jorenretel / 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 the following files is considered to be a single model:

├── dataloader.py     # implements the dataloader
├── dataloader.yaml   # describes the dataloader
├── dataloader_files/      #/ files required by the dataloader
│   └── ...
├── model.yaml        # describes the model
├── model_files/           #/ files required by the model (like weights.h5 and arch.json)
│   └── ...
└── example_files/         #/ small example files used to test the model
    └── ...

Folders named *_files are tracked by Git Large File Storage (LFS). New models are added by simply submitting a pull-request to https://github.com/kipoi/models.

Contributing models

1. Install Kipoi

1. Install git-lfs
   • conda install -c conda-forge git-lfs && git lfs install
     • alternatively see https://git-lfs.github.com/
2. Install kipoi
   • pip install kipoi
3. Run kipoi ls (this will checkout the kipoi/models repo to ~/.kipoi/models)

2. Add the model

0. cd ~/.kipoi/models
1. Write the model: Create a new folder <my new model> containing all the required files
   • Option 1: Copy the existing model: cp -R <existing model> <my new model> & edit the copied files
   • Option 2: Run kipoi init, answer the questions & edit the created files
   • Option 3: mkdir <my new model> & write all the files from scratch
2. Test the model
   • Step 1: kipoi test ~/.kipoi/models/my_new_model
   • Step 2: kipoi test-source kipoi --all -k my_new_model
3. Commit your changes
   • cd ~/.kipoi/models && git commit -m "Added <my new model>"

3. Submit the pull-request

1. Fork the https://github.com/kipoi/models repo on github (click on the Fork button)
2. Add your fork as a git remote to ~/.kipoi/models
   • cd ~/.kipoi/models && git remote add fork https://github.com/<username>/models.git
3. Push to your fork
   • git push fork master
4. Submit a pull-request (click the New pull request button on your github fork - https://github.com/<username>/models>)

See docs/contributing getting started and docs/tutorials/contributing/models for more information.

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: [email protected]:kipoi/models.git
        local_path: ~/.kipoi/models/

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