MISO

MISO
Original author(s)	Earlham Institute
Developer(s)	Earlham Institute, Ontario Institute for Cancer Research
Initial release	May 31, 2012 (0.1.6)
Stable release	2.18.0 (June 7, 2024; 6 months ago) [±]
Preview release	none [±]
Written in	Java
Operating system	platform-independent
Type	Laboratory informatics software
License(s)	GNU Public License v3.0
Website	github.com/miso-lims/miso-lims

MISO is a modular, open-source laboratory information management system (LIMS) that handles next-generation sequencing experiments, including the tracking and recording of sequencing metadata.

Product history

Development for MISO began in February 2010 by Dr. Robert Davey and the Core Bioinformatics Team of The Genome Analysis Centre (TGAC), located in the United Kingdom. The first release of MISO occurred internally on September 19, 2011, beginning with version 0.1.1 (Hydrogen). Once several revisions took place, the software was released as free open-source software on May 31, 2012, represented as version 0.1.6 (Carbon).^[1] On July 15, Dr. Davey presented MISO to attendees of the 20th Annual International Conference on Intelligent Systems for Molecular Biology, demonstrating installation, developmental insight, and future features.^[2]^[3]

Sometime in 2015, the Ontario Institute for Cancer Research (OICR) approached TGAC about MISO, noting however that "OICR did not want to fork MISO entirely." The OICR's Geospiza GeneSifter LE LIMS was proprietary—inhibiting workflow flexibility—and features they wanted weren't being added.^[4] Working together, TGAC and OICR "worked out a development plan to better support multiple institutes with the same code base."^[5]^[6] This included that addition of features such as the ability "to capture more information about samples such as tissue type" and various other types of metadata.^[7]

In June 2016, the Genome Analysis Centre announced it had rebranded itself to the Earlham Institute as "the name TGAC was no longer reflective of the evolution of the organisation and the breadth of scientific research being undertaken at the Institute."^[8]

Features

MISO is a full-featured LIMS system that concentrates on tracking samples and laboratory processes for modern DNA and RNA sequencing from a number of platforms, including Illumina, PacBio, and Oxford Nanopore. Features of MISO include^[9]^[3]^[5]:

sample log-in, batching, management, and tracking
barcode and label support
data visualization
user and group management
user-centric authentication
taxonomy lookup
broadened metadata support (reference genomes, tissues, stains, libraries, QC types, boxes and containers, arrays, etc.)
broadened sample and library management (including support for library dilutions)
project management (including support for worksets, pools, orders, sequence runs, arrays, etc.)
inventory management
instrument management
document management
workflow management

Reference the user manual for all available features.

Hardware/software requirements

Using Docker proves to be the easiest way to try MISO. Docker 18.06.0+ and, potentially, Docker Compose are required. It can be configured for plain sample mode or detailed sample mode. The software can also be installed locally, though prerequisites such as Java Development Kit 8, Tomcat 8, MySQL 5.7.7, Flyway 5.2.4, and other tools are required.

Please reference the Installation Guide for more details on installation and configuration.