Genome Engineering Tool
Project description
Edge keeps structural changes between a genome and child genomes derived from it. A user creates a modified genome by applying a sequence based operation, such as homologous recombination, to a parent genome. Users can annotate or make corrections to sequences on a genome; Edge automatically applies the changes to the appropriate regions on the derived genomes. Edge does this efficiently: making a change on a parent genome takes O(1), and is automatically propagated to the modified genomes.
Edge uses O(D) amount of storage for each modified genome, where D is the number of differences between a modified genome and its parent. The current implementation additionally keeps a cache of annotations to base pair numbers, but this cache is soft-data and is invalidated and re-built on demand.
A modified genome can be re-created by re-applying operations to a new genome (think git rebase). Currently, however, annotating a genome is not an operation. Also, applying the same operation to a genome twice results in a single child genome, not two.
Edge provides UIs to look at operations and changes, and APIs for making changes. Edge can export genome sequences and annotations as GFF files. While Edge comes with a simple UI for browsing features and sequences, the UI is primitive compared to other specialized applications.
Try it using Docker
cd docker-edge-simple bash run-server
Then checkout in your browser http://localhost:9000/edge/#/genomes
Example: to import an genome, try
cd docker-edge-simple bash add-s288c
docker-edge-simple environment includes a Docker image without NCBI and primer3. To run tests, and to use Edge for real, use docker-edge
cd docker-edge docker-compose up -d ./db-setup docker-compose run --rm edge python manage.py test
Try it without Docker
Construct your virtual env and pip install dependencies (use requirements/{dev,core}.txt).
To start a server, first update src/server/settings.py to use either sqlite or MySQL. For MySQL, create the appropriate databse. Then,
python src/manage.py syncdb --noinput python src/manage.py migrate (cd example; gunzip ecoli-mg1655.gff.gz; gunzip yeast.gff.gz) python src/manage.py import_gff 'E. coli MG1655' example/ecoli-mg1655.gff python src/manage.py import_gff 'Saccharomyces cerevisiae' example/yeast.gff python src/manage.py runserver 0.0.0.0:8000
Then set your browser to http://<your IP>:8000/edge/
You can edit genome and fragment metadata, such as name, notes, circular attributes, from Django admin. Create a Django admin superuser, then set your browser to http://<your IP>:8000/admin/
If you need BLAST support, run
cd ncbi; ./install cd ../src; python manage.py build_edge_blastdb
If you need Primer3 support, run
cd primer3; ./install
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