Maintaining data and cleaning up files

It is a good idea to keep the following guidelines in mind when you are working on your projects since this is how data should be organized when you hand it over before you leave the lab:

  • Move important data from microscope computers onto your folders in the NAS. No data should be left on the microscope computers. Please check the storage drive but also the Desktop and Documents folders. When you leave, there should be no files left that are only related to your projects (but do leave tools that others use).
  • Clean up your custom scripts in microscope software. Leave a version you were using but not other versions you may have created but not actually used.
  • Move important data from your office desktop computer onto the NAS. Again, no data should be left on the storage drive, Desktop, Documents, or other folders. When you leave, we should be able to wipe your office computer, in principle.
  • Keep an up-to-date strain and plasmid list.
  • Data structure in your NAS folder:
    • Top folder: Project-name
      • Sub-folder: Data
        • Sub-sub-folder: YYYY_MM_DD_brief-description-of-recording
          • All data related to a recording is here:
            • raw recording
            • annotations (only best one)
            • metadata (e.g., settings used for imaging, microfluidics protocol, optogenetic stimulation protocol)
            • a description file explaining any particularities of the recording (e.g., recording went bad after time point X but I used data up to X, positions 1 and 2 used but not 3)
          • Absolutely keep recordings that go into a paper.
          • Do not keep recordings that are exploratory and where you were optimizing recording parameters, if they were followed by recordings with the final protocol, which you then analyzed. So, delete recordings nobody will ever use but do keep recordings people may use. Ask me if you are unsure.
          • The recording folder name should have a short description of the experiment (e.g., X-versus-Y-constant-XYZ-two-good-positions, X-perturbation-unused-recording-but-good)
        • Sub-sub-folder: Compiled-data
          • Data extracted from recordings that was then plotted or analyzed further (e.g., summary of one or multiple recordings in a csv file)
        • Sub-sub-folder: Plots
          • Only final or important plots. Meaningful file names.
    • Top folder: Strains_and_plasmids
      • Strain list (including all organisms received from other labs or repositories)
      • Plasmid list (including all received from elsewhere)
      • Location of strains and plasmids in freezers should be indicated (e.g., Box 5)
    • Top folder: Presentations
      • Group meeting, conference, thesis defense presentations
    • Top folder: Manuscript-and-Thesis
      • Sub-folder: Manuscript-name
      • Sub-folder: Thesis
      • Tex files or Word files, figures in sub-folder
    • Top folder: Code
      • Code for extracting, analyzing, and plotting data, as organized as possible
      • It should be clear which code was used to create compiled-data files and plots
      • No code that was exploratory or creates a variant of the compiled-data files or plots that was not actually used
    • Data should be kept in first author’s NAS folder. So, if you helped with someone else’s project and they are first author, they should keep the data. No shared folders that are not associated with a first author, unless we discuss this. Exceptions for obviously shared resources such as annotated yeast images specifically for training deep learning pipeline.
    • Avoid spaces and special characters in file and folder names. Use underscore or hyphen.
    • Let’s talk if this structure does not make sense for your project or you want to suggest something else. It would be nice if everyone can follow this structure though.