Difference between revisions of "MISO"

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'''MISO''' is a modular [[laboratory information management system]] (LIMS) that handles next-generation [[sequencing]] experiments, including the tracking and recording of sequencing metadata.
'''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==
==Product history==
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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).<ref name="MISOStart" /> 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.<ref name="MISOISMB">{{cite web |url=https://www.iscb.org/cms_addon/conferences/ismb2012/technologytrack.php |title=ISMB 2012 - Technology Track Schedule |publisher=International Society for Computational Biology, Inc |date=2012 |accessdate=30 September 2012}}</ref><ref name="MISONews1">{{cite web |url=http://www.tgac.ac.uk/news/31/68/TGAC-launches-MISO-A-free-open-source-LIMS-for-NGS/ |archiveurl=https://web.archive.org/web/20120731152633/http://www.tgac.ac.uk/news/31/68/TGAC-launches-MISO-A-free-open-source-LIMS-for-NGS/ |title=TGAC launches MISO: A free open source LIMS for NGS |publisher=The Genome Analysis Centre |date=23 July 2012 |archivedate=31 July 2012 |accessdate=30 September 2012}}</ref>
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).<ref name="MISOStart" /> 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.<ref name="MISOISMB">{{cite web |url=https://www.iscb.org/cms_addon/conferences/ismb2012/technologytrack.php |title=ISMB 2012 - Technology Track Schedule |publisher=International Society for Computational Biology, Inc |date=2012 |accessdate=30 September 2012}}</ref><ref name="MISONews1">{{cite web |url=http://www.tgac.ac.uk/news/31/68/TGAC-launches-MISO-A-free-open-source-LIMS-for-NGS/ |archiveurl=https://web.archive.org/web/20120731152633/http://www.tgac.ac.uk/news/31/68/TGAC-launches-MISO-A-free-open-source-LIMS-for-NGS/ |title=TGAC launches MISO: A free open source LIMS for NGS |publisher=The Genome Analysis Centre |date=23 July 2012 |archivedate=31 July 2012 |accessdate=30 September 2012}}</ref>


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.<ref name="MasellaEnhance16">{{cite journal |title=Enhancements to MISO: An open-source community-driven LIMS  [version 1; not peer reviewed] |journal=F1000Research |author=Masella, A.; Taschuk, M.; Armstrong, H. et al. |volume=5 |issue=ISCB Comm J |page=1608 |year=2016 |doi=10.7490/f1000research.1112508.1}}</ref> Working together, TGAC and OICE "worked out a development plan to better support multiple institutes with the same code base."<ref name="MISOManual">{{cite web |url=http://miso-lims.github.io/miso-lims/usr/user-manual-table-of-contents.html |title=MISO - An open-source LIMS for NGS sequencing centres |publisher=OICR and the Earlham Institute |work=GitHub |accessdate=06 May 2019}}</ref><ref name="">{{cite web |url=https://webcache.googleusercontent.com/search?q=cache:LnbzQCp7etkJ:https://documentation.tgac.ac.uk/pages/viewpage.action%3FpageId%3D9076833+&cd=1&hl=en&ct=clnk&gl=us |archiveurl=https://web.archive.org/web/20190506193558/https://webcache.googleusercontent.com/search?q=cache:LnbzQCp7etkJ:https://documentation.tgac.ac.uk/pages/viewpage.action%3FpageId%3D9076833+&cd=1&hl=en&ct=clnk&gl=us |title=Morgan Taschuk’s Home |author=Taschuk, M. |work=Earlham Institute Spaces |date=01 February 2018 |archivedate=06 May 2019 |accessdate=06 May 2019}}</ref> 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.<ref name="OICRInter17">{{cite web |url=https://news.oicr.on.ca/2017/02/international-collaboration-cooks-up-powerful-new-software-miso/ |title=International collaboration cooks up powerful new software: MISO |work=OICR News |publisher=OICR |date=13 February 2017 |accessdate=06 May 2019}}</ref>
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.<ref name="MasellaEnhance16">{{cite journal |title=Enhancements to MISO: An open-source community-driven LIMS  [version 1; not peer reviewed] |journal=F1000Research |author=Masella, A.; Taschuk, M.; Armstrong, H. et al. |volume=5 |issue=ISCB Comm J |page=1608 |year=2016 |doi=10.7490/f1000research.1112508.1}}</ref> Working together, TGAC and OICR "worked out a development plan to better support multiple institutes with the same code base."<ref name="MISOManual">{{cite web |url=http://miso-lims.github.io/miso-lims/usr/user-manual-table-of-contents.html |title=MISO - An open-source LIMS for NGS sequencing centres |publisher=OICR and the Earlham Institute |work=GitHub |accessdate=06 May 2019}}</ref><ref name="">{{cite web |url=https://webcache.googleusercontent.com/search?q=cache:LnbzQCp7etkJ:https://documentation.tgac.ac.uk/pages/viewpage.action%3FpageId%3D9076833+&cd=1&hl=en&ct=clnk&gl=us |archiveurl=https://web.archive.org/web/20190506193558/https://webcache.googleusercontent.com/search?q=cache:LnbzQCp7etkJ:https://documentation.tgac.ac.uk/pages/viewpage.action%3FpageId%3D9076833+&cd=1&hl=en&ct=clnk&gl=us |title=Morgan Taschuk’s Home |author=Taschuk, M. |work=Earlham Institute Spaces |date=01 February 2018 |archivedate=06 May 2019 |accessdate=06 May 2019}}</ref> 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.<ref name="OICRInter17">{{cite web |url=https://news.oicr.on.ca/2017/02/international-collaboration-cooks-up-powerful-new-software-miso/ |title=International collaboration cooks up powerful new software: MISO |work=OICR News |publisher=OICR |date=13 February 2017 |accessdate=06 May 2019}}</ref>


