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This is an initial version of the companion page for the paperback
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.. _book-intro-v1: | ||
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Updates for the book *Datalad -- An Introduction* | ||
================================================= | ||
Datalad --- An Introduction to Research Data Management | ||
======================================================= | ||
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This page is the online companion to the paperback book | ||
published in 2023. | ||
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.. image:: book-intro-v1/intro-v1-cover.jpg | ||
:align: center | ||
:target: ../_images/intro-v1-cover.jpg | ||
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The book contains almost 200 references to online resources, and describes a | ||
continuously evolving software ecosystem. In order to maximize the longevity | ||
of the book, this page provides updates to references and content that are no | ||
longer in-sync with the state of the world. | ||
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.. _book-intro-v1-urls: | ||
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Errata | ||
------ | ||
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Presently, there are no known issues in the published book. | ||
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If you discovered one, please report it via the `Handbook's issue tracker | ||
<https://github.com/datalad-handbook/book/issues/new/choose>`__. Thank you! | ||
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Hyperlink URL index | ||
------------------- | ||
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.. add URL index once final | ||
The book's appendix lists URL references to online resources using two or three | ||
character alphanumeric codes. The following lists maps these codes to | ||
an up-to-date URL. | ||
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.. container:: book-v1-url-index | ||
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:71: https://7-zip.org | ||
:A1: https://apps.apple.com/us/app/xcode/id497799835 | ||
:A2: https://aws.amazon.com | ||
:A2A: https://aws.amazon.com/ecr | ||
:A2B: https://aws.amazon.com/s3 | ||
:A3: https://www.appveyor.com | ||
:B1: https://git-annex.branchable.com | ||
:B1A: https://git-annex.branchable.com/backends | ||
:B1B: https://git-annex.branchable.com/design/adjusted_branches | ||
:B1C: https://git-annex.branchable.com/git-annex | ||
:B1D: https://git-annex.branchable.com/git-annex-adjust | ||
:B1E: https://git-annex.branchable.com/git-annex-migrate | ||
:B1F: https://git-annex.branchable.com/git-annex-numcopies | ||
:B1G: https://git-annex.branchable.com/git-annex-uninit | ||
:B1H: https://git-annex.branchable.com/git-annex-wanted | ||
:B1K: https://git-annex.branchable.com/install/rpm_standalone | ||
:B1L: https://git-annex.branchable.com/internals/key_format | ||
:B1M: https://git-annex.branchable.com/projects/datalad/bugs-done/Windows__58___substantial_per-file_cost_for___96__add__96__ | ||
:B1N: https://git-annex.branchable.com/special_remotes | ||
:B1O: https://git-annex.branchable.com/tips/largefiles | ||
:B1P: https://git-annex.branchable.com/tips/owncloudannex | ||
:B1Q: https://git-annex.branchable.com/tips/using_Amazon_Glacier | ||
:B1R: https://git-annex.branchable.com/tips/using_Google_Cloud_Storage | ||
:B1S: https://git-annex.branchable.com/tips/using_box.com_as_a_special_remote | ||
:B2: https://bitbucket.org | ||
:B3: https://brew.sh | ||
:C1: http://creativecommons.org/publicdomain/zero/1.0 | ||
:C2: https://creativecommons.org | ||
:C2A: https://creativecommons.org/licenses/by-sa/4.0 | ||
:C2B: https://creativecommons.org/licenses/by/4.0/ | ||
:C2C: https://creativecommons.org/public-domain/cc0/ | ||
:C3: https://docs.conda.io | ||
:C3A: https://docs.conda.io/miniconda.html | ||
:C3B: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html | ||
:D1: https://docs.datalad.org | ||
:D1A: https://docs.datalad.org/en/latest/generated/datalad.config.html | ||
:D1B: https://docs.datalad.org/en/latest/generated/man/datalad-push.html | ||
