This is an old revision of the document!

File Management

Backup

Establish an automatic backup plan; manual backup plans are not practical
Mac: Time Machine
Linux: rsync scripts

Naming and version control
- File names
  - Do: short and informative. Include information such as project id, keyword (e.g. manuscript, report, keyword of figure/table), version or date
  - Avoid: long names that are difficult to read (e.g., full title of the manuscript)
  - Avoid: short names that are not informative (e.g., manuscript.docx, figure1.ai)
  - Avoid: space or special characters
  - Avoid: “xxx_final.docx”, “xxx_final_revised.docx”, “xxx_final_revised_typofixed.docx”, etc
- Versioning
  - Version number should be the last part of the file name; two digits should be sufficient
    - Optional: Add initials if multiple people are involved in the project
  - When in doubt, save as a new version
  - Recommended: In early versions of manuscript drafts, add a short section in the beginning of the document to explain the major changes made
  - Benefits
    - Write as much as possible without worrying if those parts will be kept in later versions
    - Throw away as much as needed to make a good story; you can always go back to previous versions to retrieve the deleted materials
- Project progress report
  - In the beginning of the document, include:
    - Name (who prepared this report?)
    - Date (when was it prepared?)
    - Project id (what is it about?)
    - Directory of relevant files (on lab servers for people to get raw data files if needed)
  - For long reports, prepare a short summary section
- Branching and merging
  - When multiple people are involved, branches may be created for each person to work on a different part
  - It is important that everyone agree with the leader on when and how to merge the branches
  - Example
    - For project “agro38”, start the main manuscript file as “agro38_ms_v01.docx”
      - ABC then saved the file as “agro38_ms_v02_ABC.docx” to work on Introduction
      - DEF creates “agro38_ms_v02_DEF.docx” to work on Materials and Methods
      - GHI creates “agro38_ms_v02_GHI.docx” to work on Figure Legend.
    - ABC being the project leader, should be responsible to set the deadline, collect the files, then merge and create “agro38_ms_v03.docx” as the starting point for the next iteration.
- Figure/table files
  - Before finalizing the order, use names without fig/table number and with a keyword (e.g., “fig_phylogeny_v02.ai”, “table_accession_v05.xlsx”)
  - After finalizing the order, put all early versions into a separate folder (e.g., “figure_stage1”), then add figure/table numbers to the file names (e.g., “fig1_phylogeny_v15.ai”)
  - If the order changed, put the previous versions into another separate folder (e.g., “figure_stage2”), then update the figure/table numbers (e.g., “fig3_phylogeny_v16.ai”)

Tracking changes
- For Word files: better to use the build-in function “Track Changes”; possible to use the “Compare Documents” functions later.
- For Google Docs: all changes are automatically tracked. Manually name and download the major versions.

Working with collaborators
- Discuss and setup a workflow
- Avoid emailing files as attachments; use a file server or file sharing service (e.g., Google Drive) instead.
- Pros and cons of setting up a file server vs. using a commercial service.

File directory structure
- Make it easy to identify the parts that need to be included in backup
- Example for personal desktops/laptops
- Example for shared servers