UCSF Guides: Reproducible Data Management: Organize and Document Data

Organizing your Research Project

Reproducible research depends on having good systems for organizing and documenting your research. These resources provide recommendations for setting up and maintaining well-organized projects.

Foundational Practices of Research Data Management
Very practical article covering best practices for research data organization, versioning, retention and storage.
A Quick Guide to Organizing Computational Biology Projects
This is a great overview of how to organize your files, keep a lab notebook, document experiments and use version control
Nine Simple Ways to Make it Easier to (Re)use Your Data
Although this comes from the field of ecology it contains great tips for making your data more understandable and easier to analyze.
File Naming Worksheet
This worksheet from Caltech Library walks you through the process of creating file names for a batch of files.

Data Standards and Documentation Tools

There are a lot of things to document as part of your research! These resources give you some ideas of what to document (reporting guidelines) and how to document them (Fairsharing metadata schemas and RRIDs) as well as how to design your research so that your data is standardized from the beginning (CDEs)

Reporting Guidelines - EQUATOR Network
Reporting guidelines are a useful tool for writing papers and documenting your research as they give you a checklist of things you need to report out in your paper (and therefore should be carefully documenting). There are guidelines for randomized trials, observational studies, qualitative research and more!
NIH CDE Repository
This repository contains Common Data Elements (CDEs) for NIH funded studies. Using these common data elements allows researchers to standardize their work and more easily compare data across studies.
FAIRsharing
A database of data and metadata standards. Useful to see if there is a data standard relevant to your area of research.
Resource Identification Portal
This portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource like a plasmid, organism, cell line or antibody so that you can correctly reference it in a paper.

Documenting Methods and Code

UCSF Guidance for Electronic and Paper Lab Notebooks
This guidance includes recommended practices for notebook organization and documentation, including considerations for maintaining digital and physical notes. The document also summarizes UCSF policies for lab notebook ownership and retention.
Protocols.io
A website for creating, organizing, and publishing research protocols. UCSF researchers have access to free premium accounts.
Open Science Framework
A free, open-source tool from the Open Science Framework designed to help researchers manage and archive their research, privately and publicly
Jupyter Notebooks
These interactive online notebooks combine live code with narrative text. Perfect for documenting computational experiments
Methods and Protocol Resources
This guide from the Library includes links to several online resources and journals that publish research protocols

Version Control

A Quick Introduction to Version Control with Git and GitHub
Heard about GitHub but not sure how it works? This article from PLoS Computational Biology walks you through the process of using Git and GitHub to track different versions of your code and data.
GitHub Cheat Sheets
One page cheat sheet with all the essential GitHub commands