Tool:Brave: Bioinformatics Reactive Analysis and Visualization Engine

Question

[Edward]

Hello everyone: I recently developed and fully open-sourced a private cloud bioinformatics analysis tool that can visualize generation parameters and runs using Docker.

• Document: https://pybrave.github.io/brave-doc/
• UI: https://pybrave.github.io/brave-ui/

Local Installation API:

git clone https://github.com/pybrave/brave.git
cd brave
pip install .
brave  --port 5008  --use-https

I am actively improving the documentation and functions, welcome to follow star.

[ATpoint]

Can you summarize in one sentence what the use case is? Is this a workflow manager?

[Edward]

This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, and workflow.

The following is an example of running metaphlan:

Creating an analysis task

Editing analysis task parameters

Generated parameters

{
  "stat_q": 0.2,
  "remove_host_reads": [
    {
      "group": "group1",
      "id": 3593,
      "analysis_result_id": "a9ec5caa-6b72-48d0-920c-db26745b51b7",
      "sample_id": "644878ea-7d51-4e20-8100-559644e91674",
      "sample_source": null,
      "file_name": "test_s2",
      "analysis_key": null,
      "component_id": "3a3aee58-805c-4ad2-8542-771ff5617385",
      "software": null,
      "analysis_version": null,
      "content_type": "json",
      "analysis_id": "b6145832-c918-42a3-8d51-b2a52065d32d",
      "project": "a4f4acb2-e119-4a9e-8c59-cdea6bff3df5",
      "request_param": null,
      "analysis_type": "upstream_analysis",
      "create_date": null,
      "analysis_result_hash": "3e15cc146ccb995d365a1f0d04efcbcc",
      "fastq1": "/ssd1/wy/workspace2/nextflow_workspace/a4f4acb2-e119-4a9e-8c59-cdea6bff3df5/59bead89-13af-4956-951a-1dcef1b3b7a3/b6145832-c918-42a3-8d51-b2a52065d32d/output/remove_hosts/test_s2/test_s2_host_removed_R1.fastq.gz",
      "fastq2": "/ssd1/wy/workspace2/nextflow_workspace/a4f4acb2-e119-4a9e-8c59-cdea6bff3df5/59bead89-13af-4956-951a-1dcef1b3b7a3/b6145832-c918-42a3-8d51-b2a52065d32d/output/remove_hosts/test_s2/test_s2_host_removed_R2.fastq.gz",
      "log": "/ssd1/wy/workspace2/nextflow_workspace/a4f4acb2-e119-4a9e-8c59-cdea6bff3df5/59bead89-13af-4956-951a-1dcef1b3b7a3/b6145832-c918-42a3-8d51-b2a52065d32d/output/remove_hosts/test_s2/test_s2.bowtie2.log"
    },
    {
      "group": "group2",
      "id": 3594,
      "analysis_result_id": "85f7d572-b04a-48da-8eb9-7589c9df3f1c",
      "sample_id": "70938e37-f540-426a-bdc3-94048889201e",
      "sample_source": null,
      "file_name": "test_s1",
      "analysis_key": null,
      "component_id": "3a3aee58-805c-4ad2-8542-771ff5617385",
      "software": null,
      "analysis_version": null,
      "content_type": "json",
      "analysis_id": "b6145832-c918-42a3-8d51-b2a52065d32d",
      "project": "a4f4acb2-e119-4a9e-8c59-cdea6bff3df5",
      "request_param": null,
      "analysis_type": "upstream_analysis",
      "create_date": null,
      "analysis_result_hash": "6117a284b167397486eb17f92c22497c",
      "sample_name": "test_s1",
      "fastq1": "/ssd1/wy/workspace2/nextflow_workspace/a4f4acb2-e119-4a9e-8c59-cdea6bff3df5/59bead89-13af-4956-951a-1dcef1b3b7a3/b6145832-c918-42a3-8d51-b2a52065d32d/output/remove_hosts/test_s1/test_s1_host_removed_R1.fastq.gz",
      "fastq2": "/ssd1/wy/workspace2/nextflow_workspace/a4f4acb2-e119-4a9e-8c59-cdea6bff3df5/59bead89-13af-4956-951a-1dcef1b3b7a3/b6145832-c918-42a3-8d51-b2a52065d32d/output/remove_hosts/test_s1/test_s1_host_removed_R2.fastq.gz",
      "log": "/ssd1/wy/workspace2/nextflow_workspace/a4f4acb2-e119-4a9e-8c59-cdea6bff3df5/59bead89-13af-4956-951a-1dcef1b3b7a3/b6145832-c918-42a3-8d51-b2a52065d32d/output/remove_hosts/test_s1/test_s1.bowtie2.log"
    }
  ],
  "metaphlan_database": {
    "db_index": "mpa_vJun23_CHOCOPhlAnSGB_202403",
    "path": "/data/wangyang/databases/metaphlan"
  },
  "groups_name": {
    "remove_host_reads": "group1-group2"
  },
  "groups": [
    "remove_host_reads"
  ],
  "pipeline_dir": "/ssd1/wy/workspace2/nextflow-fastapi/pipeline-dev",
  "metadata_form": [
    {
      "name": "group",
      "label": "group"
    }
  ]
}

View Script

Downstream analysis visualization

[Ram]

Do you have a plan to make an English version of the UI?

[Edward]

Yes, we plan to make English the primary language of the Brave UI.