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 ManagementVery practical article covering best practices for research data organization, versioning, retention and storage.
- A Quick Guide to Organizing Computational Biology ProjectsThis 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 DataAlthough this comes from the field of ecology it contains great tips for making your data more understandable and easier to analyze.
- File Naming WorksheetThis worksheet from Caltech Library walks you through the process of creating file names for a batch of files.
Data and Documentation Standards
There are a lot of things to document as part of your research! If there is a metadata standard for your discipline that is a great place to start as it will tell you what to document and how. If you know what repository you will be using for your data check and see if they recommend a data or metadata standard. Read more about metadata standards and see if there is one relevant to you below.
- NIDDK Metadata Standards Cheat SheetThis guide from NIDDK lists several common data and metadata standards for biomedical research including clinical, genomics, imaging, proteomics and more
- Metadata Standards CatalogCatalog for finding metadata documentation standards for your discipline.
- Guide to writing "Readme" style metadataGuide to writing "readme" style metadata when there isn't a metadata standard for your discipline.
- NIH CDE RepositoryThis 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.
- Create a Survey CodebookGuide to creating a detailed survey codebook using the DDI metadata documentation standard
- FAIRsharingA database of data and metadata standards. Useful to see if there is a data standard relevant to your area of research.
- Reporting Guidelines - EQUATOR NetworkReporting 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!
- Resource Identification PortalThis 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 NotebooksThis 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.ioA website for creating, organizing, and publishing research protocols. UCSF researchers have access to free premium accounts.
- Open Science FrameworkA free, open-source tool from the Open Science Framework designed to help researchers manage and archive their research, privately and publicly
- Jupyter NotebooksThese interactive online notebooks combine live code with narrative text. Perfect for documenting computational experiments
- Methods and Protocol ResourcesThis 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 GitHubHeard 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 SheetsOne page cheat sheet with all the essential GitHub commands