The EPI2ME Labs Launcher is used to start, stop, and update the EPI2MELabs notebook server, our interactive environment for bioinformatics exploration and learning. We provide executables for Windows 10, macOS, and Linux.
Below are listed all resources on which EPI2ME Labs is built. We aim for all components of EPI2MELabs to be open source (including this website) and available through our GitHub repository: https://github.com/epi2me-labs/.
If you find something is not available please contact firstname.lastname@example.org
A listing of all available notebooks is available on the Notebook Index page.
The notebooks used within EPI2ME Labs are available in their source form from the GitHub repository: https://github.com/epi2me-labs/tutorials. These are updated regularly with enhancements and fixes.
The docker container for the EPI2MELabs notebook server is hosted on dockerhub: https://hub.docker.com/r/ontresearch/epi2melabs-notebook. This source code used to build this image is contained within the git repositories nanolabs and tutorials. The notebook server is based on the docker-stacks project. The EPI2ME Labs team have added bioinformatics software as well as various Jupyter extensions (including some custom additions).
A listing of all available notebooks is available on the Workflows Index page.
All EPI2ME Labs workflows are available open-source through our
Github space; workflow projects
are named with a
The workflows can be run easily using nextflow without explicitely downloading anything from Github, for example:
nextflow run epi2me-labs/wf-artic --help
Will download our SARS-CoV-2 ARTIC sequencing workflow and display its help text. See the Workflow Quick Start for further information.
In the course of creating informative tutorials and tailored workflows, the Customer Workflows group at Oxford Nanopore Technologies has created several standalone packages that might be useful to other scientists in their own right.
Aplanat is a plotting library built on top of bokeh. It allows graphs to be contructed and displayed in notebooks with minimal boiler plate. Aplanat also provides functionality to generate static HTML report documents, as used in the EPI2ME Labs Nextflow workflows.
Fastcat is a small FASTQ utility primarily used to concatenate transparently compressed and uncompressed FASTQ files, whilst producing summaries of the input files.