233 lines
11 KiB
ReStructuredText
233 lines
11 KiB
ReStructuredText
.. _book-intro-v1:
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Datalad --- An Introduction to Research Data Management
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=======================================================
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This page is the online companion to the paperback book
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published in 2023, available from a book store near you
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(ISBN 979-8857037973), or from any amazon site (e.g.,
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`US <https://www.amazon.com/dp/B0CPDB4YMY>`_ or
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`EU <https://amzn.eu/d/e6A7nAO>`_).
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.. image:: book-intro-v1/intro-v1-cover.jpg
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:align: center
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:target: ../_images/intro-v1-cover.jpg
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The book contains almost 200 references to online resources, and describes a
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continuously evolving software ecosystem. In order to maximize the longevity
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of the book, this page provides updates to references and content that are no
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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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------
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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
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<https://github.com/datalad-handbook/book/issues/new/choose>`__. Thank you!
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Hyperlink URL index
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-------------------
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The book's appendix lists URL references to online resources using two or three
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character alphanumeric codes. The following lists maps these codes to
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an up-to-date URL.
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.. container:: book-v1-url-index
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:71: https://7-zip.org
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:A1: https://apps.apple.com/us/app/xcode/id497799835
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:A2: https://aws.amazon.com
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:A2A: https://aws.amazon.com/ecr
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:A2B: https://aws.amazon.com/s3
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:A3: https://www.appveyor.com
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:B1: https://git-annex.branchable.com
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:B1A: https://git-annex.branchable.com/backends
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:B1B: https://git-annex.branchable.com/design/adjusted_branches
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:B1C: https://git-annex.branchable.com/git-annex
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:B1D: https://git-annex.branchable.com/git-annex-adjust
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:B1E: https://git-annex.branchable.com/git-annex-migrate
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:B1F: https://git-annex.branchable.com/git-annex-numcopies
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:B1G: https://git-annex.branchable.com/git-annex-uninit
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:B1H: https://git-annex.branchable.com/git-annex-wanted
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:B1K: https://git-annex.branchable.com/install/rpm_standalone
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:B1L: https://git-annex.branchable.com/internals/key_format
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:B1M: https://git-annex.branchable.com/projects/datalad/bugs-done/Windows__58___substantial_per-file_cost_for___96__add__96__
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:B1N: https://git-annex.branchable.com/special_remotes
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:B1O: https://git-annex.branchable.com/tips/largefiles
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:B1P: https://git-annex.branchable.com/tips/owncloudannex
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:B1Q: https://git-annex.branchable.com/tips/using_Amazon_Glacier
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:B1R: https://git-annex.branchable.com/tips/using_Google_Cloud_Storage
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:B1S: https://git-annex.branchable.com/tips/using_box.com_as_a_special_remote
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:B2: https://bitbucket.org
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:B3: https://brew.sh
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:C1: http://creativecommons.org/publicdomain/zero/1.0
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:C2: https://creativecommons.org
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:C2A: https://creativecommons.org/licenses/by-sa/4.0
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:C2B: https://creativecommons.org/licenses/by/4.0/
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:C2C: https://creativecommons.org/public-domain/cc0/
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:C3: https://docs.conda.io
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:C3A: https://docs.conda.io/miniconda.html
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:C3B: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html
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:D1: https://docs.datalad.org
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:D1A: https://docs.datalad.org/en/latest/generated/datalad.config.html
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:D1B: https://docs.datalad.org/en/latest/generated/man/datalad-push.html
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:D1C: https://docs.datalad.org/en/latest/generated/man/datalad-status.html
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:D1D: https://docs.datalad.org/en/latest/modref.html
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:D1E: https://docs.datalad.org/projects/container
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:D1F: https://docs.datalad.org/projects/gooey
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:D1G: https://docs.datalad.org/projects/osf
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:D3: https://datasets.datalad.org
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:D4: https://datalad.org
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:D5: https://docs.docker.com/desktop/install/windows-install/
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:D6: https://hub.docker.com
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:D7: https://neuro.debian.net
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:D7A: https://neuro.debian.net/install_pkg.html?p=datalad