:D1C: https://docs.datalad.org/en/latest/generated/man/datalad-status.html | ||
:D1D: https://docs.datalad.org/en/latest/modref.html | ||
:D1E: https://docs.datalad.org/projects/container | ||
:D1F: https://docs.datalad.org/projects/gooey | ||
:D1G: https://docs.datalad.org/projects/osf | ||
:D3: https://datasets.datalad.org | ||
:D4: https://datalad.org | ||
:D5: https://docs.docker.com/desktop/install/windows-install/ | ||
:D6: https://hub.docker.com | ||
:D7: https://neuro.debian.net | ||
:D7A: https://neuro.debian.net/install_pkg.html?p=datalad | ||
:D7B: https://neuro.debian.net/pkgs/datalad.html | ||
:D8: https://www.debian.org/index.en.html | ||
:D9: https://www.docker.com/get-started | ||
:F1: https://f1000research.com/posters/7-1965 | ||
:F2: https://figshare.com | ||
:G1: https://git-scm.com | ||
:G1A: https://git-scm.com/book/en/v2 | ||
:G1B: https://git-scm.com/book/en/v2/Customizing-Git-Git-Configuration | ||
:G1C: https://git-scm.com/book/en/v2/Git-Internals-Environment-Variables | ||
:G1D: https://git-scm.com/book/en/v2/Git-Internals-Git-References | ||
:G1E: https://git-scm.com/book/en/v2/Git-Internals-The-Refspec | ||
:G1F: https://git-scm.com/book/en/v2/Git-Tools-Rewriting-History | ||
:G1G: https://git-scm.com/book/en/v2/Git-on-the-Server-Getting-Git-on-a-Server | ||
:G1H: https://git-scm.com/docs/git-cat-file | ||
:G1K: https://git-scm.com/docs/git-config | ||
:G1L: https://git-scm.com/docs/git-config#Documentation/git-config.txt-corefileMode | ||
:G1M: https://git-scm.com/docs/git-push#Documentation/git-push.txt---force | ||
:G1N: https://git-scm.com/docs/git-reflog | ||
:G1O: https://git-scm.com/download/win | ||
:G2: https://github.com | ||
:G2A: https://github.com/ReproNim/neurodocker | ||
:G2B: https://github.com/andrewringler/git-annex-turtle | ||
:G2C: https://github.com/datalad-datasets/bmmr-t1w-250um | ||
:G2D: https://github.com/datalad-datasets/longnow-podcasts | ||
:G2E: https://github.com/datalad-handbook/DataLad-101 | ||
:G2F: https://github.com/datalad-handbook/book/issues/new | ||
:G2G: https://github.com/datalad-handbook/midterm_project | ||
:G2H: https://github.com/datalad-handbook/repro-paper-sketch | ||
:G2K: https://github.com/datalad-handbook/resources | ||
:G2L: https://github.com/datalad/datalad-installer | ||
:G2M: https://github.com/myyoda/talk-principles | ||
:G2N: https://github.com/newren/git-filter-repo | ||
:G2O: https://github.com/psychoinformatics-de/studyforrest-data-phase2 | ||
:G2P: https://github.com/settings/tokens | ||
:G2Q: https://github.com/swaroopch/byte-of-python/releases/download/vadb91fc6fce27c58e3f931f5861806d3ccd1054c/byte-of-python.pdf | ||
:G3: https://docs.github.com | ||
:G3A: https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent | ||
:G3B: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens | ||
:G3C: https://docs.github.com/en/get-started/getting-started-with-git/about-remote-repositories | ||
:G3D: https://docs.github.com/en/get-started/quickstart/fork-a-repo | ||
:G3E: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/addressing-merge-conflicts/resolving-a-merge-conflict-using-the-command-line | ||
:G3F: https://docs.github.com/en/repositories/working-with-files/managing-large-files/about-large-files-on-github | ||
:G4: https://github.blog/2015-02-06-git-2-3-has-been-released | ||
:G5: https://gin.g-node.org/G-Node/Info/wiki | ||
:G6: https://www.gnu.org | ||
:G6A: https://www.gnu.org/savannah-checkouts/gnu/bash/manual/bash.html#Pattern-Matching | ||
:G6B: https://www.gnu.org/software/sed/manual/sed.html | ||
:G7: https://about.gitea.com | ||
:G8: https://about.gitlab.com | ||
:G9: https://developer.github.com/changes/2020-02-14-deprecating-password-auth | ||
:G10: https://drive.google.com/drive/my-drive | ||
:G11: https://gist.github.com/netj/8836201 | ||
:G12: https://gogs.io | ||
:G13: https://jonas.github.io/tig | ||
:G14: https://miykael.github.io/nipype_tutorial/notebooks/introduction_neurodocker.html | ||
:G15: https://raw.githubusercontent.com/datalad/datalad.org/7e8e39b1/content/asciicast/seamless_nested_repos.sh | ||
:G16: https://try.github.io | ||
:G17: https://www.go-fair.org | ||
