Rendeiro group

Lab manual





Research

Project life cycle

Initializing a project

  1. Register your project in the lab's project register:
    1. Go to https://cemmat.sharepoint.com/sites/rendeirolab and find the 'Lab project register.xlsx' or directly here.
    2. Start a new row for your project and increment the Project ID by one.
    3. Choose an intuitive name for the project, avoiding adding personal information e.g. collaborator names.
  2. Create a project directory structure from the lab's template: cookiecutter gh:rendeirolab/_project_template
  3. Create a git repository on GitHub (https://github.com/rendeirolab) with the same name as the project, make a first commit and push to Github.
  4. Create a directory for the project in the CeMM cluster at: /research/groups/lab_rendeiro/projects/
    1. Create a directory inside called data to store raw data.
  5. Create a directory for the project in the CeMM cluster at: /nobackup/groups/lab_rendeiro/projects/
    1. Create a soft link between /research/.../data and /nobackup/.../data
  6. Create a cemm_metadata.json file in /research/groups/lab_rendeiro/projects/$PROJECT/
  7. Create a cemm_metadata.json file in /nobackup/groups/lab_rendeiro/projects/$PROJECT/

You can find various metadata JSON templates at /research/groups/lab_rendeiro/projects/_templates/.

Make sure to validate your JSON files, e.g.:

# pip install jsonvalidate
wget http://metadata.int.cemm.at/latest/cemm_metadata_schema.json
jsonvalidate -i cemm_metadata.json cemm_metadata_schema.json

Developing a project

[!CAUTION] TODO

Maintaining files for a project

Make sure to maintain your metadata JSON files, in line with the existing data on disk.

Reporting research

No powerpoint!

Publications

[!CAUTION] TODO

Authorship

[!CAUTION] TODO

Tools and technologies of standard use within the lab

File types of digital data

Below are the preferred types of technology to be used in the lab:

  • documentation: Markdown
  • programming language: Python
  • image files: OME-TIFF
  • tabular form files: CSV (or csv.gz), Parquet
  • plots: SVG, PDF

Engaging in new projects

[!CAUTION] TODO

Meta-science

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