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:D7B: https://neuro.debian.net/pkgs/datalad.html
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:D8: https://www.debian.org/index.en.html
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:D9: https://www.docker.com/get-started
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:F1: https://f1000research.com/posters/7-1965
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:F2: https://figshare.com
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:G1: https://git-scm.com
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:G1A: https://git-scm.com/book/en/v2
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:G1B: https://git-scm.com/book/en/v2/Customizing-Git-Git-Configuration
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:G1C: https://git-scm.com/book/en/v2/Git-Internals-Environment-Variables
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:G1D: https://git-scm.com/book/en/v2/Git-Internals-Git-References
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:G1E: https://git-scm.com/book/en/v2/Git-Internals-The-Refspec
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:G1F: https://git-scm.com/book/en/v2/Git-Tools-Rewriting-History
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:G1G: https://git-scm.com/book/en/v2/Git-on-the-Server-Getting-Git-on-a-Server
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:G1H: https://git-scm.com/docs/git-cat-file
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:G1K: https://git-scm.com/docs/git-config
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:G1L: https://git-scm.com/docs/git-config#Documentation/git-config.txt-corefileMode
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:G1M: https://git-scm.com/docs/git-push#Documentation/git-push.txt---force
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:G1N: https://git-scm.com/docs/git-reflog
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:G1O: https://git-scm.com/download/win
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:G2: https://github.com
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:G2A: https://github.com/ReproNim/neurodocker
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:G2B: https://github.com/andrewringler/git-annex-turtle
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:G2C: https://github.com/datalad-datasets/bmmr-t1w-250um
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:G2D: https://github.com/datalad-datasets/longnow-podcasts
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:G2E: https://github.com/datalad-handbook/DataLad-101
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:G2F: https://github.com/datalad-handbook/book/issues/new
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:G2G: https://github.com/datalad-handbook/midterm_project
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:G2H: https://github.com/datalad-handbook/repro-paper-sketch
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:G2K: https://github.com/datalad-handbook/resources
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:G2L: https://github.com/datalad/datalad-installer
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:G2M: https://github.com/myyoda/talk-principles
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:G2N: https://github.com/newren/git-filter-repo
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:G2O: https://github.com/psychoinformatics-de/studyforrest-data-phase2
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:G2P: https://github.com/settings/tokens
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:G2Q: https://github.com/swaroopch/byte-of-python/releases/download/vadb91fc6fce27c58e3f931f5861806d3ccd1054c/byte-of-python.pdf
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:G3: https://docs.github.com
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:G3A: https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent
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:G3B: https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens
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:G3C: https://docs.github.com/en/get-started/getting-started-with-git/about-remote-repositories
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:G3D: https://docs.github.com/en/get-started/quickstart/fork-a-repo
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:G3E: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/addressing-merge-conflicts/resolving-a-merge-conflict-using-the-command-line
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:G3F: https://docs.github.com/en/repositories/working-with-files/managing-large-files/about-large-files-on-github
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:G4: https://github.blog/2015-02-06-git-2-3-has-been-released
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:G5: https://gin.g-node.org/G-Node/Info/wiki
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:G6: https://www.gnu.org
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:G6A: https://www.gnu.org/savannah-checkouts/gnu/bash/manual/bash.html#Pattern-Matching
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:G6B: https://www.gnu.org/software/sed/manual/sed.html
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:G7: https://about.gitea.com
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:G8: https://about.gitlab.com
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:G9: https://developer.github.com/changes/2020-02-14-deprecating-password-auth
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:G10: https://drive.google.com/drive/my-drive
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:G11: https://gist.github.com/netj/8836201
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:G12: https://gogs.io
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:G13: https://jonas.github.io/tig
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:G14: https://miykael.github.io/nipype_tutorial/notebooks/introduction_neurodocker.html
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:G15: https://raw.githubusercontent.com/datalad/datalad.org/7e8e39b1/content/asciicast/seamless_nested_repos.sh
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:G16: https://try.github.io
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:G17: https://www.go-fair.org
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:G18: https://www.google.com
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:H1: https://hochschulcloud.nrw
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:H2: https://www.howtogeek.com/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor
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:I1: https://imagemagick.org
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:I1A: https://imagemagick.org/index.php
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:I1B: https://imagemagick.org/script/download.php
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:I2: https://imgflip.com/memesearch?q=cat
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:I3: https://ipython.org
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:L1: https://singularity.lbl.gov
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:L2: https://www.linuxjournal.com/content/globstar-new-bash-globbing-option
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:M1: https://learn.microsoft.com
