The Turing Way
Welcome
Guide for Reproducible Research
Overview
Definitions
Added advantages
Resources
Open Research
Open Data
Open Source Software
Open Hardware
Open Access
Open Notebooks
Open Scholarship
Checklist
Resources
Version Control
General Workflow
Getting Started with Git
Git Commit Command
Retrieving and Comparing Versions
Git Branches
Merging Branches in Git
Git Commands to Work on GitHub
Summary Table of Git Commands
Version Control for Data
Personal Stories
Checklist for Version Control
Resources for Version Control
Licensing
Software Licenses
License Compatibililty
Data Licenses
Resources
Checklist
Research Data Management
Research Data
The FAIR Principles and Practices
Data Storage and Organisation
Data Organisation in Spreadsheets
Documentation and Metadata
Sharing and Archiving Data
Research Data Management Toolkits
Personal Impact Stories
Checklist
Resources
Reproducible Environments
Ways to capture computational environments
Package management systems
YAML files
Binder
Virtual machines
Containers
Checklist
Resources
BinderHub
Introduction to BinderHub
Compute Resources
Build Your Own BinderHub
Resources for BinderHub
Code quality
Code Style and Formatting
Checklist and Resources
Code Testing
General guidance for testing
Types of tests
Challenges and exceptional cases
Checklist for code testing
Resources for code testing
Code Reviewing Process
Motivation for code reviewing
Recommendations for code reviewing
Code review workflow
Checklist for code reviewing
Resources for code reviewing
Continuous Integration
Continuous integration options
Continuous integration with Travis
Best practices and recommendations
Checklist
Resources
Reproducible Research with Make
Learn "Make" by examples
Debugging Makefiles
Case Study of a Reproducible Paper
Including numerical results and tables
Resources for "Make"
Appendix
Research Compendia
Credit for Reproducible Research
Risk Assessment
Complexity and Impact of Risk Assessment
Summary of Risk Assessment
Case Studies
A Statistical Methods Manuscript
Guide for Project Design
Personas and Pathways
Persona Creation Tool
Contributor Pathways
File Naming Convention
Guide for Communication
Community Communications for Open Source Projects
Issue Tracking
Communication Channels
Further Reading
Guide for Collaboration
Collaborating on GitHub
README and Project Communication
Roadmapping
Getting Contributors
Reviewing GitHub Contributions
Checklist and resources
Managing a New Community and Team
Guide to Planning a Community
Addressing Technical Issues
Valuing Diversity and Differences
Leadership in Data Science
Personal Stories of Leadership
Remote Collaboration
Organising Remote Meetings
Guidelines for Remote Collaboration
Tools for Remote Collaboration
Organising Online Coworking Calls
Organising Remote Conferences
Chairing Remote Events
Participating in Remote Events
Managing Distributed Teams
Informal Coffee Chats
Perceived Pros and Cons
Guide for Ethical Research
Ethical Decisions in Preclinical Research
Community Handbook
Code of Conduct
Code of Conduct in Detail
Incident Reporting Guideline
Enforcement Manual
Acnowledgements
Style Guide
Citing and Referencing External Resources
Cross-Referencing Sections and Chapters
Using Figures
Glossary, Special Blocks and More Styling
Maintaining Consistency
Formatting
Structure
Language
Acknowledging Contributors
Community Members and Shared Ownership
Record of Contributions
Different Contributions and Acknowledgements
Monthly Newsletters
A Process of Creating a newsletter
Newsletter's Style Guide
The Turing Way Newsletter Template
Book Dash Events
Application and Review Process
Selection and Preparation Process
The Book Dash Main Event Plans
Community Coworking Calls
Background, Motivations, and Techniques
Online Collaboration Cafe
Weekly Coworking Calls
Organising coworking calls
Template Collection
Book Dash Issue Template for Planning
Book Dash Template for Pre-event Call
Book Dash Template for Shared Notes
Book Dash Template for Feedback
Online Collaboration Cafe Templates
Weekly Coworking Call Template
Template for Drafting Newsletters
Afterword
Glossary
Bibliography
Contributors Record
repository
open issue
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
Y
A
Acceptance Testing
Add
Authors
B
Binder
Binderhub
Binderize
Branch
Bug
Build
C
Checkout
Citizen Science
Clone
Code Coverage
Code of Conduct
Code Review
Commit
Commit Message
Communication Channel
Community Member
Computational Environment
Conda
Container
Continuous Delivery
Continuous Deployment
Continuous Integration
Contributing Guidelines
Contributors
D
Data repository
Digital Object Identifier
DMP
Docker Container
Docker Image
Docker Registry
Dockerfile
E
End to End Test
Equitable, Diverse and Inclusive Practices
F
FAIR
G
Generalisable
Git
Github
GitLab
H
Head
Helm
Human Readable
I
Image
Integration Testing
Issue Tracking
Issues
J
Job
JupyterHub
K
Kubernetes
L
License
M
Machine Readable
Main
Maintainers
Makefile
Merge
Merge Conflict
Metadata
Mock Test
O
Open Access
Open Access publishing (gratis)
Open Access Publishing (libre)
Open data
Open Educational Resources
Open License
Open Notebooks
Open Project
Open Scholarship
Open Source Hardware
Open Source Software
ORCID
Owner
P
Package Management System
Pattern
Persistent Identifier
Persona
Persona Canvas
Phony Target
Power Users
Prerequisite
Project Design
Pull Request
Push
R
RDM
README
Recipe
Regression Test
Rendered Output
Replicable
repo2docker
Repository
Reproducible
Research Compendia
Research Data Management
Research Ethics
Review
Risk Assessment
Risk Matrix
Roadmapping
Robust
Rule
Runtime Test
S
Self Archiving
SHA
Smoke Testing
Staged
Stochastic Code
Syntax
System Testing
T
Target
Test Driven Development
Test Stub
Test Suite
Testing Framework
Travis
U
Unit
Unit Testing
V
Virtual Machine
Y
YAML