poldrack
commented
3 years ago 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 notifications@github.com 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 Stanford, CA 94305
poldrack@stanford.edu http://www.poldracklab.org/
franklin-feingold
MarioMalicki
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 https://github.com/DSI-CORES/OpenByDesign/pull/15Learning more about the Open Science community/ - addressed in https://github.com/DSI-CORES/OpenByDesign/pull/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]