understood that research is a research Prodoc and it's already possible to cite soft they're not a publication or paper ballots after the software itself like that you can cite data you can also start citing soft and this is this is what's important for you because in a few years possibly there will be some the to some some some
analyzes how impact for yourself there might have been and if others have start using it and are able to cite it and then it's your credit somehow and you can show that you have maybe you've written less papers than others but sad software has been quite influential and has been used in other papers that others have written so there is a change in the system and you should start applying it as soon as possible so you have another research product which is for all 4 flail you for you OK reffing talking about that why opening softened so scope matters sustainability verifiability of research offer improved the perception of software so if you started doing suffer publications means softer will be understood in a different way for example by by funding authorities are you open up research Sophus is a key building block in open science so we of open access papers we of Open Data and now we have open source which is part of open signs now you can link suffer publications the scientific reputation system through consistent application of the wise for example and you can do a bit more there this is part of the aims of the D. E. R. is the movement in in Germany and new Shong once
said untill there's a radical change in the way that academic credit is given the principal record of scientific research is still peer reviewed publication given that software is a fundamental part of doing science we agree with that in the digital age the question we often ask is Where can I published papers which a primary focus on my research on my scientific software so what we have
is we have suffered jewels and repositories as suffer use
their individual policies and you can have a comprehensive list for example which is provided by the softer Sustainability Institute we can have a look at it parents
relatives which John social I publish my software we are not talking about a softer publication it's more work around but if you like to do the work around you find many journals general journals engineering humanities social science Image Processing informatics Life Sciences of the Physical Sciences Geosciences suit you will definitely
find their usual which helps you to write something about yourself that this is the 1 thing and of course the other thing
as that their digital
repositories which you can use to minted DUI for source code copy so far like Sununu do it's just minting at you I am a copy all software released
packages we have software and source code repositories are most likely you won't have a DUI there but you have code there and solve for a project management where the suffer development really happens it's get top or give left for example and you have some sort of foundation so if you have reached a specific might MIT maturity and then it's in an
environment for a free and open-source software projects for example the apogee foundational the Eclipse Foundation and of course you have few institutes some institutes already offer the option that software or code repositories can used for digital repositories minting you wise to solve the software itself that can be used as well so
there are many channels where you can start providing your software in a way that it it's also that you get the acknowledgment in the in the scientific reputation system this is
something I will skip we can dive into the offer publications when we go to the data size search we will find that there our suffer publications they list approximately 60 thousand there is you can see it's more than 60
thousand words that are if you look on the right time it's still the filter you can see we have selected software as a resource types so others are doing it already to date is slide shows a long list of 60 solvent suffer publications which is quite a lot but I also have to say and when we
go and tools in nodal so which basically is their digital repository which is having more is hosting or is listing on minting due wise forceful software now we can see trigger the same
search here it's listing 15 thousand words just this software resource type and also just for the data centers in order but if you go to the nobles yourself you will find an inconsistency for example when
we go to Synote unused to search there
there's just saying that that 20 thousand
it 20 found 20 thousand results which all software so there is an inconsistency between data side and some older which basically results from that a few people for example is signed
this and this is the resource types software to data which is a company to soft so they make a publication for the software say resource types offer and then the provided data and say it's also resource type of software because it's part of the soft and can be used with this
often but in fact it's data so if you're using that's a nodal and publishing yourself
a yourself all the data for softer be careful what you select because you have all things in your own hands however by some arise that means Zinn noted currently has the the biggest amount of softer publications available which have a d y for example we can take that 1 click on it for example we see that there is a
D Y you can even see that this is piece of software is a supplement to another publication and you can see lot the content of its what's in there and you can see that there are different versions of the piece of software and they even provide you information to cite that stuff cite areas and you can start using that by copy and paste and put it if you use the softer in a paper to produce results we can use that part in the citations and a reference list of paper OK
and as you can see is a no-no itself has 20 thousand and the next 1 is fictional Bioconductor with 5 4 3 thousand so Synote who currently is the choice the place to publish software OK
citations so data site office citations that that's for copy and paste after the alignment we have seen a similar thing just like known what did we say data
side for example yeah we can click
this a status site that the search result again we can use the site as well here and you can use the APA hovel at analyze Vancouver in you just need to copy and paste and you can put in your reference list and you should stop doing that as well if you publish a softer and you get a do why you have a copy and paste that you can put in the paper that you have written where you're using your own software once
advantageous so the that that was the 1
area this just telling you
OK but Sophus citations
starts at your screen the for all this out minting at you Y so when you start to bundling your package and this of force 11 and the specific group who have defined a few principles and you can also
think about what the software what is data but we don't need to talk about that in respect to citations just additional