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."<ref name="NRPTheGenome16">{{cite web |url=https://www.norwichresearchpark.com/news/genome-analysis-centre-tgac-has-changed-its-name-earlham-institute |title=The Genome Analysis Centre (TGAC) has changed its name to the Earlham Institute |publisher=Norwich Research Park |date=29 June 2016 |accessdate=06 May 2019}}</ref>
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."<ref name="NRPTheGenome16">{{cite web |url=https://www.norwichresearchpark.com/news/genome-analysis-centre-tgac-has-changed-its-name-earlham-institute |title=The Genome Analysis Centre (TGAC) has changed its name to the Earlham Institute |publisher=Norwich Research Park |date=29 June 2016 |accessdate=06 May 2019}}</ref>
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==Features==
==Features==


Features of MISO include<ref name="MISOPoster">{{cite web |url=http://cdn.f1000.com/posters/docs/250776676 |format=PDF |title=MISO: an open-source LIMS for small-to-large sequencing centres |author=Davey, Robert; Xingdong, Bian; Thanki, Anil; Caccamo, Mario |publisher=Faculty of 1000 Ltd |date=2012 |accessdate=30 September 2012}}</ref><ref name="MISONews1" /><ref name="MISOManual" />:
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<ref name="MISOPoster">{{cite web |url=http://cdn.f1000.com/posters/docs/250776676 |format=PDF |title=MISO: an open-source LIMS for small-to-large sequencing centres |author=Davey, Robert; Xingdong, Bian; Thanki, Anil; Caccamo, Mario |publisher=Faculty of 1000 Ltd |date=2012 |accessdate=30 September 2012}}</ref><ref name="MISONews1" /><ref name="MISOManual" />:


* sample log-in, batching, management, and tracking
* barcode and label support
* data visualization
* user and group management
* user-centric authentication
* user-centric authentication
* extensive laboratory tracking
* barcode and print support
* taxonomy lookup
* taxonomy lookup
* monitoring and reporting of analytical processes
* data visualization
* user and group management
* notifications
* automated data/metadata submissions
* broadened metadata support (reference genomes, tissues, stains, libraries, QC types, boxes and containers, arrays, etc.)
* 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)
* broadened sample and library management (including support for library dilutions)
Line 52: Line 49:
* document management
* document management
* workflow management
* workflow management
* alerts
 
* extensibility
Reference the [https://miso-lims.readthedocs.io/projects/docs/en/latest/user_manual/ user manual] for all available features.


==Hardware/software requirements==
==Hardware/software requirements==
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==Videos, screenshots, and other media==
==Videos, screenshots, and other media==


The [http://miso-lims.github.io/miso-lims/usr/user-manual-table-of-contents.html user manual] is also full of useful information.
The [http://miso-lims.github.io/miso-lims/usr/user-manual-table-of-contents.html user manual] is full of useful information about the LIMS.


==Entities using MISO==
==Entities using MISO==
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==Further reading==
==Further reading==


* {{cite web |url=http://cdn.f1000.com/posters/docs/250776676 |format=PDF |title=MISO: an open-source LIMS for small-to-large sequencing centres |author=Davey, Robert; Xingdong, Bian; Thanki, Anil; Caccamo, Mario |publisher=Faculty of 1000 Ltd |date=2012}}
* {{cite journal |title=MISO: an open-source LIMS for small-to-large sequencing centres |journal=F1000Posters |author=Davey, R.; Xingdong, B.; Thanki, A.; Caccamo, M. |volume=3 |page=931 |year=2012 |url=https://f1000research.com/posters/1092116}}
* {{cite journal |title=MISO: an open source LIMS for sequencing centres |journal=F1000Posters |author=Davey, R. |volume=3 |page=940 |year=2012 |url=https://f1000research.com/slides/1092117}}
* {{cite journal |title=Enhancements to MISO: An open-source community-driven LIMS  [version 1; not peer reviewed] |journal=F1000Research |author=Masella, A.; Taschuk, M.; Armstrong, H. et al. |volume=5 |issue=ISCB Comm J |page=1608 |year=2016 |doi=10.7490/f1000research.1112508.1}}
* {{cite journal |title=Enhancements to MISO: An open-source community-driven LIMS  [version 1; not peer reviewed] |journal=F1000Research |author=Masella, A.; Taschuk, M.; Armstrong, H. et al. |volume=5 |issue=ISCB Comm J |page=1608 |year=2016 |doi=10.7490/f1000research.1112508.1}}
* {{cite web |url=https://www.youtube.com/watch?v=znrRsPip5D0 |title=MISO LIMS: HTS Management by Earlham Institute and Ontario Institute for Cancer Research |author=Masella, A.; Taschuk, M.; Armstrong, H. et al. |date=2016 |publisher=YouTube |accessdate=08 May 2019}}


