GVMV: an interactive web server for gene variant map viewer

Description

GVMV is an interactive web platform for generating customizable gene variant maps. It integrates gene features, protein domain annotations, and variant information into a single visualization. GVMV supports common annotation formats (GFF, BED, VCF, etc.) and allows users to adjust element positions, modify variant labels, switch domain prediction databases, highlight specific variants, and export high‑resolution SVG/PNG figures—all via simple mouse clicks and drag‑and‑drop, with no programming required. The tool works across a wide range of species and is freely accessible at https://gvmv.eurekaomics.cn.

---

Deployment with Docker Compose

Prerequisites

• Docker (≥ 20.10)
• Docker Compose (≥ 2.0)

Quick Start

1. Clone the repository

git clone https://github.com/BioLiu/GVMV.git
cd GVMV

2. Configure environment variables

Copy the example environment file:

cp .env.example .env

Important:

1. Open the .env
2. Set a valid email address for NCBI_EMAIL (the email must be registered with NCBI to comply with their E-utilities usage policy).
3. If you need to access GVMV from other devices on your local network, append the local IP address (e.g., 192.168.x.x) to the ALLOWED_HOSTS list.

3. Build and start all services

docker compose up -d

4. Verify the deployment

Wait about 10 seconds, then check container status:

docker compose ps

A healthy deployment shows all services Up:

NAME             IMAGE                 COMMAND                   SERVICE          CREATED          STATUS          PORTS
varview-celery   gvmv-varview-celery   "celery -A celery_ta…"   varview-celery   12 seconds ago   Up 10 seconds   
varview-django   gvmv-varview-django   "gunicorn VarViewDja…"   varview-django   12 seconds ago   Up 10 seconds   0.0.0.0:8000->8000/tcp, [::]:8000->8000/tcp
varview-mysql    mysql:8               "docker-entrypoint.s…"   varview-mysql    12 seconds ago   Up 11 seconds   33060/tcp, 0.0.0.0:33060->3306/tcp, [::]:33060->3306/tcp
varview-nginx    gvmv-varview-nginx    "/docker-entrypoint.…"   varview-nginx    12 seconds ago   Up 10 seconds   80/tcp, 0.0.0.0:8080->8080/tcp, [::]:8080->8080/tcp
varview-redis    redis:7-alpine        "docker-entrypoint.s…"   varview-redis    12 seconds ago   Up 11 seconds   0.0.0.0:63790->6379/tcp, [::]:63790->6379/tcp

5. Perform database migration

docker compose exec varview-django python manage.py migrate

Important: This step creates the necessary database tables. GVMV will not work correctly if migrations are not applied.

6. Access the application

Open your browser and go to: http://localhost:8080

Citation

If you use GVMV in your research, please cite our GitHub repository as: Shen, Y., & Liu, C. (2026). GVMV: Gene Variant Map Viewer [Software]. GitHub. https://github.com/BioLiu/GVMV

License

This project is distributed under the MIT License.
Please note that the tool accesses the NCBI E-utilities and SMART APIs; therefore, any use of this tool is subject to the terms and conditions set forth by NCBI and SMART. It is the user's responsibility to review and adhere to those policies.

Contact & Support

For questions or bug reports, please open an issue on GitHub.

Data Privacy Statement

The public server processes data in real-time for visualization purposes only. Data is retained for a maximum of 48 hours from the time of task creation, after which it is automatically deleted. We do not distribute or share any user-submitted variant data or sequences. For sensitive data, we recommend using the local deployment version.