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.

[Istvan Albert]

I visited the website, but I couldn't understand what problem the software solves.

You need to do a much better job of communicating the purpose and value of the work.

[Yang]

Thanks for the reply, I simply recorded the screen and used brave to integrate fastqc analysis. You can click the link below to view. In general, brave can quickly develop visual analysis applications based on cloud applications, and manage and real-time monitor docker processes.

[Yang]

Thanks for the reply, I simply recorded the screen and used brave to integrate fastqc analysis. You can click the link below to view. In general, brave can quickly develop visual analysis applications based on cloud applications, and manage and real-time monitor docker processes.

https://pybrave.github.io/brave-doc/

[Istvan Albert]

We don't have 6 minutes to watch something without even knowing what it does.

I would recommend that you provide a brief explanation of what problem you are trying to solve, and within just a few lines of text, convince people that it is worth spending effort.

what you have today is a cryptic statement "Bioinformatics Reactive Analysis and Visualization Engine" I have no idea whatsoever what that is, why I should care.

I still don't know what this tool does, frankly.

Who is your audience? What does one need to run it? etc

[ATpoint]

Seconding this, I also felt completely lost what this actually does. @OP, you need to learn to make sharp, concise bulletpoints advertising your software, so anyone immediately knows what it is. Or it gets lost in the daily software traffixc.