====== File Management ======
  * Guidelines that Chih-Horng Kuo (chk@gate.sinica.edu.tw) developed for our group members. Suggestions are welcome.
  * Related information: 
    * [[tutorials:scientific_presentation|Scientific Presentations]]
    * [[tutorials:scientific_writing|Scientific Writing]]

===== Backup =====
  * <color #ff0000>Critical!</color>
  * File loss happens. Not __IF__, but __WHEN__.
  * Establish an automatic backup plan; manual backup plans are not practical
    * Mac: Use "Time Machine" to back up automatically to another hard drive
    * Linux: Use rsync scripts with a cron job

===== 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. 
  * Setting up a file server vs. using a commercial service
    * File server:
      * Pros: Full control, large storage, no vendor lock-in
      * Cons: Requires hardware, set up, and maintenance
    * File sharing service
      * Pros: Easy, low cost
      * Cons: Limited space, less control over structure, potential data leakage.

===== File directory structure =====
  * Make it easy to identify the parts that need to be included in backup
  * Example for personal desktops/laptops
    * A few top level folders with clear naming for easy backup/restore (e.g., work_files, personal_files)
  * Example for shared servers
    * Depends on the research group, for example: data/, lab_doc/, project/, conference/
    * Clear rules, communication, and enforcement are all very important 

===== 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)
      * Short names that are not informative (e.g., manuscript.docx, figure1.ai)
      * Space or special characters (can cause problem across systems)
      * Names such as "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")
    * Very important to save the files in editable formats (e.g., .ai, not just .jpg)

===== Tracking changes =====
  * For Word files: Use the build-in function "Track Changes" by default when collaborating; possible to use the "Compare Documents" functions later.
  * For Google Docs: All changes are automatically tracked. Manually download the major versions and save with meaningful names (e.g., "agro38_ms_v05_ABC.docx")

===== Metadata =====
  * Metadata = data that explains your files: what they are, where they came from, how to use them.
  * Examples 
    * For the raw data file of a gel image (20250509_1428.jpg), add a text file (20250509_1428.txt or 20250509_1428.docx) to explain what this image is (when, whom, which project, content of each lane, why generate this, main conclusion, etc)
    * For a set of raw data files (e.g., Sanger sequencing results), or a file folder, provide a "readme.txt" to explain the content