diff --git a/_sidebar.md b/_sidebar.md index c007197..b3e11f5 100644 --- a/_sidebar.md +++ b/_sidebar.md @@ -30,9 +30,6 @@ * [Copyright](/intellectual_property_and_licensing/copyright.md) * [Software Licenses](/intellectual_property_and_licensing/software_licenses.md) * [Examples](/intellectual_property_and_licensing/examples.md) -* [Publishing](/citable_software/publishing_results.md) - * [Making software citable](/citable_software/making_software_citable.md) - * [eScience Conferences, Journals, and Workshops](/citable_software/conferences_journals_workshops.md) * [Contributing to this Guide](/CONTRIBUTING.md) * NLeSC specific * [Chapter Owners](/chapter_owners.md) diff --git a/citable_software/conferences_journals_workshops.md b/citable_software/conferences_journals_workshops.md deleted file mode 100644 index 0ab3404..0000000 --- a/citable_software/conferences_journals_workshops.md +++ /dev/null @@ -1,35 +0,0 @@ -#e-Science Conferences, Journals, and Workshops - -This is a list of Conferences, Journals, and Workshops related to eScience. - -## Conferences - -* [The IEEE International Conference on eScience](https://escience-conference.org/) Yearly (computer science) conference on eScience. - -* [UK Conference of Research Software Engineers](https://rsecon2022.society-rse.org/). - -* [German Conference of Research Software Engineers](https://www.de-rse.org/en/conf2019/index.html). - -* The [European Geosciences Union General Assembly (EGU)](http://www.egu.eu/) has a track by the [Division on Earth and Space Science Informatics (ESSI)](http://www.egu.eu/essi/home/). - -* [Free Open Source Software for GeoInformatics](https://2019.foss4g.org/) - -* [International Conference on Computational Science](https://www.iccs-meeting.org/iccs2019/) - -* [PASC Conference](https://pasc19.pasc-conference.org) - - -There is also a [page with a list of upcoming events](https://www.esciencecenter.nl/events/) on the eScience Center website. - -## Journals - - -* [SoftwareX](http://www.journals.elsevier.com/softwarex/). - -* [Journal of Open Research Software](http://openresearchsoftware.metajnl.com/). - -* [Journal of Open Source Software](https://joss.theoj.org) - -See [A list at the Software Suistainability Institute](http://www.software.ac.uk/resources/guides/which-journals-should-i-publish-my-software). - -## Workshops diff --git a/citable_software/making_software_citable.md b/citable_software/making_software_citable.md deleted file mode 100644 index 8ef9e63..0000000 --- a/citable_software/making_software_citable.md +++ /dev/null @@ -1,70 +0,0 @@ -# Making software citable - -Digital Object Identifiers are globally unique identifiers which can point to -any digital object, such as a version of a paper, a version of software etc. -This has the advantage that it is unambigous and standardized. For papers, using -DOIs is commonplace, and a DOI is usually provided by the publisher. For -software, you can make your own DOI with [Zenodo](https://zenodo.org/): - -1. You can tell people how to cite your software by including a ``CITATION.cff`` -file in the root of your repository (You can read up on the rationale of -``CITATION.cff`` files in [this -blog](https://www.software.ac.uk/blog/2017-12-12-standard-format-citation-files)). -However, writing ``CITATION.cff`` files by hand is a bit tedious and -error-prone, so instead go to -https://citation-file-format.github.io/cff-initializer-javascript/ and fill in -the provided web form. -1. Make a [Zenodo](https://zenodo.org/) account and link it with your GitHub account as explained on [guides.github.com/activities/citable-code](https://guides.github.com/activities/citable-code/). -1. You can tell Zenodo what metadata you want to associate with the software by -including a ``.zenodo.json`` file in the root of your repository, but writing -that file by hand is also error-prone. Therefore it is advisable to just generate it -from the ``CITATION.cff`` file. To do so, you'll need a command line tool -``cffconvert`` which you can install [from -PyPI](https://pypi.org/project/cffconvert/) by: - - ```bash - pip install --user cffconvert - ``` -1. Make sure that your ``CITATION.cff`` is valid YAML by copy-pasting the -contents to http://www.yamllint.com/. -1. Make sure that your ``CITATION.cff`` is valid CFF, by: - - ```bash - # (in the repository's root directory) - cffconvert --validate - ``` - - If the command does not return anything, that means the CFF is valid. - -1. Generate the ``.zenodo.json`` file using ``cffconvert`` as follows: - - ```bash - cffconvert --ignore-suspect-keys --outputformat zenodo --outfile .zenodo.json - ``` -1. On Zenodo, make sure to 'Flip the switch' to the ``on`` position on the -GitHub repository that you want to make a release of. -1. Go to your Github repository, use the _Create a new release_ button to create -a release on GitHub. -1. Zenodo should automatically be notified and should make a snapshot copy of -the current state of your repository (just one branch, without any history), and -should also assign a persistent identifier (DOI) to that snapshot. - - **when things don't work** - - In case the GitHub-Zenodo integration does not work as expected, there are - two places to go and look for information: - 1. On GitHub: - - go to ``https://github.com///`` - - select ``Settings`` - - select ``Webhooks`` - - select select the Zenodo webhook (may require GitHub login) - - scroll down to ``Recent deliveries`` - - click on one of the listed deliveries for details on the request, the response, and to request redelivery. - 1. On Zenodo: - - go to ``https://zenodo.org/account/settings/github/`` - - select the repository that you want to see the diagnostic information of - - click on one of the releases to