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Tool: Brave: Bioinformatics Reactive Analysis and Visualization Engine

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

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.

docker r nextflow python react
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written by Edward • Edward

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

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written by ATpoint ATpoint

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.

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written by Istvan Albert Istvan Albert

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/

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written by Yang • Yang

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

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written by Istvan Albert Istvan Albert

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.

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written by ATpoint ATpoint

Thanks for the reply and suggestions. This software is a bit similar to galaxy. Recently, I am adding an application store for pipelines, software, files and scripts, and packaging the brave program into docker so that pipelines, software, files or scripts can be run in three steps.

In addition, since Brave implements the structural definition of Bioinformatics analysis, the cromwell pipeline can be automatically generated by the visual connection software later (cromwell seems to be easier to automatically generate than nextflow).

enter image description here

In addition, Brave is for private clouds and cannot be directly applied. You must install the back-end API.

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written by Edward • Edward

2 answers

I recently updated some of the code and I would like to reintroduce this GitHub open source project:

BRAVE is a visual bioinformatics workflow platform, similar to Galaxy, that enables intuitive configuration and visualized execution of both upstream and downstream data analyses.

It provides an interactive interface that allows users to quickly develop upstream Nextflow analysis pipelines and downstream visualization scripts using containerized applications such as RStudio, VS Code, and Jupyter.

Once a Nextflow pipeline or visualization script is developed, it can be published to a GitHub repository as a BRAVE “store” app, allowing other analysts to download and use it. Each app maintains isolation, reproducibility, and scalability, leveraging containerized execution to ensure consistent and reliable analyses.

For more information, see: https://pybrave.github.io/brave-doc/ or https://github.com/pybrave/brave

enter image description here

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written by Edward • Edward

This is a good start, but if one clicks on Launch Brave, it launches a modal HTML window that asks questions such as API, Authorization, GitHub token, etc.

Who would start adding authorization tokens to a new website they visit the first time?

Your demonstration animation is way too quick and crytpic.

I have no idea what it shows! I have no idea what it does. What are these quick popups and page changes supposed to show?

Slow down, it is a documentation site, not a TikTok video.

Don't rush it - otherwise it will be like TikTok nobody recalls anything 10 seconds later.

Explain what it does step by step on the reader's pace.

You got the gist of my message, but you are still miles away from what a tutorial should be like

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written by Istvan Albert Istvan Albert

I still have no idea what it does at all. Please don't take this as personal criticism, but you really have to advertise better for anyone to even check it out.

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written by ATpoint ATpoint

I have not given up on this project. I have updated a lot of code recently. You can install it with one click through the following script to see the effect.

curl -s https://raw.githubusercontent.com/pybrave/brave/refs/heads/master/install.sh  | bash

I will add detailed documentation later, and I plan to rewrite the entire backend code using golang in the future.

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written by Edward • Edward

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