Open Science

I am passionate about open science and FAIR data, and try to align my scientific work with collaborative practices that are reproducible, transparent, inclusive, and kind (the Openscapes Approach). My graduate thesis involves developing an open source R package (morphmat) and I am always excited to contribute to open source software and connect with others who frequently work on similar projects.

My engagement with open science

• Volunteer on the fundraising committee for the Society for Open, Reliable, and Transparent Ecology and Evolutionary biology (SORTEE)
• Data & Code Editor for PCI Ecology and PCI Evolutionary Biology (part of the Peer Community In community)
• Peer reviewer for the Journal of Open Source Software, a diamond open access journal for research software packages

Open Science Resources

• The Turing Way comprehensive online book/guide
• Opensciency - A core open science curriculum
• Good Enough Practices in Scientific Computing Carpentries curriculum 
• ESIIL learning portal: Open Reproducible Science 
  • Tools for Open and Reproducible Science 
  • How To Organize Your Project: Best Practices for Open Reproducible Science
• Openscapes Champions Lesson Series; https://openscapes.org/resources 
• NMFS Open Science Resource Book
• SORTEE resources
  • SORTEE Workshop and Webinar series resources on OSF 
  • Reproducible Environments in R slides
• OER Commons; Open Scholarship Knowledge Base
• Our Curriculum | Open Climate Science for Agriculture 
• EU Open Source Solutions Catalogue  
• Teaching Open Science: Slide Set | ZBW MediaTalk 
• Easing Into Open Science: A Guide for Graduate Students and Their Advisors
• CyVerse Foundational Open Science Skills curriculum/roadmap
• Toolbox - Open Science Center - LMU Munich 
• Research Data Services - University of Iowa Libraries 
• Sherry Lake’s Zotero library of data management resources

FAIR data & data management

FAIR data: https://www.go-fair.org/fair-principles/ 

• ESIP Biological Data Cluster (BDS) Primer Guide
• How to make your data FAIR | OpenAIRE 
• The FAIR principles - Research Data Management Support - Utrecht University 
• The FAIR Cookbook
• Preparing FAIR data for reuse and reproducibility (includes FAIR checklist)
• FAIR Cheat Sheets: to publish your research data and software FAIR
• Nine simple ways to make it easier to (re)use your data
• Eight Principles of Good Data Management
• Australian Research Data Hub - Resources
  • Making Data FAIR | ARDC 
  • https://ardc.edu.au/resource/fair-data-self-assessment-tool/ 
• Data Mobilization/Darwin Core workshop (MBON)
• Interoperable - FAIR Data - LibGuides at UCD Library 
• FAIR in ML, AI-ready data, & Reproducibility
• EarthCube FAIR training materials
• FAIR²
• Reporting Summary | Nature 
• Research data life cycle - ETH Zurich 
• DataONE Data Management Skillbuilding Hub
• Supporting Scientific Data
• Research Data Documentation Methods handout (Briney, 2022)
• https://fairsharing.org/
• https://infoguides.pepperdine.edu/datacuration
• Research data management - UK Data Service 
• Data versioning
  • Versioning - UK Data Service 
  • Recommendations on Data Versioning 
• Metadata, data dictionaries, & READMEs
  • Documentation & metadata | MIT Data management 
  • Metadata - Research Data Management - LibGuides at UCD Library
  • Documentation and Metadata - The Turing Way
  • Metadata Creation | U.S. Geological Survey 
  • UNC Libraries Metadata for Data Management: Basic Elements 
  • Key Concepts - Metadata Basics - LibGuides at University of Texas at Austin 
  • Research Guides at University of California Irvine 
    • Describing Data - Research Data Management 
  • Tabular strategies for metadata in ecology, evolution, and the environmental sciences 
  • Dryad What’s in a README? Why your README matters
  • UC Irvine Libraries Research Data Management: README Files 
  • Metadata - Research Data Services - University of Iowa Libraries 
    • Spreadsheet Data Structure 
  • University of Helsinki Making a research project understandable - Guide for data documentation
  • Standards
    • Dublin Core Metadata Generator 
    • Metadata Standards in the Geosciences 
    • Controlled Vocabulary and Taxonomies 
    • Pepperdine Managing Data Sets: Metadata Standards 
    • Data Standards | U.S. Geological Survey 
    • UNC Libraries Metadata for Data Management: Standards/Schema 
      • Controlled Vocabularies 
    • LibGuides at University of Texas at Austin
      • Cross-Disciplinary Standards 
      • Domain-Specific Standards  
      • Controlled Vocabularies
    • Research Data Alliance Metadata Standards Catalog & tool index
  • Harvard Data Management
    • Data Dictionary
    • README Files
  • Cornell Data Services
    • eCommons: Cornell’s Digital Repository: Metadata tips 
    • Writing READMEs for Research Data 
    • Writing READMEs for Research Code & Software 
    • https://cornell.app.box.com/v/ReadmeTemplate
  • Data dictionaries
    • OSF How to Make a Data Dictionary
    • 10. Creating data/variable dictionary (FAIR Cookbook) 
    • Data Dictionaries | U.S. Geological Survey 
    • https://library.ucmerced.edu/data-dictionaries 
• Repositories
  • Generalist Repository Comparison Chart 
  • Repository of Research Data Repositories https://www.re3data.org/ 
  • https://geo-data-support.sites.uu.nl/open-science-open-data/open-repositories/ 
  • https://oad.simmons.edu/oadwiki/Data_repositories Organized by subject
  • Geo data - support for researchers | Repository Comparison 
  • Best Practices for Data Submission in Generalist Repositories: A Checklist
  • How to Archive Your Work FAIRly on Zenodo
• Data papers
  • https://www.gbif.org/data-papers 
  • Sharing your data through a Data Article - The Turing Way
  • Data Papers - The Turing Way 
• Sensitive data
  • J-Pal Guide To De-Identifying Data
• Data ethics
  • Local Contexts
  • CARE Principles for Indigenous Data Governance
  • Data Ethics in the Participatory Sciences Toolkit
  • Data Co-Ownership Template 
  • Data ownership & sharing decision tree 
  • De-identification when making datasets FAIR: Two worked examples from the behavioral and social sciences

