hackathon/index.html at master · aging-slayers/hackathon · GitHub

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    <title>Aging SLAYers Hackathon Team</title>
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        <div class="inner"><h1>Longevity hackathon</h1>
<p>This is a project to showcase results obtained for the <a href="https://forimmortality.ai/ru/">Longevity hackathon</a></p>
<h1>Drug Research Platform</h1>
<p>A Streamlit-based web application for biomedical drug research and discovery, integrating multiple pharmaceutical and biomedical databases for comprehensive drug analysis and exploration.</p>
<h2>📸 Slides for the presentation</h2>
<p>Feel free to find them <a href="https://www.figma.com/proto/3vflh9xhpQ9hv4irNHTPyU/SLAY-Longevity-Priority.-%D0%93%D1%80%D0%B0%D1%84%D0%B8%D0%BA%D0%B8?node-id=0-1&amp;p=f&amp;viewport=623%2C906%2C0.16&amp;t=F4tHTfWUBOR6brma-0&amp;scaling=min-zoom&amp;content-scaling=fixed&amp;starting-point-node-id=10%3A2">here</a>.</p>
<h2>📖 More resources</h2>
<p>Project repository <a href="https://github.com/aging-slayers/hackathon">here</a>.</p>
<p>Live demo <a href="https://slay.nb3.me">here</a>.</p>
<br />
<h2>🚀 Features</h2>
<ul>
<li><strong>Multi-Database Integration</strong>: Combines data from DrKG, DrugBank, MeSH, SIDER, DOID, and HGNC</li>
<li><strong>Interactive Web Interface</strong>: Built with Streamlit for intuitive data exploration</li>
<li><strong>Containerized Deployment</strong>: Docker-based setup for consistent environments</li>
<li><strong>Knowledge Graph Analysis</strong>: Leverages drug repurposing knowledge graphs</li>
<li><strong>Disease Ontology Integration</strong>: Incorporates structured disease classifications</li>
</ul>
<h2>📋 Prerequisites</h2>
<ul>
<li>Docker and Docker Compose</li>
<li>Make (optional, for convenience commands)</li>
<li>Minimum 4GB RAM recommended</li>
<li>At least 2GB free disk space for data and containers</li>
</ul>
<h2>🗂️ Data Structure</h2>
<p>The application integrates the following biomedical databases:</p>
<pre><code>data/
├── doid/                    # Disease Ontology
│   └── doid.obo            # Disease classifications and relationships
├── drkg/                    # Drug Repurposing Knowledge Graph
│   ├── drkg.tsv            # Main knowledge graph data
│   ├── graph.gml           # Graph structure file
│   ├── relation_glossary.tsv # Relationship definitions
│   └── relation_glossary.xlsx
├── drugbank/                # DrugBank Database
│   └── drugbank_vocabulary.csv # Drug nomenclature and metadata
├── hgnc/                    # Human Gene Nomenclature Committee
│   └── HGNC_complete_set.tsv # Official gene symbols and names
├── mesh/                    # Medical Subject Headings
│   └── desc2025.xml        # Medical terminology hierarchy
├── sider/                   # Side Effect Resource
│   └── meddra_all_indications.tsv # Drug side effects and indications
├── drugbank_vocabulary.csv  # Additional drug vocabulary
└── entity_name_mapping.json # Entity name mappings across databases</code></pre>
<h3>Database Sources</h3>
<ul>
<li><strong>DOID</strong>: <a href="https://disease-ontology.org/">Disease Ontology</a> - Standardized disease classifications</li>
<li><strong>DrKG</strong>: <a href="https://github.com/gnn4dr/DRKG">Drug Repurposing Knowledge Graph</a> - Comprehensive biomedical knowledge graph</li>
<li><strong>DrugBank</strong>: <a href="https://go.drugbank.com/">DrugBank Database</a> - Pharmaceutical knowledge base</li>
<li><strong>HGNC</strong>: <a href="https://www.genenames.org/">HUGO Gene Nomenclature Committee</a> - Official gene symbols</li>
<li><strong>MeSH</strong>: <a href="https://www.nlm.nih.gov/mesh/">Medical Subject Headings</a> - NLM's controlled vocabulary</li>
<li><strong>SIDER</strong>: <a href="http://sideeffects.embl.de/">Side Effect Resource</a> - Drug side effects database</li>
</ul>
<h3>Google Drive Access files</h3>
<p>Place the following files in the <code>access/</code> directory to enable Google Drive access:
<code>access/service_account.json</code>.
Instructions on creating a Google Drive client and connecting it to the code can be found <a href="https://developers.google.com/workspace/sheets/api/quickstart/python">here</a>.</p>
<h2>🛠️ Installation &amp; Setup</h2>
<h3>Option 1: Using Make (Recommended)</h3>
<pre><code class="language-bash"># Clone the repository
git clone &lt;repository-url&gt;
cd &lt;project-directory&gt;

