This Docker image provides a minimal Python environment with AlphaGenome and common data science libraries installed. It is designed to replicate a similar environment to Google Colab for offline or local development.
- alphagenome
- matplotlib
- pandas
- numpy
- flask
- Docker installed (https://docs.docker.com/get-docker/)
To build the Docker image:
docker build -t alphagenome-web .This will create an image named alphagenome-web.
To start an interactive Web app inside the container with your API key, you can pass it as an environment variable:
docker run -it --rm -p 8080:8080 \
-v $(pwd):/alphagenome \
-e API_KEY=your_real_api_key_here \
alphagenome-webAlternatively, create a .env file in this directory with the following content:
API_KEY=your_real_api_key_here
Then run the container using:
docker run -it --rm -p 8080:8080 \
-v $(pwd):/alphagenome \
--env-file .env \
alphagenome-webOnce the application is running, you can open a web interface where you can input a DNA sequence and run the analysis by visiting http://localhost:8080/ in your browser.
| Output Type | Description | Data / Interpretation |
|---|---|---|
| ATAC | Identifies regions of open chromatin using Tn5 transposase | Open chromatin; regulatory accessibility |
| CAGE | Captures transcription start sites (TSS) via 5' capped RNAs | Promoter activity; precise TSS location |
| DNASE | Maps DNase I hypersensitive sites | Regulatory elements like enhancers and promoters |
| RNA_SEQ | Measures gene expression via RNA sequencing | Transcript abundance; splicing patterns |
| CHIP_HISTONE | ChIP-seq for histone modifications | Epigenetic marks (e.g., H3K27ac, H3K4me3) indicating active regions |
| CHIP_TF | ChIP-seq for transcription factors | TF binding sites; regulatory network inference |
| SPLICE_SITES | Annotated or predicted splice donor/acceptor sites | Exon-intron boundaries; splicing signals |
| SPLICE_SITE_USAGE | Quantitative usage level of splice sites | Splicing dynamics; isoform switching |
| SPLICE_JUNCTIONS | Inferred exon junctions from RNA-seq reads | Alternative splicing patterns |
| CONTACT_MAPS | Chromatin interaction data (e.g., Hi-C, Micro-C) | 3D genome organization; enhancer-promoter loops |
| PROCAP | High-resolution identification of transcription start sites via run-on cap | Active transcription initiation; enhancer activity |
This project is licensed under the MIT License. See the LICENSE file for details.