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The Turing Way
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Welcome
Guide for Reproducible Research
Overview
Definitions
Added Advantages
Barriers
Resources
Open Research
Open Data
Open Source Software
Open Source Hardware
Open Access
Open Notebooks
Open Scholarship
Checklist
Resources
Version Control
Version Control Workflow
Version Control and Branches
The Git Version Control Software
Git for Research Projects
Git Using the Command Line
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
License Compatibililty
Ethics-informed Licensing
Data Licenses
Hardware Licenses
Machine Learning Model Licenses
Case Studies: Choosing an ML License
Checklist
Research Data Management
Research Data
Finding Data
Data Management Plan
The FAIR Principles and Practices
Personal data management
Data Storage and Organisation
Data Organisation in Spreadsheets
Documentation and Metadata
Methods and Protocols
Electronic Lab Notebooks (ELNs)
Data Curation
Data Visualisation
Data Repositories
Sharing and Archiving Data
Data Article
Checklist
Personal Impact Stories
Resources
Reproducible Environments
Capturing Computational Environments
Package Management Systems
YAML
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
Writing Robust Code
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
Reusable Code
Overview of Code Reuse
Detailed Recommendations for Code Reuse
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 and 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
Collaborative project documentation
Reproducibility Methods
Version Control and Documentation
Sharing Your Research Work
Project Design Checklist
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
Sensitive Data Projects
Types of Sensitive Data
Personal Data
Confidential Data
Biological Data
Metadata
Combined Datasets
Managing Sensitive Data Projects
Informed consent
Data Privacy Strategies
Sharing Sensitive Data
Resources
Working on Sensitive Data Projects
Working with Trusted Research Environments
Privacy Preserving Machine Learning
Keeping Sensitive Files Secure
Sharing Your Jupyter Notebook
Removing Sensitive Data From GitHub
Further Recommendations
Data Governance
Data Governance for the Machine Learning Pipeline
BigCode Data Governance Case Study
Guide for Communication
Overview of Guide for Communication
Principles of Communicating with Wider Audiences
Communicating Accessibly
Resources and Recommendations
Open Scholarship
Open Education
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 X
Managing multiple X accounts
Research Objects in Action
Lifecycle
Implementation
Making Research Objects Citable
Steps for Making Research Objects Citable
Citing Research Objects
Software citation with CITATION.cff
Create a CITATION.cff using CFFinit
Linking Research Objects
ORCID to Collect your Research Objects
Checklists and Resources
Publishing Different Article Types
Data Papers
Methods Papers
Micropublishing
Registered Reports
Software Papers
Communications in Open Source Projects
Issue Tracking
Communication Channels
Authorship and Contributions on Academic Articles
Overview of Academic Authorship
Types of Authorship Misconduct
Discipline Specific Authorship Traditions
Large and Equitable Authorships
Tips on How to Get Authorship Right
Personal Stories - Authorship on Interdisciplinary Projects
Personal Stories - Large Collaborative Research Community
Resources
Peer Review
Peer Review
Open Peer Review
Guidance on Peer Review for a Journal
Guidance on Code Review
Resources
Binder
Zero-to-Binder
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
Organising Meetings
Organising Online Coworking Calls
Organising Conferences
Registration Forms
Template for Registration Form
Chairing Events
Participating in Events
Informal Coffee Chats
Tools for Facilitating Collaboration
Facilitating Stakeholder Engagement
Managing a New Community and Team
Guide to Planning a Community
Addressing Technical Issues
Valuing Diversity and Differences
Teamwork
Academic-Industry Collaborations
Establishing an Academic-Industry Collaboration
Community Building in an Academic-Industry Collaboration
Turing-Roche Community Activities Personal Story
Team Manual
On and Offboarding Team Members
Open Leadership in Data Science
Important Features of Leadership
Building Healthy Leadership Skills
Creating Leadership Opportunities
Personal Story from Running a Hackathon
Personal Story of Leadership by a Data Librarian
Research Infrastructure Roles
Community Managers Overview
Data Stewards Overview
Data Steward Personal Story
Data Wrangler Overview
Research Software Engineers Overview
Research Software Engineering Personal Story
Research Application Manager Overview
Research Infrastructure Developer Overview
Remote Collaboration
Pros and Cons
Guidelines for Remote Collaboration
Managing Distributed Teams
Useful Resources
Hybrid Collaboration
Challenges faced during Hybrid Collaboration
Guidelines for Hybrid Collaboration
Resources
Shared Ownership in Open Source Projects
Project Ownership
Shared Ownership Models
Challenges with Applying Ownership Models Retroactively
Nudging for a Better Default
Sustainability of Open Source Projects
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
Research Ethics for Social Data
Data Feminism
Activism for Researchers
Unionisation
Whistleblowing
Cultural change
The Environmental Impact of Digital Research
Case study - Robodebt
Case study - Google Workers
Internal Policy Advocacy
Self-Reflection
Identity and Positionality
Power and Privilege
Self-Reflection Prompts
Resources
Data-Hazards
Introduction
How To Use
Case Study
Ethical Considerations for Open Source Governance Models
Community Handbook
Code of Conduct
Code of Conduct in Detail
Incident Reporting Guideline
Enforcement Manual
Acknowledgements
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
Build the Turing Way Book locally
Contributing and Developing Chapters - Templates and Workflow
Templates
Workflow
Acknowledging Contributors
Community Members and Shared Ownership
Record of Contributions
Different Contributions and Acknowledgements
Translation and Localisation
Translation of Open Source Projects
Welcome to the Translation and Localisation Team of
The Turing Way
!
Embark on Your Localisation Journey
Your Gateway to Crowdsourced Localisation
Infrastructure
Publishing Contributors
External Link Checking
DNS
Accessibility
Event Organising
Alt text
Communication Platforms
Quick Start Guide for Slack
Slack Welcome Guide
Monthly Newsletters
A Process of Creating a newsletter
Newsletter's Style Guide
The Turing Way Newsletter Template
Book Dash Events
Application and Review Process
Book Dash Logistics
Working With an Illustrator
Participant Selection Process
Book Dash Main Event Plans
After the Book Dash
Community Coworking Calls
Background, Motivations, and Techniques
Online Collaboration Cafe
Weekly Coworking Calls
Organising coworking calls
Fireside Chat Series
Fireside Chat Planning Checklist
Fireside Chat Roles and Responsibilities
Giving a Turing Way Talk
Template Collection
Book Dash Main Shared Document
Book Dash Pre-event Onboarding
Book Dash GitHub Session
Book Dash Template for Shared Notes
Book Dash Template for Feedback
Online Collaboration Cafe Templates
Weekly Coworking Call Template
Template for Drafting Newsletters
Template for Fireside Chat Shared Notes
Afterword
Legal Disclaimer
Contributors Record
Collaborators
Sub-projects, Working Groups, Informal Initiatives
Glossary
Bibliography
Repository
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