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MISO

MISO (Managing Information for Sequencing Operations) is a new open-source Lab Information Management System (LIMS) under development at TGAC, specifically designed for tracking next-generation sequencing experiments.

Sequencing centres differ not only in terms of their scale and output, but also their requirements for information management. Sequencing platforms are becoming more accessible, and the efficient storage of genomic metadata is vital for large and small sequencing centres alike. Off-the-shelf solutions are often very expensive and not cost-effective for the smaller centre. Furthermore, support contracts are often required, and the extensibility of these systems is not in the hands of the metadata generators. In terms of implementation, as well as the desire to tailor an information system in-house, data formats can change and platforms can evolve rapidly. These are valid concerns for both large centres characterised by high-throughout data production and smaller scale laboratories with constrained expenditure for IT solutions, and potentially project specific metadata requirements.

Hence, we are developing MISO, an open-source LIMS for recording sequencing metadata. We are using freely available tools that are industry standard, well documented, and easy to set up on minimal hardware. As a bare system, MISO can store relevant metadata based on a wide array of NGS sequencing platforms (e.g. Illumina GA, HiSeq and MiSeq, Roche 454, ABI SOLiD and PacBio RS) and public repository data submission schemas (e.g. the Sequence Read Archive at the EBI), and has many features common to bespoke and proprietary LIMS, such as secure authentication, fine-grained access control, barcode tracking, and reporting.

Availability

Virtual Image

For getting MISO up and running with the minimum of fuss, we have put together a VirtualBox image that includes a guest OS (Ubuntu) with all the required dependencies and software pre-installed. Please refer to the Documentation for instructions, and be aware that this download is 1GB in size.

https://repos.tgac.bbsrc.ac.uk/miso/latest/MISO_Image.ova

Install from pre-built package

Please follow the instructions in the README to grab the web application package (WAR file) and associated dependencies.

Source Code

For the more geeky types, MISO source code is now available at the link below. We are always happy to accept new contributors and patches, so please get in contact!

https://github.com/TGAC/miso-lims

A JIRA issue tracking system and a Confluence documentation management system will be available in due course. Until these are live, you can consult the PDF User Manual to find out how to use MISO. A Developer Manual is under construction.

Documentation

https://documentation.tgac.ac.uk/

Issue Tracker

https://tracker.tgac.ac.uk/

Demo Installation

Finally, there is a demo MISO install available that the community can play around with:

http://miso-demo.tgac.ac.uk

Features
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MISO provides all of these elements:

  • Authentication – user-centric access control to designated areas Laboratory tracking – project description, sample receipt, library prep, run construction, and barcoding
  • Printing – can connect to barcode printers and print barcodes for the relevant objects inside MISO
  • Bioinformatics pipelines – monitoring and reporting of analytical processes, ability to interact directly with computing clusters via a simple analysis server
  • Reporting – accurate statistics from library preparation and sequencing processes
  • Data Visualisation – tree-structured status diagrams, run status and resource calendar, MISO can easily show the status of each project and its elements
  • Submission – automated packaging of sequencing data and metadata, deployment of these data to remote public repositories
  • Notification – automated import of run metadata and notification of change of run status
We are working on new plugin features to enable MISO to be extendable, making it easier for the community to contribute more features.
Implementation

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We have chosen a relational database model to underpin MISO. Currently this is MySQL, but can be replaced with any other RDBMS (data access objects will obviously have to be constructed for each persistence store). Object relational mapping (ORM) via data access objects (DAOs) is achieved through Spring's JDBC Templates, which enable fine-grained control over queries over the underlying database.

We use simple Java beans, or Plain Old Java Objects (POJOs), to represent the objects in the database, and we construct concrete relationships between them in business logic space.

We have developed a RESTful web application from the Spring 3 MVC framework and, as such, MISO can support a number of view technologies. It comes with a user-friendly interface built on Java Server Pages (JSP) which is designed specifically for lab technicians, but can be queried programmatically using the REST URLs. This means helpful web services, such as remote custom reporting, are available.

We use D3.js for data visualisation in MISO.


 

SRA

MISO is heavily modelled upon the submission schemas specified by the SRA and is therefore able to automatically generate and deploy the required completed XML documents. We are currently working on automated data delivery solutions to user-configured submission endpoints.


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