see the _Payload_ Zenodo received from GitHub, as well as the _Metadata_ that Zenodo has associated with your release, or _Errors_ if there were any. - -1. Use the DOI whenever you refer to your software, be it in papers, posters, or -even tweets and blogs. -1. Add the software's Zenodo badge to your repository's README. \ No newline at end of file diff --git a/citable_software/publishing_results.md b/citable_software/publishing_results.md deleted file mode 100644 index 2fc3576..0000000 --- a/citable_software/publishing_results.md +++ /dev/null @@ -1,68 +0,0 @@ -# Publishing Scientific Results - -## Ready-to-go demos -For many projects, we will prepare attractive demos. We want to be able to show a working demo at any moment in time. Therefore, we want to have special branches in git that contain fully stand-alone demos, including a slide deck, that can just be checked out and used directly. - -## Handling datasets and results -Assuming you have only the software in a (private) git repo, you might want to also add and share with others the data and results related to that software: -* Add also the data and figures using git lfs ([Git Large File Storage](https://git-lfs.github.com/)). -* If not, make the repo public. - -## Available archival / preprint servers or services -* [arXiv](http://arxiv.org/) (physics, mathematics, computer science, quantitative biology, quantitative finance, statistics) -* [bioRxiv](http://biorxiv.org/) (biology) -* [PeerJ Preprints](https://peerj.com/archives-preprints/) (biological and medical sciences) -* [CogPrints](http://cogprints.org/) (psychology, neuroscience, linguistics, and other fields related to cognition) -* [figshare](https://figshare.com/) (all disciplines) -* [GitHub](https://github.com/) (all disciplines) -* [Social Science Research Network](http://www.ssrn.com/en/) (cognitive sciences, economics, humanities, law and more) - -## Data storage and preservation - -We strongly advise to store your research data in a secure location where regular back-ups of the data are made, before you start working with the data. If it is logistically impossible to store the data in a secure location immediately after data collection then here are some tips on how to improve data preservation in the time window in between data collection and data arrival at a secure location. For example, you collect data on humans in an environment without (secure) internet connection and need to temporarily store your data offline on a laptop before being able to upload it to a data archive. - -### Planning data storage - -We recommend that you start as early as possible to think how are you managing your data during and after your project. Some questions you should ask yourself are: - - - What data am I using in my project ? Think about measurements coming from experiments (performed by you or by third parties), but also interviews, statistical information, etc. - - Where is my data coming from ? How is it being collected ? - - Where and how is this information being stored ? - - Does my data comply with the required standards applicable ? For example think of the FAIR principles, GDPR, or other ethical restrictions. - -These type of considerations should usually be covered by your data management plan, if your funding agency requires so. And when it is not required by your funding agency, it is probably a good idea to have a data management plan for yourself. If you are writing a data management plan, considering using [DMPOnline](https://dmponline.dcc.ac.uk/). - -### Tips for short term storage - -#### Checksum and sign your data archive: - -- Do a checksum on your files to check preservation of integrity. This means you will need to store the checksum somewhere, usually they are tiny, so they can be provided along with the data. In fact, some Linux distributions provide the checksum of the iso image so you can check your image when you download it. Storing checksums within the filename is not common practice anymore. A lot of data formats allow storing the checksum in the file; ie. the metadata part contains the checksum of the data part. - -#### File permissions and location: - -- If you need to work with your data, but do not plan to change it then set file access permissions to read only. -- Try to avoid processing files that are also being synced with a cloud platform (like dropbox or onedrive). -- Try to make a back-up if possible and store this back-up at a different physical location. - -#### Specific remarks on person identifiable information: - -- Do not do anything without consulting your privacy consultant. - -### Tips for long term storage - -For long term storage we advise researchers based in The Netherlands to explore the services of [SURFsara website](https://userinfo.surfsara.nl/), the Collaborative organization for ICT in Dutch education and research, including but not exclusively: -- [Surfdrive](https://www.surf.nl/en/surfdrive-store-and-share-your-files-securely-in-the-cloud) for secure data sharing up to 250 GB. -- [Data archive](https://userinfo.surfsara.nl/systems/data-archive) for long term storage of extremely large datasets. - -For researchers outside the Netherlands alternative data storing platforms include: -- https://www.re3data.org -- https://zenodo.org/ -- http://rd-alliance.github.io/metadata-directory/standards/ - -## Research Data Management Resources -### 23 Things: Support for Research Data -- [Updated version for the Dutch Community by the LCRDM task group RDA/23 Things](https://doi.org/10.5281/zenodo.3465896 -) -- [Audience-specific versions by the Dutch Community](https://doi.org/10.5281/zenodo.3773663) -- [Field guides to Research Data Management an intteractive tool](https://23things.sites.uu.nl/) -