# Build and start all services
make</code></pre>
<h3>Option 2: Using Docker Compose Directly</h3>
<p>Don't forget to place Google Drive client JSON file.</p>
<pre><code class="language-bash"># Set environment variables
export UID=$(id -u)
export GID=$(id -g)

# Build and start
./run.sh</code></pre>
<h2>🚀 Usage</h2>
<h3>Accessing the Application</h3>
<p>Once the containers are running, access the Streamlit application at:</p>
<pre><code>http://localhost:8501</code></pre>
<h3>Available Make Commands</h3>
<pre><code class="language-bash">make help     # Show all available commands
make build    # Build all containers
make up       # Start containers in detached mode
make down     # Stop all containers
make logs     # View container logs
make ps       # Show container status
make restart  # Restart services
make clean    # Clean volumes (⚠️ removes data)</code></pre>
<h3>Development Commands</h3>
<pre><code class="language-bash"># Access container shell
make shell SERVICE=streamlit_app

# View logs in real-time
make logs

# Restart specific service
make restart SERVICE=streamlit_app</code></pre>
<h2>🔧 Configuration</h2>
<h3>Port Configuration</h3>
<ul>
<li><strong>Streamlit App</strong>: Port 8501 (configurable in docker-compose.yml)</li>
</ul>
<h3>Volume Mounts</h3>
<ul>
<li><code>./streamlit_app</code> → <code>/app/streamlit_app</code> (Application code)</li>
<li><code>./data</code> → <code>/app/data</code> (Database files)</li>
<li><code>./access</code> → <code>/app/access</code> (Access control files)</li>
</ul>
<h2>📁 Project Structure</h2>
<pre><code>.
├── docker-compose.yml      # Docker services configuration
├── Dockerfile             # Container build instructions
├── Makefile               # Development convenience commands
├── requirements.txt       # Python dependencies
├── project_config.py      # Project configuration
├── streamlit_app/         # Streamlit application code
│   └── root_page.py       # Main application entry point
├── app/                   # Core application modules
├── research_scripts/      # Research and analysis scripts
├── data/                  # Database files (see structure above)
└── access/                # Access control and authentication</code></pre>
<h2>🤝 Contributing</h2>
<ol>
<li>Fork the repository</li>
<li>Create a feature branch: <code>git checkout -b feature-name</code></li>
<li>Make your changes</li>
<li>Test with: <code>make build &amp;&amp; make up</code></li>
<li>Submit a pull request</li>
</ol>
<h2>📄 License</h2>
<p>This project is licensed under the MIT License.</p>
<h2>📧 Team and contacts</h2>
<ol>
<li><a href="https://github.com/bioinvlad">Vlad Maksimov</a>, team leader</li>
<li><a href="https://github.com/vikachok">Victoria Nersisyan</a>, biologist</li>
<li><a href="https://github.com/Smirness">Viktor Smirnov</a>, bioinformatician</li>
<li><a href="https://github.com/NetBUG">Oleg Urzhumtsev</a>, programmer, ML engineer & maintainer</li>
<li><a href="https://github.com/mikprin">Mike Solovyanov</a>, programmer & maintainer</li>
<li><a href="https://www.behance.net/nikkondr">Nikita Kondratev</a>, designer and researcher</li>
</ol>
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