information but force 11 I think you have been talking about that as a community to have facilities changed Tao would improve knowledge creating sharing self as part of that and there's the Sophus citation group which produced a consolidated set off citation principles and the citation principles I think in the south 6 and had it not only which are general statements we will have a look at them and their
use cases in discussions how to make use of them so principle 1 is the importance of software should be considered a Likud to mate and citable product it's a research up call the same importance as citations of other research I other research products so in the reference list of a John logical and should not be omitted or separated should be cited on the same basis as any other research product to this basically means if your writing a piece of paper which is based on data which is
based on software you will end up with 3 publications already in in your paper you can cite a data and you can cite the softly have used than credit attribution it's
portant in research software citation should facilitate given credits and attribution to all contributors unique identification as the identification is principal free of sulfur citation should include a method for identification recognized at least by the community of the corresponding domain experts but it would be better if it's also recognized by the general public researchers and we have 3 other principles persistence so unique identifiers and metadata describing to soften its disposition should persist accessibility suffer citations should facilitate access to the software itself and specificity Sophus citations should facilitate identification of and access to with the specific version of software that was used so not just the general into the
software appears my GitHub blink please don't do that way please use to specific version that has been used in the paper you can use
citation files or citations you've of Wiles the first one is it plain text file name citation I think you have been talking about that yesterday as well as so he just like the license file you put a citation file in the root directory off your coat we have an example and since there is no
real standard hold to handle now when we
go to this example with the citation file or you can use citation click it and
you can see that the citation for is a bit more extensive possibly then you have seen yesterday but the most important thing is that there's the fish entry and there's much more information there where this belongs to you the of your and of information than to site of the piece of softened publication please use and they provide a copy and paste string the even say that this string might be modified in the citation style of a publication and so on and so on and at the bottom and
they say why they are doing that and they refer to the false 11 document referring to the principles and how to implement them we have another
example yes we have more examples which is very important for you because this is a practice which is just being adopted by many researchers who of writing software and if you want to become such a research as
well then you of course would like to look at how while this doing that we can make a search on a filenames citations
What's interesting OK and then you would see at all the different citations files which are in other produce and you can click on them and check how others are
doing that get some experience with it get ideas how to design your own citation file which a little and yeah at the
end or plus columns open size
that way Tao OK perfect and then you have a list
of great when you have a list of citations file and you just can look how others are doing that and you can
see this 1 only contains the petition tree OK so it's a 1st entry for you how
to wear at the citation flies and then we have the the citation file format because this 1 is a human readable information normally that's that's I mean it's a bit entry so it could also be mission readable but mainly it's mainly meant for being the human readable and the citation 5 forward is you invention readable to because it uses the the yet another mark up
language and we have an example here as well for the for specific
Python converter and as you can see
now we don't have a citation file now we have a citation you of f file and when we look into that we have a
specific syntax and it tells us something about the authors are the date released a door some key words licenses also in their message title and the version so it's a different type of how to do things basically that means for you things are just changing so you should if you all don't know no 1 knows which of these formats all of which of these approaches may survive over the next years you should start using both of them
to support future future use we
also known the next 1 is that there are
also other times I think you also have been talking about could make bit and J. no the files this provides a way of describing describing
mention readable information of the semantic context again they are examples there's a coke made Jazan file here and as you can
see there is much more information in year but basically it says also different persons on bolster of me with their names so than e-mail address and also with the orchid so these are the country Office and contributed so so there's a different differentiation it's a long list in that case of contributers it's even also differentiating that there's a maintainer and there's also some some information on continuous integration development start to use funding so it's a really express a file rate can put much more metadata in which are then not only mainly mention readable but for developers it's also human readable what
else and the next thing is that you have read me and for example which is displayed in in in at 1st in and get up and other like it that hosting web sites and to there you can also
include a small section whole to site or 2 site and publications please use and you provide a copy and paste in the bed and if possible you can even add it you why batch you have copy and paste possibilities for example in some how to apply it to you Ibatan README file and get up and it might things
coming up over the next years as well also currently you that the reputation SIFT system in science and research changes are you're part of that change and you should be aware of what happens and if you want to to be flexible and to address the final decision may be you should consider the citation fired you should consider see if f file if you like you can play around with these coat-maker Jazan used to read me file because this is the 1st thing people see and you should stay up-to-date because there might be a new attempts new approaches over the next 1 2 or 3 years they also use some
higher wait wait wait wait explore for example this year remember this is so nodal and so you have this side as information and you also have export section at the bottom and you already have a languages listing Jazan
LD and you can see that they already integrators information somehow so basically it's it's something that just coolers and the different providers offer publication in systems or a
