Lab Data Organization - neuropsytox/Documentation GitHub Wiki

Lab Data Organization

The purpose of this document is to describe the minimum organization and documentation expected of all lab members for research projects they are undertaking.

We have the Synology Storage Server called Zinana (Otomi goddess) with around 40 TB but it will run out quickly. All staff and students will save their projects within tezca, austin and gioria from the main cluster. Inside misc there will be 3 folders, animal, human, cross. Inside each of those you can have your project created. Certain folders will be backed up daily. Other will not.

Directory example:

├── 1-ProjectManagement
│   ├── 1-Proposal
│   ├── 2-Preregistrations
│   ├── 3-Finance
│   │   ├── Expenses
│   │   └── Funding
│   ├── 4-Reports
│   └── 5-Other
├── 2-Ethics
│   ├── 1-EthicsApproval
│   └── 2-ConsentForms
├── 3-Experiment
│   ├── analysis
│   ├── code
│   ├── data
│   ├── derivatives
│   └── preprocessed
└── 4-Dissemination
    ├── 1-Presentations
    ├── 2-Publications
    │   ├── communications
    │   └── paper
    │       └── figures
    ├── 3-Posters
    └── 4-Other

Top-level directory: <Recognizable name of project>

  • something that others would recognize if at all possible
  • no spaces

Notes: Use relative paths in scripts as opposed to absolute, so that the entire project folder can be moved elsewhere and still operate

PHD, MSc, BSc projects should have that in the name.

Example names of projects:

  • PHD-ALE-ALCOHOL

  • SUDMEX-TMS

If it's an "umbrella" project, subproject folders may be stored inside.

Contents

README

  • describes purpose of project
  • contact information of any collaborators
  • specific organizational details of directory structure not covered by this document
  • chronological log of major events in the project

Second level folders

There will be 5 folders created:

  • 1-ProjectManagement/

  • 2-Ethics/

  • 3-Experiment/

  • 4-Dissemination/

  • 5-Other/

Each folder will have subfolders.

1-ProjectManagement/ will have the following folders inside:

  • 1-Proposal/
  • 2-Preregistrations/
  • 3-Finance/
  • 4-Reports
  • 5-Other/

2-Ethics/ will have the following folders inside:

  • 1-EthicsApprovals/
  • 2-ConsentForms/

3-Experimentwill have the following folders inside:

data/

  • README per data type
    • Describe specific naming conventions for the project of raw data as well as how it is organized
    • Describe what data is present
    • A log of any unexpected events or deviations from proper data collection procedures for specific measurements or subjects
  • Some kind of quality control document
    • CSVs or similar corresponding to the quality control of the raw data
    • Should contain notes as to why data is excluded
  • Different type of data will have different folders and we must use the BIDS framework. https://bids-specification.readthedocs.io/en/stable/

Raw data will be stored elsewhere in Synology and will only be available writable by me, Eduardo. Therefore, it is recomended to transform the data to BIDS and ask me to store it as raw data. It will have it own path for your READ ONLY use.

code/

  • You can store code here in any format.

preprocessed/

  • Data from data/ preprocessed or otherwise transformed into more usable form
  • README per data type
    • Document what actions were taken
    • E.g. for behavioural data explain manual reformatting
    • Document renaming or such
    • Okay to exclude data QC failures

derivatives/

  • Contains processing pipelines/results from things such as fMRIprep
  • README per processing type
    • Document commands used
    • Version of pipeline or date downloaded
    • Inputs used for pipeline
      • Which files (what kind)
      • Which atlases, etc
  • Quality control output per data type
    • CSV or equivalent
    • Notes describing failure mode

analysis/

  • README describing the general methods of analysis
    • Versions of software (modules) used
  • R or python scripts (or other)
    • Scripts must run from beginning to end to reproduce figures from scratch
  • Keep old scripts and name with date
    • Don't delete old attempts at analysis if not fruitful

4-Dissemination/ will have the following folders inside:

  • 1-Presentations
  • 2-Publications
  • 3-Posters
  • 4-Other

2-Publications will have the following folders inside:

paper/

  • Copy of submitted paper version
  • Submission letter
  • BibTeX export of references used in paper submission
  • Copy of referee reports
  • Replies to referees
  • Copy of resubmit

paper/figures/

  • Figure files submitted with paper
  • README describing any manual work undertaken on figured generated from scripts (changes made, merging done, etc)

For collaborator projects communications/

  • Print to PDF copies of emails between you and the collaborator going over project details

Everything from these folders will be backed up except for

├── 3-Experiment
│   ├── data
│   └── preprocessed