itaskiran/models

Model zoo for genomics

Kipoi models

This repository hosts predictive models for genomics and serves as a model source for Kipoi. Each folder containing model.yaml is considered to be a single model.

Contributing models

1. Install kipoi:

pip install kipoi

2. Run kipoi ls. This will checkout the kipoi/models repo to ~/.kipoi/models)

3. Follow the instructions on contributing/Getting started.

Using models (to predict, score variants, build new models)

To explore available models, visit http://kipoi.org/models. See kipoi/README.md and docs/using getting started for more information on how to programatically access the models from this repository using CLI, python or R.

Configuring local storage location

This model source (https://github.com/kipoi/models) is included in the Kipoi config file (~/.kipoi/config.yaml) by default:

# ~/.kipoi/config.yaml
model_sources:
    kipoi:
        type: git-lfs
        remote_url: git@github.com:kipoi/models.git
        local_path: ~/.kipoi/models/
        auto_update: True

If you wish to keep the models stored elsewhere, edit the local_path accordingly.