Gene Knowledge Base Web Service

Table of Contents

1. Overview
2. Project structure
3. Setup and Installation
4. Usage
5. FAQ
6. Contacts

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Overview

This project provides a Flask-based web service to visualize differences in protein activity levels interactively, which includes:

• an interactive volcano plot with clickable points to view boxplots
• boxplots (Young vs. Old) with additional points representing the protein concentration value in each sample
• scientific paper titles and URLs where the selected gene name was reported

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Project Structure

.
├── assets
│   └── style.css               # CSS file for styling
├── data
│   └── NIHMS1635539-supplement-1635539_Sup_tab_4.xlsx  
│       # Main Excel file containing:
│       # - "S4B limma results" sheet (for volcano plot data)
│       # - "S4A values" sheet (for boxplot data)
├── main.py                     # Main Flask + Dash application entry point
├── requirements.txt            # Python dependencies for the project
└── README.md

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Setup and Installation

1. Clone the repository:

git clone git@github.com:YaroslavMayorov/gene_knowledge.git
cd gene_knowledge

2. Create a virtual environment:

python3.10 -m venv venv

Linux / MacOs

source venv/bin/activate

Windows (Command Prompt (cmd.exe))

venv\Scripts\activate

Windows (PowerShell)

venv\Scripts\Activate.ps1

3. Install dependencies:

pip install -r requirements.txt

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Usage

1. Launch the web service:

python main.py

2. Open a browser:

   Go to the address that is displayed in the console, usually this http://127.0.0.1:8050 .

3. Interact with the volcano plot:

   Hover over the pointы to see information about the gene's symbol, p-value and fold change. Use sliders to move the threshold lines to highlight significant points.

4. Click on the point to see the boxplot:

   The canvas will appear, which shows comparison between protein concentraction in young and old samples for selected gene.

5. Viewing medical publication with MyGene.info:

   When you select a gene, you will see the links and the pubmed id of scientific articles on this gene. By default only 5 links are showed. Click on the button to show all. Click again to hide.

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FAQ

Why did I choose this internship?

I studied in a biology-focused class, so I have a strong background in biology. I am especially interested in aging and ways to combat age-related diseases. I have long wanted to work in bioinformatics, and this internship is a great opportunity for me.

For about two years, I have been working with Flask, developing various web applications, from simple projects to multi-page websites. You can see one of my projects here: arthouserooms.pythonanywhere.com.

I also completed a data analysis course from Tinkoff and a machine learning specialization from Yandex, which gave me valuable experience working with pandas and matplotlib. In addition, I prepared for the DANO Olympiad in data analysis, so I have a solid understanding of statistics, data processing, and interpretation.

I really want to join your team, because this topic is really close to me. I am ready to learn new things and help develop a useful tool for biological data research. I would be grateful for the opportunity to be part of this project!

What if port is unavailable?

By default server is on port 8050. Change the port in main.py (line 380):

app.run_server(port=free_port)

What python version should I use?

Python 3.10 is recommended. Earlier versions may work but could introduce compatibility issues.

Why did you choose plotly?

• Support interactive graphics

• Clear documentation – lots of examples, easy to understand.

• Dash compatibility – allows you to create full-fledged web pages using lists directly in Python.

• Simply graphs created by few lines, but deep customization is available too.

Why do you use Dash and Flask at the same time? Dash is build on Flask.

Dash is built on Flask, but by default, it creates its own Flask instance internally. The Flask instance is needed to integrate the Dash application into a larger Flask app. This is important when working on real projects.

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Contacts

If you have any questions, feel free to contact me:

• Email: sasha.val2006@gmail.com
• Telegram: @thedreamertype