Quick start¶

This page provides details to start using the CryoET Data Portal.

Contents

Installation.
Python quick start.

Installation¶

Requirements¶

The CryoET Data Portal Client requires a Linux or MacOS system with:

Python 3.7 to Python 3.11.
Recommended: >16 GB of memory.
Recommended: >5 Mbps internet connection.
Recommended: for increased performance, use the API through an AWS-EC2 instance from the region us-west-2. The CryoET Portal data are hosted in a AWS-S3 bucket in that region.

Python¶

(Optional) In your working directory, make and activate a virtual environment or conda environment. For example:

python -m venv ./venv
source ./venv/bin/activate

Install the latest cryoet_data_portal package via pip:

pip install -U cryoet-data-portal

Python quick start¶

Below are 3 examples of common operations you can do with the client. Check out the examples page for more code snippets.

Browse data in the portal¶

The following iterates over all datasets in the portal, then all runs per dataset, then all tomograms per run

from cryoet_data_portal import Client, Dataset

# Instantiate a client, using the data portal GraphQL API by default
client = Client()

# Iterate over all datasets
for dataset in Dataset.find(client):
    print(f"Dataset: {dataset.title}")
    for run in dataset.runs:
        print(f"  - run: {run.name}")
        for tvs in run.tomogram_voxel_spacings:
            print(f"    - voxel spacing: {tvs.voxel_spacing}")
            for tomo in tvs.tomograms:
                print(f"        - tomo: {tomo.name}")

And outputs the name of each object:

Dataset: S. pombe cells with defocus
  - run: TS_026
    - voxel spacing: 13.48
        - tomo: TS_026
...

Find all tomograms for a certain organism and download preview-sized MRC files:¶

The following iterates over all tomograms related to a specific organism and downloads each tomogram in MRC format.

import json

from cryoet_data_portal import Client, Tomogram

# Instantiate a client, using the data portal GraphQL API by default
client = Client()

# Find all tomograms related to a specific organism
tomos = Tomogram.find(
    client,
    [
        Tomogram.tomogram_voxel_spacing.run.dataset.organism_name
        == "Schizosaccharomyces pombe"
    ],
)
for tomo in tomos:
    # Access any useful metadata for each tomogram
    print(tomo.name)

    # Print the tomogram metadata as a json string
    print(json.dumps(tomo.to_dict(), indent=4))

    # Download a tomogram in the MRC format (uncomment to actually download files)
    # tomo.download_mrcfile()

Downloads display a progress bar by default:

TS_026
{
    "id": 121,
    "tomogram_voxel_spacing_id": 1,
    "name": "TS_026",
... more output ...