Data management (plans)

• Research Data Management - The Turing Way 
  • Data Management Resources - The Turing Way 
• Primer on Data Management: What you always wanted to know 
• Ten Simple Rules for Creating a Good Data Management Plan
• MIT OpenCourseWare Data Management
  • Write a data management plan | MIT
• Guidelines for Effective Data Management Plans
• UC Irvine Libraries Data Management Plans 
• Data Management Plan Resources and Examples (ICPSR)
• Example Plans (University of Minnesota)
• Management of NOAA Data & Information (NAO 212-15B)
  • NOAA Data Management Plan template
  • Guidelines for DMPs: Templates and Examples for the NOAA Restoration Center 
  • NOAA OCM Data Management and Sharing Plan Review Form 
• OER Commons Data Management course 
• Cornell Writing a data management (and sharing) plan 
• Pepperdine Managing Data Sets: Writing a Data Management Plan 
• Data Management Plans - Research Guides at University of Michigan Library 
  • Data Management Plan Resources and Examples (UMich) 
• British Ecological Society Guide to Data Management 
• Research Data Management cheat sheets 
• Creating a data management plan (DMP) document - OSF Support 
• Data Management in Large-Scale Education Research (book, Crystal Lewis)
• UK Data Service Data management checklist 
• https://resourcelibrary.openenvironmentaldata.org/ 
  • Open Env. Data Project - Community Data Playbook 
• Dryad’s Quickstart Guide to Data Sharing simple infographic
• Data management planning - Research Data Management Support - Utrecht University 
• https://esipfed.github.io/esipDMP/ 
• Project & file organization
  • Setting up a FAIR and reproducible project - Heidi Seibold
  • TIER Protocol 4.0 | Project TIER 
  • File Naming & Organization - University of Iowa Libraries 
  • File Naming Conventions | Harvard Data Management 
  • Organize Files and Data | U.S. Geological Survey
  • File management – Cornell Data Services 
  • Organizing Data - Research Guides at University of California Irvine 
  • MIT Libraries Organize your files | Data management
  • Generating file tree diagrams
    • tree.nathanfriend.com: ASCII folder structure diagrams
    • Project Tree Generator: generate a file tree from a GitHub repository URL
    • Tree Maker: creates file trees using Markdown

