Multiscale Genomics

Virtual Research Environment- Supporting the 3D/4D genomics community with tools to integrate navigation from sequence to 3D/4D chromatin dynamics data.

Full details of the project can be found on the MuG website.

From this site there are links to all of the documentation for each of the repositories within the MuG GitHub. Each set of documents contains details about the installation and usage both for an end user and for developers creating workflows.

If you want to develop tools and workflows that can run within the VRE please checkout the HOWTO section of the site. This lists how to write a workflow, tool, the configuration files and testing that the workflow works. Please also read about how to apply the Apache2.0 license to your code and a document on Coding Standards that you should adher to to ensure the best chance of your workflow being integrated with the VRE as smoothly as possible.



MuG Virtual Research Environment. MuG VRE is a web application aimed to allow MuG users to access MuG data and explore and exploit it together with its own data via a selection of tools and visualizers. It is written in PHP, HTML and Javascript.

GitHub VRE

Development APIs


Data Management API. This API tracks files within the VRE and contains meta data about how the file was generated with access to the file geneology.

GitHub mg-dm-api


Tool API. This API provides the interface between the pyCOMPSs architecture and the tool. It provides a standard way for all tools to be wrapped to allow for a common interface layer.

GitHub mg-tool-api



Workflows for processing FASTQ data. These workflows can handle ChIP-seq, MNase-Seq, RNA-Seq and Whole Genome BiSulphate Sequencing (WGBS). There are also scripts for generating the inditial set of indexes for given genome assemblies. There are also workflows for processing Hi-C data to generate adjacency matrices and calculate TAD regions

GitHub mg-process-fastq


Workflows for processing results files into an indexed form for use in a RESTful interface.

GitHub mg-process-files



The root RESTful server. This provides links to the main root end points. Each end point is a provides a unique function within the defined URL so that the service as a whole appears seamless to the end user.

GitHub mg-rest-service


RESTful interface to the DM API along with end-points to manage the stored files and track the relevant metadata.

GitHub mg-rest-dm


RESTful interface to the DM API along with end-points to servicing out regions from basic file based data, such as Bed, Wig and TSV files.

GitHub mg-rest-file


Interface for RESTfully querying adjacency matrices generated by the TADbit workflows developed in mg-process-fastq.

GitHub mg-rest-adjacency


Interface for RESTfully querying 3D models generated by the TADbit workflows developed in mg-process-files.

GitHub mg-rest-3d


Set of common functions that are required by the RESTful interfaces for interacting with the DM API.

GitHub mg-rest-util

Indices and tables