Repositories list

• challenges-capsules

  Public
  Python

  •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

• codeocean-sdk-python

  Public
  Code Ocean Python SDK

  Python

  •

  MIT License

  •4•10•1•1•Updated Mar 28, 2026Mar 28, 2026

• codeocean-mcp-server

  Public
  Code Ocean MCP Server

  Python

  •

  MIT License

  •1•3•0•0•Updated Mar 9, 2026Mar 9, 2026

• user-docs

  Public
  User documentation for Code Ocean computational research platform.

  0•0•0•0•Updated Feb 27, 2026Feb 27, 2026

• scrna-visualization-template

  Public
  Python

  •0•0•0•0•Updated Dec 5, 2025Dec 5, 2025

• fip-analysis-template

  Public template
  Jupyter Notebook

  •0•0•0•0•Updated Nov 25, 2025Nov 25, 2025

• go-mlflow

  Public
  Golang MLflow SDK

  Go

  •

  MIT License

  •0•0•0•0•Updated Nov 19, 2025Nov 19, 2025

• r-seurat-demo

  Public template
  0•0•0•0•Updated Nov 7, 2025Nov 7, 2025

• infra-aws-vpc-system-requirements

  Public
  Python

  •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

• single-cell-tutorial

  Public template
  Jupyter Notebook

  •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

• amazon-ebs-autoscale

  Public
  Don't run out of disk space on your EC2 instance when generating or working with large files. Automatically add EBS volumes to a filesystem mount point in respo…

  Shell

  •

  MIT License

  •61•0•0•0•Updated Sep 14, 2025Sep 14, 2025

• strands-agent-with-codeocean-mcp-server-and-streamlit-demo

  Public
  A simple demo showing how to use code ocean mcp server with local agents and a simple streamlit chat interface

  Python

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

• co-support

  Public
  Code Ocean Support Command-Line

  Python

  •0•1•0•0•Updated May 21, 2025May 21, 2025

• seurat-demo

  Public template
  HTML

  •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

• pipeline-training-prep

  Public
  Python

  •0•1•0•0•Updated Jan 14, 2025Jan 14, 2025

• AIBS_training

  Public
  HTML

  •0•0•0•0•Updated Aug 26, 2024Aug 26, 2024

• aibs-patch-seq

  Public template
  Jupyter Notebook

  •0•1•0•0•Updated Jun 25, 2024Jun 25, 2024

• aibs_thalamus_merfish

  Public template
  Jupyter Notebook

  •2•0•0•0•Updated Apr 6, 2024Apr 6, 2024

• co-apps-mutect-preprocess

  Public
  Shell

  •0•0•0•0•Updated Nov 29, 2023Nov 29, 2023

• co-apps-gatk-mutect2-tumor-only

  Public
  Shell

  •0•0•0•0•Updated Nov 28, 2023Nov 28, 2023

• co-apps-gatk-mutect2

  Public
  Shell

  •0•0•0•0•Updated Nov 28, 2023Nov 28, 2023

• co_aux_tools

  Public
  Convenince tools for working in Code Ocean capsules and pipelines.

  Python

  •

  MIT License

  •0•4•0•0•Updated Nov 9, 2023Nov 9, 2023

• co-apps-combfold-prepare-fasta

  Public
  This capsule outputs fasta files which can be input for AlphaFold Multimer or ColabFold.

  Shell

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 5, 2023Oct 5, 2023

• co-apps-combfold-combinatorial-assembly

  Public
  The CombFold Combinatorial Assembly algorithm assembles paired subunit structures into a single large complex.

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 5, 2023Oct 5, 2023

• text-notification

  Public
  Add text notifications to your Code Ocean workflows.

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 3, 2023Oct 3, 2023

• casule_databricks_data_asset_generation

  Public
  Python

  •0•0•0•0•Updated Jul 17, 2023Jul 17, 2023

• capsule_databricks_data_connector

  Public
  This tool is designed to create a connection between Code Ocean and your SQL Warehouse in Databricks.

  Python

  •0•0•0•0•Updated Jul 17, 2023Jul 17, 2023

• capsule_mysql_r_odbc

  Public
  Capsule to connect to MySQL from RStudio

  R

  •0•0•0•0•Updated Jul 13, 2023Jul 13, 2023

• capsule_databricks_r_odbc

  Public
  Databricks connector to RStudio

  R

  •0•0•0•0•Updated Jul 7, 2023Jul 7, 2023

• coding_workshop

  Public
  Shell

  •0•0•0•0•Updated Apr 18, 2023Apr 18, 2023