Training & Collaborative Resources for Ongoing Projects

This repo consolidates various resource lists for more and less related projects.

Collaboration

I use the following resources to coordinate work with colleagues:

• Google Drive: Each project has a dedicate Google Doc with meeting agendas and near-term tasks or goals. We also compile tables, draft manuscripts and slideshows, and prepare other materials in Docs, Sheets, or other formats. No sensitive or unpublished content may be posted here.
• Zotero: Zotero is a reference manager with a web interface and a downloadable app. It facilitates shared annotations of PDFs and BibTeX exports of reference lists. Each project maintains its own Zotero Group. Each member must have a Zotero account.
• GitHub: All projects involve collaborative version control. For simplicity, i use this one service for all projects. Each member must have a GitHub account.
• Overleaf: Higher-speed collaborative LaTeX documents may be prepared here. Each collaborator will need an account.

Software

Version control

• Git
  • GitHub
  • Bitbucket

Programming languages

• The R Project for Statistical Computing
  • RStudio
  • Tidyverse
  • Tidymodels

Specialized tools

• Ripser by Ulrich Bauer
• GUDHI
• ReebGraphPairing by Junyi Tu, Mustafa Hajij, and Paul Rosen
• TDA by Brittany T. Fasy, Jisu Kim, Fabrizio Lecci, Clement Maria, David L. Millman, Vincent Rouvreau
• tdaverse by Raoul Wadhwa, Matt Piekenbrock, Cory Brunson, and several contributors

Data sets

• PhysioNet – maintains the MIMIC-IV database and its previous versions
• UCI Machine Learning Repository – lots of small-to-medium-sized data sets with associated tasks

Training

Workshops

• UF Health Center Libraries: UF librarians conduct workshops on software tools, systematic reviews, reproducible analysis, and much more; check upcoming workshops or the workshop calendar
• UF Carpentries Club: See the Events tab for upcoming workshops, or subscribe to the mailing list

Books

Methods

• Topological data analysis for genomics and evolution by Rabadán and Blumberg – a gradual introduction to topological data analysis with a focus on biological applications; check UF Libraries for PDFs

Software

• Introduction to R for Health Data Science by Matthew Sperrin – brief looks at many facets of data science, with extensive section references
• R Programming for Data Science by Roger D. Peng – a comprehensive introductory text using base R and tidyverse, ultimately geared toward programming
• R for Data Science by Hadley Wickham and Garrett Grolemund – the definitive introduction to the tidyverse package collection
• An Introduction to R by the R Core Team – a comprehensive reference text for base R with detailed explanations
• Software for Data Analysis by John Chambers – a published and more accessible variation on the previous book

Tutorials

• Git/GitHub Tutorial
• Data Camp: Modeling with tidymodels in R

Fora

In addition to journals and conferences run by professional organizations, we may also present work locally.

• University Math Society
• Undergraduate Research Symposium
• College of Medicine Research Day
• Florida Undergraduate Research Conference
• Medical Student Reseearch Day
• Journal of Undergraduate Research