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:M1A: https://learn.microsoft.com/en-us/windows/win32/fileio/naming-a-file
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:M1B: https://learn.microsoft.com/en-us/windows/wsl/install
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:M2: https://mit-license.org
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:M3: https://www.monkeyuser.com/2017/step-by-step-debugging
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:N1: https://neurostars.org
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:N2: https://the-turing-way.netlify.app
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:N2A: https://the-turing-way.netlify.app/reproducible-research/renv/renv-containers.html
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:N2B: https://the-turing-way.netlify.app/reproducible-research/testing
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:O1: https://osf.io
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:O2: https://owncloud.com
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:O3: https://www.openvim.com
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:P1: https://docs.python.org
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:P1A: https://docs.python.org/3/library/pdb.html#debugger-commands
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:P1B: https://docs.python.org/3/tutorial/classes.html
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:P1C: https://docs.python.org/3/tutorial/classes.html#method-objects
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:P1D: https://docs.python.org/3/tutorial/venv.html
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:P2: https://knowledge-base.psychoinformatics.de
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:P2A: https://knowledge-base.psychoinformatics.de/kbi/0003
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:P2B: https://knowledge-base.psychoinformatics.de/kbi/0022
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:P3: https://pandas.pydata.org
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:P4: https://phdcomics.com/comics/archive.php?comicid=1531
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:P5: https://pip.pypa.io
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:P6: https://pypi.org
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:P7: https://seaborn.pydata.org
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:P8: https://www.python.org/downloads
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:S1: http://scripts.sil.org/OFL
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:S2: https://docs.sylabs.io
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:S2A: https://docs.sylabs.io/guides/3.4/user-guide/build_a_container.html
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:S2B: https://docs.sylabs.io/guides/3.4/user-guide/installation.html
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:S3: https://p7zip.sourceforge.net
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:S4: https://scikit-learn.org
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:S5: https://singularity-hub.org
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:S6: https://sourceforge.net/projects/linuxcommand/files/TLCL/19.01/TLCL-19.01.pdf/download
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:S7: https://stackoverflow.com/q/2221658/10068927
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:S8: https://sylabs.io/docs
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:T1: https://tldp.org/LDP/Bash-Beginners-Guide/Bash-Beginners-Guide.pdf
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:T2: https://tug.org/fonts/licenses/GUST-FONT-LICENSE.txt
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:U1: https://packages.ubuntu.com/datalad
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:U2: https://ubuntu.com
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:W1: https://en.wikipedia.org
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:W1A: `<https://en.wikipedia.org/wiki/Cat_(Unix)>`_
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:W1B: https://en.wikipedia.org/wiki/Continuous_integration
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:W1C: `<https://en.wikipedia.org/wiki/Docker_(software)>`_
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:W1D: https://en.wikipedia.org/wiki/GNOME_Keyring
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:W1E: https://en.wikipedia.org/wiki/Group_identifier
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:W1F: https://en.wikipedia.org/wiki/Hash_function
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:W1G: https://en.wikipedia.org/wiki/Here_document
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:W1H: https://en.wikipedia.org/wiki/High-throughput_computing
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:W1K: https://en.wikipedia.org/wiki/Iris_flower_data_set
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:W1L: `<https://en.wikipedia.org/wiki/Make_(software)>`_
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:W1M: https://en.wikipedia.org/wiki/Monorepo
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:W1N: https://en.wikipedia.org/wiki/NTFS
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:W1O: `<https://en.wikipedia.org/wiki/Pipeline_(Unix)>`_
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:W1P: https://en.wikipedia.org/wiki/Recursive_acronym
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:W1Q: https://en.wikipedia.org/wiki/Sed
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:W1R: `<https://en.wikipedia.org/wiki/Singularity_(software)>`_
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:W1S: https://en.wikipedia.org/wiki/Standard_streams
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:W1T: `<https://en.wikipedia.org/wiki/Standard_streams#Standard_input_(stdin)>`_
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:W1U: `<https://en.wikipedia.org/wiki/Standard_streams#Standard_output_(stdout)>`_
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:W1V: https://en.wikipedia.org/wiki/Superuser
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:W1W: https://en.wikipedia.org/wiki/Terminal_pager
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:W1X: https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux
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:X1: https://xkcd.com
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:X1A: https://xkcd.com/1205
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:X1B: https://xkcd.com/1722
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:X1C: https://xkcd.com/1833
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:X1D: https://xkcd.com/2083
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:X1E: https://xkcd.com/979
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:Z1: https://zenodo.org
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Sources
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-------
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The PDF version of the published book is built from customized LaTeX sources,
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originally generated with Sphinx. The sources are available from
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https://github.com/datalad-handbook/book-datalad-intro
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