OpenbyDesign TOC and tracking migration from psych-open-science to OpenByDesign
#3
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15 of 28 tasks
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I think I would probably prefer to have the web page files stored in a
separate repository, or in a gh-pages branch, rather than storing them in
the root with the source files in a subdirectory. that will help keep
things cleaner, I think.
…On Tue, Sep 8, 2020 at 4:52 PM Franklin Feingold ***@***.***> wrote:
This ticket intends to track our progress for converting
psych-open-science <https://github.com/poldrack/psych-open-science-guide>
documents into our domain-general content. The file organization is a
proposed initialization - we can move around the modular pieces later
We can store the source document under a src folder. Our naming scheme
can follow 01_introduction.md. If a section has multiple files, these
files can be stored in a folder following the same naming scheme. For
example 02_sample is the folder with 01_subsample.md and 02_subexample.md
within.
This schema makes our organization more modular and easy to fit into our
rendering solution - Jupyter Book <https://jupyterbook.org/intro.html>.
We can store the generated html files at the root. Within the file, I have
listed a proposed initial set of sections denoted by :. We can initialize
a CODEOWNERS file for community members to maintain their files of
interest.
Section 0: Introduction to the Open By Design handbook
- What is "Open Science" and why should I join?
- The components of Open Science practices
- How this book is organized
- Contributors
- License
Learning more about the Open Science community/
- Open Science resources: Blogs, Books, Courses, People/Twitter
handles, podcasts, foundational papers, talks
- Doing Open Science: Tools/Platforms, Initiatives/Collaborations,
Organizations/Centers/Labs, Societies/Conferences, Hackathons, Journals,
Funding & Grants
Section 1: Research practices (practical)
- Pre-registration: What is pre-registration, Why is pre-registration
important?, When can/should one pre-register their research?, Getting
started, Examples, FAQ, Resources
- Reproducible data analysis: Committing to reproducibility,
Prerequisities, Getting started, Advanced steps, Examples, FAQ, Resources
- Reproducible modeling: Why should I share my model?, Sharing the
model weights, Examples, FAQ, Resources
- Reproducible manuscript: Prerequisites, Getting started, Advanced
topic: Containerizing and automating your reproducible manuscript,
Examples, FAQ, Resources
- Reproducible project: Why is a reproducible project important? What
makes up a reproducible project? Checklist, Examples, FAQ, Resources
Sharing research objects beyond the text/
- Code sharing: Why should I share my code?, Prerequisities,
Readability, Distributing your work, Getting started, When you are ready to
publish your work, Examples, FAQ, Resources
- Data sharing: Why should I share my data?, Why doesn't everyone
share their data?, What are "metadata" and why are they important?, The
FAIR principles for open data, Getting started, Examples, FAQ, Resources
Section 2: Open Science infrastructure
- Computer literacy: File systems, Files, Command line, Editing text
files
- UNIX: Makefiles
- Computing languages: Python, R
- Git
- Version Control
- Collaborating with GitHub: Introduction, Repository initialization,
Project communication, Working with contributors, Tips and FAQ, Resources
- Reproducible environments: Package manager, Interactive notebooks,
Containerization
- Code testing: Types of tests
- Code reviewing: Guidelines, Checklist, Resources
- Continuous integration: Introduction, Examples
- High-Performance Computing resources: Introduction, Examples
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Russell A. Poldrack
Albert Ray Lang Professor of Psychology and Professor (by courtesy) of
Computer Science
Director, DSI Center for Open and Reproducible Science
Building 420
Stanford University
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poldrack@stanford.edu
http://www.poldracklab.org/
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sounds good! edited this issue to have the web page files pushed to the |
franklin-feingold
changed the title
psych-open-science to OpenByDesignOpenbyDesign TOC and Tracking migration from psych-open-science to OpenByDesign
franklin-feingold
changed the title
OpenbyDesign TOC and Tracking migration from psych-open-science to OpenByDesignOpenbyDesign TOC and tracking migration from psych-open-science to OpenByDesign
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My suggestion would be to restructure the book in the following way: Chapter 0: Introduction
Chapter 2: Open study conduct and reporting
Chapter 3: Other aspect of open science
alternatively we can mention in intro we will not be covering this in detail |
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posting here - perhaps may you please share what the subsections may look like? describing similar to how I did above? |
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I didn't want to add subsections initially, as I am not sure there is agreement on the current chapters -e.g. what subsections all chapters should have. I really love your idea - and would expect all to start with: What is X? Why do X? Guide to doing X. Case examples. FAQ. Additional resources. |
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that sounds good! adding a reminder note: update the TOC to reflect this consistent organization |
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UI rendering: https://dsi-cores.github.io/OpenByDesign/README.html
This ticket intends to convey our handbook organization and track our progress for converting psych-open-science documents into our domain-general content. The file organization is a proposed initialization - we can move around and link together the modular pieces after the migration is complete.
We can store the source document under a
srcfolder. Our naming scheme can follow01-introduction.md. If a section has multiple files, these files can be stored in a folder following the same naming scheme. For example02-sampleis the folder with01-subsample.mdand02-subexample.mdwithin.This schema makes our organization more modular and easy to fit into our rendering solution - Jupyter Book. We can store the generated html files on the
gh-pagesbranch. Within the file, I have listed a proposed initial set of sections denoted by:. We can initialize aCODEOWNERSfile for community members to maintain their files of interest.The handbook organizational scheme will be: Chapter -> Section -> Topic
edit 4/6: incorporated a redesign of Chapters 1, 2, and 3
Chapter 0: Introduction to the
Open By Designhandbook - addressed in #15Learning more about the Open Science community/ - addressed in #16
Chapter 1: Research practices (practical)
Sharing research objects beyond the text/
Chapter 2: Open Science infrastructure
[Edit 9/20]: Proposing a layer of organization above these sections: Computer Literacy, Programming, and Project Management. This additional layer will enhance our management of this section and focus on further extensions and development.
Computer Literacy/
Programming/
Project Management/
Chapter 3: Examples
Collection of Open Science examples. Include the previous psych examples
Open Science practices in research/
[Organized by domain]
[Open Science software and toolboxes/
[Organized by domain]
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