What does 1.0 take? MISO-LIMS after 9 years of development
Creators: name: Taschuk, Morgan
name: Armstrong, Heather
name: Cooke, Dillan
name: Masella, Andre
name: Varsava, Alexis
name: Jorgensen, Lars
Publisher: name: F1000 Research Limited
Year: 2019

description: MISO is a laboratory information management system designed for eukaryotic sequencing operations. It supports genomic, exomic, transcriptomic, methyl-omic, and CHiP-seq protocols; long reads and short reads; and microarrays. MISO incorporates a wide feature set useful for both large and small facilities to track their lab workflows in great detail. MISO has two primary goals: 1) to allow laboratory technicians to record their work accurately, without having to adapt their protocols to match the system’s model, with a minimum of data entry overhead and 2) to keep the associated metadata valid and structured enough to use for automation and other downstream applications.<br><br><i>History</i><br>The software was developed by Robert Davey’s lab at the Earlham Institute in Norwich, UK, with the first release in 2011. By 2015, development had slowed to primarily maintenance activities. Our group was looking for a new LIMS and so approached the MISO development team with the intent of developing it to meet specific goals.<br><br><i>Goal 1: Record laboratory activities </i><br>MISO is flexible enough to keep up with rapidly evolving research protocols and methods while simultaneously providing input validation and reducing the pain of data entry. Our detailed sample hierarchy mimics actual laboratory processes for receiving tissues, creating stocks and aliquots, propagating to sequencing libraries, pooling and loading onto a sequencer. Quality control measures, volume, and concentrations can be recorded for each entity. Everything corresponding to a physical specimen is also barcoded, located by freezer and shelf, and tracked by changelogs. MISO supports new instruments like the Illumina NovaSeq, 10X Chromium, and Oxford Nanopore PromethION, added more extensive location tracking, and has improved overall performance.<br><br>We improved UI interfaces to simplify data entry by providing a spreadsheet-like bulk entry interface for every entity in MISO with functions like fill-down and auto-increment. If more power is necessary, MISO allows exporting and importing Excel spreadsheets. MISO also provides automatic name generators based on project names and templates to automatically fill in values for standard laboratory protocols.<br><br><i>Goal 2: Facilitate analysis automation</i><br>A major goal of MISO was to encourage laboratory technicians to enter information in enough detail and with sufficient rigor to automate downstream analysis, particularly base calling and alignment. MISO provides in-browser validation to ensure that controlled vocabulary stays consistent. MISO also implements Pinery, which is a LIMS abstraction layer to allow read-only access to the metadata required for analysis and reporting.<br><br><i>Other associated software</i><br>MISO is intended for laboratory technicians, and so does not have billing, detailed inventory control, or reporting functions built in. However, we’ve built other software to fill these needs. Pinery: a read-only view of MISO’s sample, lane and library data that can be used for a variety of functions, including billing, reporting, and querying. Run Scanner: reads information from sequencing instrument directories and can report on the status of past and active sequencing runs in a computationally amenable format Shesmu: a decision-driven action launching system that can take information from MISO and Pinery and launch analysis jobs Ramen: a detailed inventory tracking system <br><i>Availability and Installation</i><br>The project is open-source and licensed under GPL-3.0 on Github: https://github.com/miso-lims/miso-lims. MISO is most easily installed using Docker Compose. Detailed instructions are available on the website to start MISO in a ‘production’ capacity within a few minutes with persistent storage, SSL encryption, and the features mentioned above. A detailed user manual and comprehensive walkthroughs are also available for training.<br><br><i>Future directions</i><br>MISO is used in production by several institutions, including the Ontario Institute for Cancer Research. After 8 years of development, we consider MISO feature-complete and are preparing a 1.0 release for late 2019.