Ecological Metadata Language (EML)

• EML Specification
• Read and Write Ecological Metadata Language Files • EML (rOpenSci)
  • EML R package overview • LivingNorwayR 
• Understand the EML schema | NCEAS Data Team Reference Guide 
• Creating Metadata for Publication | EML 
• Standard Units for EML 2.2.0 

Computational reproducibility

• Checklist: https://fairerdata.github.io/FAIRER-Aware-REPRODUCIBILITY-Assessment/ 
• British Ecological Society A Guide to Reproducible Code in Ecology and Evolution
• Building reproducible analytical pipelines with R (book by Bruno Rodrigues, 2023)
• NMFS Open Science Best Coding Practices in R
• https://www.repro4everyone.org/resources 
• CRAN Task View: Reproducible Research 
• Ecological Forecasting Initiative Reproducible Forecasting Workflows
• Course: Reproducible Research in Computational Ecology
• Reproducible Research Data & Project Management in R book/course
• TADA (Transferable, Accessible, Documented and Annotated): Simple guidelines to improve code sharing
• Readable, Reliable, Reusable: A Guide to Clean R Code (Jacci Ziebert)
• Example of code appendix for paper (Heiss)
• Documenting Your Code - Research Data Services - University of Iowa Libraries 
• Code review
  • GitHub - OxfordCodeReviewNet/forum 
  • codecheck 
  • GitHub - SORTEE/peer-code-review / Peer Code Review - SORTEE 
  • A checklist template for R code review
• Docker
  • R Docker tutorial by ropenscilabs
  • An Introduction to Docker for R Users - Colin Fay 
  • Docker Curriculum 
  • Rocker Project 

Git/GitHub

• ​​Happy Git and GitHub for the useR (book) 
• GitHub Skills 
• Practical R+Git Workflow materials (NMFS Open Science)
• GitHub Good Practices (NMFS-OpenSci) mostly NOAA-specific
• NOAA Fisheries Integrated Toolbox GitHub Resources

Organizations: Open science, synthesis research, etc.

• National Socio-Environmental Synthesis Center (SESYNC) Resources
• Society for Open, Reliable, & Transparent Ecology & Evolutionary Biology (SORTEE)
• Center for Open Science
  • Open Science Framework (OSF)
• FORCE11
• Research Data Alliance
• Make Data Count 
• The Dataverse Project
• Open Source Hardware Association (OSHWA)
• Gathering for Open Science Hardware (GOSH)
• CERN Open Science
• Open Environmental Data Project
  • Socio-Environmental Knowledge Commons (SEEKCommons) 
    • Zotero Library
• ASU Biodiversity Knowledge Integration Center
• USGS Science Analytics and Synthesis (SAS) Program
• Biodiversity Collections Network
• Climate Informatics
• Earth Science Information Partners (ESIP)
• Global Sustainability Coalition for Open Science Services (SCOSS)
• Center for Scientific Collaboration and Community Engagement 
• Open Modeling Foundation 

Open access publishing

• DAFNEE, a Database of Academia Friendly jourNals in Ecology and Evolution
• Open Access Button
• https://guides.lib.uiowa.edu/open 

• Article funding
  • Springer Funding for Open Access Articles
  • AMS: Open Access Funding 
  • OA publication funds - Open Access Directory 
  • The Limnology and Oceanography Letters Early Career Publication Honor
  • simon.net.nz APCs | How much did it cost to publish in that journal? 
  • PLOS journals institutional agreements
    • PLOS Publication Fee Assistance (PFA) program
  • Cambridge open access waivers and discounts 
  • Free Journal Network current member journals 
  • BES APC Waivers and Discounts 
  • https://publications.copernicus.org/for_authors/financial_support.html 
  • List of journals that don’t suck – Mario Angst 
  • https://freejournals.org/current-member-journals/ 
  • Journals – MathOA
• Books
  • Funding open access books | Open science | Springer Nature 
  • List of Funding Sources for Open Access Books
  • Publishers of OA books - Open Access Directory 
  • Funds for Open Access Scholarly Books 
  • https://sloan.org/programs/public-understanding/books 
• Registered Reports
  • COS | Registered Reports 
  • List of PCI RR-friendly Journals 

For statistics and coding-related links, see my more general Resources list