SelectZyme-app

Web application to host the pre-calculated demo analyses by SelectZyme from huggingface

Install

git clone https://github.com/ipb-halle/SelectZyme-app.git
cd SelectZyme-app
docker-compose up
docker-compose down  # shut down services when desired

Access the server from your browser at: localhost/

Development

This project uses the following tools to improve code quality:

• ruff

License

MIT License

Citation

This repository contains the source code for the application hosted at https://selectzyme.app.ipb-halle.de/, showing selected pre-calculated case studies for the manuscript:

Felix Moorhoff¹, David Medina-Ortiz¹, Alicja Kotnis¹, Ahmed Hassanin^1,2, Mehdi D. Davari^1,*,
“Visualize, Explore, and Select”: A protein Language Model-Based Approach Enabling Navigation of Protein Sequence Space for Enzyme Discovery and Mining
Journal 2026, 61, 3463-3476
https://doi.org/10.64898/2026.03.23.712833

¹_{Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany}
²_{Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, 71526 Assiut, Egypt}
^*_{Corresponding author}

Server deployment @ IPB

In order to automatically (re-)start the service (e.g. with a cronjob) please perform these steps:

./sz.sh install  # register service 1st time
./sz.sh start
systemctl status sz.service  # test status
./sz.sh stop  # stop service

Use sz.sh update to update the service.

Additional notes on the current workflow to build docker images with a workflow: Because of a restricted company network, images (github: packages) are build using a CI workflow. The packages appear in the repo on the right, clicking on them you can change the visibility. They should inherit visibility from the repo but the company can have restrictions so ask the organization owner to enable public visibility of your package (image).

sequenceDiagram
    actor User
    participant BP as Infrastructure Proxy
    participant SDP as Proxy (nginx)
    participant SDA as Selectzyme App

    User->>+BP: Request resource
    BP->>+SDP: Forward request (e.g., to selectzyme-proxy.selectzyme-network)
    SDP->>+SDA: Proxy request to Selectzyme App
    SDA-->>-SDP: App response
    SDP-->>-BP: Forward response
    BP-->>-User: Response

Loading

Architecture

graph TD;  
    B[Demo analysis] --> D[data/demo/:/app/data_container/];
    C[Petase analysis] --> E[data/petase/:/app/data_container/];
    
    A[Proxy - Nginx] -->|/demo/| B[Demo analysis];
    A[Proxy - Nginx] -->|/petase/| C[Petase analysis];
    
    subgraph Docker Network;
        A[Proxy - Nginx];
        B[Demo analysis];
        C[Petase analysis];
    end

Loading