The Turing Way
Welcome
Guide for Reproducible Research
Overview
Definitions
Added Advantages
Barriers
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
Interactive, Visual Git
Git Commands to Work on GitHub
Summary Table of Git Commands
Version Control for Data
Personal Stories
Checklist
Resources
Licensing
Software Licenses
License Compatibililty
Data Licenses
Checklist
Research Data Management
Research Data
Data Management Plan
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
Capturing Computational Environments
Package Management Systems
YAML
Binder
Virtual Machines
Containers
Resources and Checklist
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
Overview of Testing Types
Smoke Testing
Unit Testing
Integration Testing
System Testing
Acceptance and Regression Testing
Runtime Testing
Test Driven Development
Challenges and Exceptional Cases
Checklist for Code Testing
Further Recommendations
Code Reviewing Process
Motivation for code reviewing
Recommendations for code reviewing
Code review workflow
Checklist for code reviewing
Resources for code reviewing
Continuous Integration (CI)
Intro to Continuous integration (CI)
Getting started with GitHub actions
Building a Block of a Github actions
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
Risk Assessment
Complexity and Impact of Risk Assessment
Summary of Risk Assessment
Case Studies
A Statistical Methods Manuscript
Guide for Project Design
Overview of Project Design
Planning for Project Design
Communication and Collaboration
Reproducibility Methods
Version Control and Documentation
Sharing Your Research Work
Creating Project Repositories
Landing Page - README File
Roadmapping
Contributors and Communication Pathways
Participation Guidelines
Advanced Structure for Data Analysis
Further Recommendations
Personas and Pathways
Persona Creation Tool
Contributor Pathways
File Naming Convention
Code Styling and Linting
Guidelines for Code Styling
Writing Human Readable Code
Code Styling Tools
Guide for Communication
Overview of Guide for Communication
Principles of Communicating with Wider Audiences
Communicating Accessibly
Resources and Recommendations
Blogs for Research Communication
Building a Webpage for Blogs
Personal stories - Blogs
Lay Summaries
Personal Stories - Lay summaries
Podcasts for Research Communication
Personal Stories - Podcasts
Presenting Posters and Conference Talks
Presenting at Remote Events
Personal stories - Presenting Outside of Your Discipline
Social Media for Research Communications
Tips for starting with twitter
Managing multiple twitter accounts
Making Research Objects Citable
Steps for Making Research Objects Citable
Citing Research Objects
Linking Research Objects
ORCID to Collect your Research Objects
Checklists and Resources
Communications in Open Source Projects
Issue Tracking
Communication Channels
Guide for Collaboration
Getting Started With GitHub
Motivation for Using GitHub
First steps on Github
Using more Github features
Advanced Github features
Maintainers and Reviewers on GitHub
Project Maintenance
Ownership and Permissions
Reviewing Contributions
Merging Contributions
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
Shared Ownership in Open Source Projects
Project Ownership
Shared Ownership Models
Challenges with Applying Ownership Models Retroactively
Nudging for a Better Default
Guide for Ethical Research
Introduction to Research Ethics
Research Ethics Committees Workflows
Ethical Decisions in Preclinical Research
Law, Policy and Human Rights in Ethics
Ethics and law
Human rights
Further Recommendations
Activism for Researchers
Unionisation
Whistleblowing
Case study - Robodebt
Case study - Google Workers
Internal Policy Advocacy
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
Custom Styling
Maintaining Consistency
Formatting
Structure
Language
Contributing and Developing Chapters - Templates and Workflow
Templates
Workflow
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
Legal Disclaimer
Glossary
Bibliography
Record of Contributions
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Bibliography
ΒΆ
This file consist of a complete bibliography for this book sorted alphabetically
Glossary
Record of Contributions