digital repositories and also called repositories and they're just figuring out how how it can be used by us by the developers by humans but also how it can be used by the system's itself stool to to communicate these metadata information in a way that they are findable under different platforms so there's no real solution right now and everyone is start playing around with that so please stop playing with it as well it then experimental definitely their integrated it's quite progress of that you can find adjacent Yonsei ANSA nodal observations experimental and no 1 knows where this will and maybe they drop this in the year and say it didn't
it isn't something that is applied by the community as you said dictation is something you have to experiment with it and if you like to support a future use which might be dropped you should consider all these I mean it's a bit of effort but it's not so much it's a citation file you can if you like it's the but the stuff and some you re human readable bill part if you like you can really put the seas f file and it's so it's a bit more information you have the G. Jason el-Deen that's a bit more look I would say or use because this 1 is
automatically generated from your metadata so you can use Synote as a publication platform and then you have the Jays know the stuff and can take that out and you have of course something like a README where you just put the copy and paste very prominent for the batch but that it has been published of
course this was a generic approach I think yesterday in the days before you have been using
all intron for example and if you have addressed probably also the citation of citing R and R packages and publications so you can use
citation and citation is
reading for example we
have a citation finally of a description file for example from the 2 we can look at Mitre and it has this information and crime and you get some
dictation formation and this is a call
and and copy and paste information
and this 1 is generated by a a a the citation file and by the
description file as you can see this is the citation fire in it's a different citation fire than we have seen before and it's integrating our a side entry which is a manual which is a book and which is a collection of his and when you look at the manual then this is information which is shown
also at the 1st point you and this information as detection tree so there are community practices
and you should really consider these Community praxis for example if you are practices if you opt for example using intron because they have been or there's still supported it in Gulu school so for example when we look at Google school of for this person weakened
far into that there are tons of publications paper publications and just in between there's a piece of software that's basically the idea
that you have also publication and that you're not just listing your papers and a bit of a data you have published but all the software that is published
next thing metadata for publications if you use a Nobel there's a long list where you can
start adding your files so you can say which communities are involved Apple type would be softer than your basic information like information about you the license the funding related alternative identifiers contributers references a joint where this might have been mentioned a conference or something like that book a thesis or a different story can select subjects so the outcomes of metadata you can select you should make use of it as as as good as possible and it's basically up to
you it's also connected to get up at night and if you have shown a perfect and
there's also further reading how we can apply metadata but basically if you go the so no this is from from my knowledge the most advanced platform because it's all in your hands and they provide a lot of options to add metadata then you have some sort of boy visioning internodal which is pretty cool as well what I would say because Goya visioning allows you to cite all versions and a specific version of record and allows to edit and update the records Phys after the initial publication so when you publish an AB load on a for the 1st time you get to would you wise the first one is a specific version of the record and the other 1 is you y representing all versions of direct court and again which do you why should I use and citations to ensure that other researchers can access the ECSEC research artifacts for reproducibility you should use the the the the specific you wife was specific version and by default also XTEND's in order were generates the citation for the for the for
the latest so we can have a look at an example I can see this is the
standard example forms in there on the left is to crowed on the idea of the visions and you can see there's been all 9 regions site all versions this is the 1 catches all do you y which is 5 9 20 20 and then you have a specific specific do you I for the for this vision for the latest version 2 don't you and you have a different you on year on so it's quite flexible but it's 1 entry it's 1 landing page and if you select 1 of these do you wise and that you eyes resolved the landing page you end up in a page where get all of the versions which is excellent this is exactly what you want trying so best
practices for Sophus citations as a publish it if it's on up then follow specific stair steps there otherwise submitted to Synote or somewhere else of the appropriate metadata and get it you wife rated create a citation fire before that update a README file and a secondary work-around might be that you write a paper about it and you should also consider what you do when you said someone else's software in a paper which has not a GUI and coach or just a snippet a citations that you just can't copy and paste then you should do it on your own to have a good practice check what the contribute is what is the name is there you were al for this piece of software and then build your own citations snippet and put it in the reference list of your publications where you use of someone else to wrap up this
if we look at all of this stuff is to select the proven and strong license check the compote ability for the license use additional license provisions if required for example in the case that you would allow the others as can follow through modifications if they are published somewhere else so that the code is available without redistribution and structure the soft the project under the released put a specific documentation on the dependencies and licenses we have been talking about these dock folder at tribute others work enable citation publish get a
DUI and don't be shy you why really is just a number to use it and publish whenever you want
and ensure that all delusions or releases
can be referred at all and individually so this is the version next on and the most important thinkers starts somehow you with the recommendations given spend time to make your own experiences and talked with others about that and then all the
time things will evolve it's I would say it's fairly new but it's new enough so that everyone helps to apply the current change in the scientific applications
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