Workflow Examples for Documentation

[dgmccart]

Running list of workflows to address in documentation:

• [ ] Download the data and run these commands to get the structure of a ribosome (involved because it includes many sub-tasks) (2 - pipeline is not public) - Utz to follow up about status of this work
• [ ] Using object relationship such as how to search all tomograms from the same camera model that produces its companion tilt series (1)
• [x] Find all datasets/Runs that have raw frames associated with them (1)
• [x] Identify all membrane annotations using GO Terms (1)
• [ ] Download a single tomogram and its associated annotations from s3 - delayed till Feb

Notes: 3 API improvements identified during Kandarp's UXR session + 1 directly from Utz. Should be completed by mid-Feb. (e.g. allowing download of individual annotations using API) - Jun to share Github ticket

• Download the data and run these commands to get the structure of a ribosome
• most of the annotations are of ribosomes + easy example. Download tomogram + tilt series, start with the tilt series (or could start with the frames), Note: Developing a pipeline for the ML Challenge that could do this
• Using object relationship such as how to search all tomograms from the same camera model (2-3 camera types; each camera has its own characteristics; folks may want to test pipelines using data from different cameras) that produces its companion tilt series
• Building queries based on graphql client. GraphQL is not familiar for many users, so having lots of examples is essential.
• Find all datasets/Runs that have raw frames associated with them
• For folks who need the raw frames for their process. Frames --> tilt series --> tomograms --> pick particles --> reconstruction based on the tilt series
• Identify all membrane annotations using GO (gene ontology) Terms - all annotations are associated with a GO term; e.g. mitochondrial membrane vs lipid bilayer membrane
• Download a single tomogram and its associated annotations from s3 --> may be blocked by changes to the API client; show difference between .mrc and .zarr formats - show a comparison

[uermel]

• [ ] Find all datasets/Runs that have raw frames associated with them
• [ ] Identify all membrane annotations using GO Terms

[uermel]

• [ ] Download a single tomogram and its associated annotations from s3