:G18: https://www.google.com | ||
:H1: https://hochschulcloud.nrw | ||
:H2: https://www.howtogeek.com/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor | ||
:I1: https://imagemagick.org | ||
:I1A: https://imagemagick.org/index.php | ||
:I1B: https://imagemagick.org/script/download.php | ||
:I2: https://imgflip.com/memesearch?q=cat | ||
:I3: https://ipython.org | ||
:L1: https://singularity.lbl.gov | ||
:L2: https://www.linuxjournal.com/content/globstar-new-bash-globbing-option | ||
:M1: https://learn.microsoft.com | ||
:M1A: https://learn.microsoft.com/en-us/windows/win32/fileio/naming-a-file | ||
:M1B: https://learn.microsoft.com/en-us/windows/wsl/install | ||
:M2: https://mit-license.org | ||
:M3: https://www.monkeyuser.com/2017/step-by-step-debugging | ||
:N1: https://neurostars.org | ||
:N2: https://the-turing-way.netlify.app | ||
:N2A: https://the-turing-way.netlify.app/reproducible-research/renv/renv-containers.html | ||
:N2B: https://the-turing-way.netlify.app/reproducible-research/testing | ||
:O1: https://osf.io | ||
:O2: https://owncloud.com | ||
:O3: https://www.openvim.com | ||
:P1: https://docs.python.org | ||
:P1A: https://docs.python.org/3/library/pdb.html#debugger-commands | ||
:P1B: https://docs.python.org/3/tutorial/classes.html | ||
:P1C: https://docs.python.org/3/tutorial/classes.html#method-objects | ||
:P1D: https://docs.python.org/3/tutorial/venv.html | ||
:P2: https://knowledge-base.psychoinformatics.de | ||
:P2A: https://knowledge-base.psychoinformatics.de/kbi/0003 | ||
:P2B: https://knowledge-base.psychoinformatics.de/kbi/0022 | ||
:P3: https://pandas.pydata.org | ||
:P4: https://phdcomics.com/comics/archive.php?comicid=1531 | ||
:P5: https://pip.pypa.io | ||
:P6: https://pypi.org | ||
:P7: https://seaborn.pydata.org | ||
:P8: https://www.python.org/downloads | ||
:S1: http://scripts.sil.org/OFL | ||
:S2: https://docs.sylabs.io | ||
:S2A: https://docs.sylabs.io/guides/3.4/user-guide/build_a_container.html | ||
:S2B: https://docs.sylabs.io/guides/3.4/user-guide/installation.html | ||
:S3: https://p7zip.sourceforge.net | ||
:S4: https://scikit-learn.org | ||
:S5: https://singularity-hub.org | ||
:S6: https://sourceforge.net/projects/linuxcommand/files/TLCL/19.01/TLCL-19.01.pdf/download | ||
:S7: https://stackoverflow.com/q/2221658/10068927 | ||
:S8: https://sylabs.io/docs | ||
:T1: https://tldp.org/LDP/Bash-Beginners-Guide/Bash-Beginners-Guide.pdf | ||
:T2: https://tug.org/fonts/licenses/GUST-FONT-LICENSE.txt | ||
:U1: https://packages.ubuntu.com/datalad | ||
:U2: https://ubuntu.com | ||
:W1: https://en.wikipedia.org | ||
:W1A: `<https://en.wikipedia.org/wiki/Cat_(Unix)>`_ | ||
:W1B: https://en.wikipedia.org/wiki/Continuous_integration | ||
:W1C: `<https://en.wikipedia.org/wiki/Docker_(software)>`_ | ||
:W1D: https://en.wikipedia.org/wiki/GNOME_Keyring | ||
:W1E: https://en.wikipedia.org/wiki/Group_identifier | ||
:W1F: https://en.wikipedia.org/wiki/Hash_function | ||
:W1G: https://en.wikipedia.org/wiki/Here_document | ||
:W1H: https://en.wikipedia.org/wiki/High-throughput_computing | ||
:W1K: https://en.wikipedia.org/wiki/Iris_flower_data_set | ||
:W1L: `<https://en.wikipedia.org/wiki/Make_(software)>`_ | ||
:W1M: https://en.wikipedia.org/wiki/Monorepo | ||
:W1N: https://en.wikipedia.org/wiki/NTFS | ||
:W1O: `<https://en.wikipedia.org/wiki/Pipeline_(Unix)>`_ | ||
:W1P: https://en.wikipedia.org/wiki/Recursive_acronym | ||
:W1Q: https://en.wikipedia.org/wiki/Sed | ||
:W1R: `<https://en.wikipedia.org/wiki/Singularity_(software)>`_ | ||
:W1S: https://en.wikipedia.org/wiki/Standard_streams | ||
:W1T: `<https://en.wikipedia.org/wiki/Standard_streams#Standard_input_(stdin)>`_ | ||
:W1U: `<https://en.wikipedia.org/wiki/Standard_streams#Standard_output_(stdout)>`_ | ||
:W1V: https://en.wikipedia.org/wiki/Superuser | ||
:W1W: https://en.wikipedia.org/wiki/Terminal_pager | ||
:W1X: https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux | ||
:X1: https://xkcd.com | ||
:X1A: https://xkcd.com/1205 | ||
:X1B: https://xkcd.com/1722 | ||
:X1C: https://xkcd.com/1833 | ||
:X1D: https://xkcd.com/2083 | ||
:X1E: https://xkcd.com/979 | ||
:Z1: https://zenodo.org |
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