handbook/docs/perma/book-intro-v1.rst

.. _book-intro-v1:

Datalad --- An Introduction to Research Data Management
=======================================================

This page is the online companion to the paperback book
published in 2023, available from a book store near you
(ISBN 979-8857037973), or from any amazon site (e.g.,
`US <https://www.amazon.com/dp/B0CPDB4YMY>`_ or
`EU <https://amzn.eu/d/e6A7nAO>`_).

.. image:: book-intro-v1/intro-v1-cover.jpg
   :align: center
   :target: ../_images/intro-v1-cover.jpg

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.

.. _book-intro-v1-urls:

Errata
------

Presently, there are no known issues in the published book.

If you discovered one, please report it via the `Handbook's issue tracker
<https://github.com/datalad-handbook/book/issues/new/choose>`__. Thank you!

Hyperlink URL index
-------------------

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.

.. container:: book-v1-url-index

   :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


Sources
-------

The PDF version of the published book is built from customized LaTeX sources,
originally generated with Sphinx. The sources are available from
https://github.com/datalad-handbook/book-datalad-intro