==External links==
==External links==


* [https://miso-lims.github.io/miso-lims/ MISO website]
* [https://github.com/miso-lims/miso-lims MISO on Github]
* [https://github.com/miso-lims/miso-lims MISO on Github]
* [https://miso-lims.github.io/walkthroughs/ MISO walkthroughs]


==References==
==References==

Latest revision as of 19:30, 13 December 2023

MISO
Original author(s) Earlham Institute
Developer(s) Earlham Institute, Ontario Institute for Cancer Research
Initial release May 31, 2012 (2012-05-31) (0.1.6)[1]
Stable release

2.18.0  (June 7, 2024; 5 months ago (2024-06-07))

[±]
Preview release none [±]
Written in Java
Operating system platform-independent
Type Laboratory informatics software
License(s) GNU Public License v3.0[1]
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.

Videos, screenshots, and other media

The user manual is full of useful information about the LIMS.

Entities using MISO

  • Earlham Institute
  • Ontario Institute for Cancer Research

Further reading

  • Masella, A.; Taschuk, M.; Armstrong, H. et al. (2016). "Enhancements to MISO: An open-source community-driven LIMS [version 1; not peer reviewed]". F1000Research 5 (ISCB Comm J): 1608. doi:10.7490/f1000research.1112508.1. 


External links

References

  1. ↑ 1.0 1.1 1.2 "MISO 0.1.6RC User Manual" (pdf). The Genome Analysis Centre. 2012. pp. 2–3. Archived from the original on 29 April 2016. https://web.archive.org/web/20160429075804/http://www.tgac.ac.uk/misofiles/MISO-01.6.RC-User_Manual.pdf. Retrieved 06 May 2019. 
  2. ↑ "ISMB 2012 - Technology Track Schedule". International Society for Computational Biology, Inc. 2012. https://www.iscb.org/cms_addon/conferences/ismb2012/technologytrack.php. Retrieved 30 September 2012. 
  3. ↑ 3.0 3.1 "TGAC launches MISO: A free open source LIMS for NGS". The Genome Analysis Centre. 23 July 2012. Archived from the original on 31 July 2012. https://web.archive.org/web/20120731152633/http://www.tgac.ac.uk/news/31/68/TGAC-launches-MISO-A-free-open-source-LIMS-for-NGS/. Retrieved 30 September 2012. 
  4. ↑ Masella, A.; Taschuk, M.; Armstrong, H. et al. (2016). "Enhancements to MISO: An open-source community-driven LIMS [version 1; not peer reviewed]". F1000Research 5 (ISCB Comm J): 1608. doi:10.7490/f1000research.1112508.1. 
  5. ↑ 5.0 5.1 "MISO - An open-source LIMS for NGS sequencing centres". GitHub. OICR and the Earlham Institute. http://miso-lims.github.io/miso-lims/usr/user-manual-table-of-contents.html. Retrieved 06 May 2019. 
  6. ↑ Taschuk, M. (1 February 2018). "Morgan Taschuk’s Home". Earlham Institute Spaces. Archived from the original on 06 May 2019. https://web.archive.org/web/20190506193558/https://webcache.googleusercontent.com/search?q=cache:LnbzQCp7etkJ:https://documentation.tgac.ac.uk/pages/viewpage.action%3FpageId%3D9076833+&cd=1&hl=en&ct=clnk&gl=us. Retrieved 06 May 2019. 
  7. ↑ "International collaboration cooks up powerful new software: MISO". OICR News. OICR. 13 February 2017. https://news.oicr.on.ca/2017/02/international-collaboration-cooks-up-powerful-new-software-miso/. Retrieved 06 May 2019. 
  8. ↑ "The Genome Analysis Centre (TGAC) has changed its name to the Earlham Institute". Norwich Research Park. 29 June 2016. https://www.norwichresearchpark.com/news/genome-analysis-centre-tgac-has-changed-its-name-earlham-institute. Retrieved 06 May 2019. 
  9. ↑ Davey, Robert; Xingdong, Bian; Thanki, Anil; Caccamo, Mario (2012). "MISO: an open-source LIMS for small-to-large sequencing centres" (PDF). Faculty of 1000 Ltd. http://cdn.f1000.com/posters/docs/250776676. Retrieved 30 September 2012. 
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