Difference between revisions of "MISO"

From LIMSWiki
Jump to navigationJump to search
(corrected spelling, removed outdated features (no longer exist in MISO), added links to other sites)
(6 intermediate revisions by 2 users not shown)
Line 6: Line 6:
| caption                =  
| caption                =  
| collapsible            =  
| collapsible            =  
| author                =  
| author                = Earlham Institute
| developer              = The Genome Analysis Centre
| developer              = Earlham Institute, Ontario Institute for Cancer Research
| released              = {{Start date|2012|05|31}} (0.1.6)<ref name="MISOStart">{{cite web |url=https://web.archive.org/web/20160429075804/http://www.tgac.ac.uk/misofiles/MISO-01.6.RC-User_Manual.pdf |format=pdf |title=MISO 0.1.6RC User Manual |publisher=The Genome Analysis Centre |date=2012 |pages=2–3 |accessdate=30 September 2012}}</ref>
| released              = {{Start date|2012|05|31}} (0.1.6)<ref name="MISOStart">{{cite web |url=http://www.tgac.ac.uk/misofiles/MISO-01.6.RC-User_Manual.pdf |archiveurl=https://web.archive.org/web/20160429075804/http://www.tgac.ac.uk/misofiles/MISO-01.6.RC-User_Manual.pdf |format=pdf |title=MISO 0.1.6RC User Manual |publisher=The Genome Analysis Centre |date=2012 |pages=2–3 |archivedate=29 April 2016 |accessdate=06 May 2019}}</ref>
| discontinued          =  
| discontinued          =  
| frequently updated    = yes<!-- Release version update? Don't edit this page, just click on the version number! -->
| frequently updated    = yes<!-- Release version update? Don't edit this page, just click on the version number! -->
Line 19: Line 19:
| genre                  = [[Laboratory informatics]] software
| genre                  = [[Laboratory informatics]] software
| license                = GNU Public License v3.0<ref name="MISOStart" />
| license                = GNU Public License v3.0<ref name="MISOStart" />
| website                = [https://miso-lims.github.io/miso-lims/ https://miso-lims.github.io/miso-lims/]
| website                = [https://github.com/miso-lims/miso-lims github.com/miso-lims/miso-lims]
}}
}}


'''MISO''' is a [[laboratory information management system]] (LIMS) that handles next-generation [[sequencing]] experiments, including tracking and recording sequencing metadata. It is open-source and  freely available on Github<ref name="repository">{{cite web |url=https://github.com/miso-lims/miso-lims|title=miso-lims/miso-lims : MISO: An open-source LIMS for NGS sequencing centres|accessdate=7 May 2019</ref>.  
'''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.


==History==
==Product history==


MISO development began in 2010 by the Davey group at Earlham Institute. The first beta, free open-source version community release became available in 2012 <ref name="first_release">{{cite web |url=https://github.com/miso-lims/miso-lims/releases/tag/0.1.6|title="Release 0.1.6 on Github"|date=26 July 2012|accessdate=7 May 2019}}</ref><ref name="first_user_manual">{{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=7 May 2019}}</ref><ref name="MISONews1">{{cite news |url=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 |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>


In 2015, the Ontario Institute for Cancer Research (OICR) chose MISO as their new LIMS system and began to develop it to meet their needs<ref name="repo_contributions">{{cite web|url=https://github.com/miso-lims/miso-lims/graphs/contributors?from=2014-04-26&to=2016-06-17&type=c|title=Contributors to miso-lims/miso-lims|accessdate=7 May 2019}}</ref>. The teams at Earlham and OICR worked out a development plan to better support multiple institutes with the same code base<ref name="collab-article">{{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}}</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>


==Features==
==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. The full list of features is available in the User Manual<ref name="manual">{{cite web | url=https://miso-lims.github.io/miso-lims/usr/user-manual-table-of-contents.html|title="MISO: User Manual"|accessdate=7 May 2019}}</ref>.
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
| STYLE="vertical-align:top;"|
* barcode and label support
{| class="wikitable collapsible" style="border-style:none;" background="#ffffff" border="0" cellpadding="0" cellspacing="0"
* data visualization
|-
* user and group management
  ! colspan="2"| Product: [https://miso-lims.github.io/miso-lims/ MISO LIMS]
* user-centric authentication
|-
* taxonomy lookup
  | style="background-color:white; border-style:none;"| {{Databox LIMSfeature
* broadened metadata support (reference genomes, tissues, stains, libraries, QC types, boxes and containers, arrays, etc.)
| sample_login_man  = Y <ref name="manual" />
* broadened sample and library management (including support for library dilutions)
| sample_track      = Y <ref name="manual" />
* project management (including support for worksets, pools, orders, sequence runs, arrays, etc.)
| sample_batch      = Y <ref name="manual" />
* inventory management
| task_event_sched  =
* instrument management
| manual_entry      = Y <ref name="manual" />
* document management
| multiple_view      = Y <ref name="manual" />
* workflow management
| data_analysis      =
| data_sharing      = Y <ref name="manual" />
| custom_fields      = Y <ref name="manual" />
| query              = Y <ref name="manual" />
| import_data        = Y <ref name="manual" />
| data_linking_int  = Y <ref name="manual" />
| data_linking_ext  = Y <ref name="manual" />
| eln_support        =
| export_msexcel    = Y <ref name="manual" />
| export_raw        = Y <ref name="manual" />
| data_warehouse    =
| deadline_control  =
| production_control =
| project_task_man  =
| inventory_man      = Y <ref name="manual" />
| document_man      = Y <ref name="manual" />
| case_man          =
| workflow_man      =
| spec_man          =
| customer_man      = Y <ref name="manual" />
| billing_man        =


| reg_compliance    =
Reference the [http://miso-lims.github.io/miso-lims/usr/user-manual-table-of-contents.html user manual] for all available features.
| qa_qc              = Y <ref name="manual" />
| performance_eval  =
| audit_trail        = Y <ref name="manual" />
| chain_custody      = Y <ref name="manual" />
| roles_security    = Y <ref name="manual" />
| data_norm          =
| data_val          = Y <ref name="manual" />
| data_encrypt      =
| version_control    =
| data_backup        =
| enviro_monitoring  =


| custom_reporting  =  
==Hardware/software requirements==
| report_printing    =
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.
| label_support      = Y <ref name="manual" />
| barcode_support    = Y <ref name="manual" />
| export_pdf        =  
| export_msword      =
| export_htmlxml    =
| fax_integration    =
| email_integration  =


| admin_manage      = Y <ref name="manual" />
Please reference the [https://github.com/miso-lims/miso-lims/blob/develop/docs/_posts/2016-01-11-installation-guide.md Installation Guide] for more details on installation and configuration.
| modular            =
 
| instrument_inter  = Y <ref name="manual" />
==Videos, screenshots, and other media==
| mobile_device      =
 
| alarms_alerts      =  
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.
| work_timetrack    =  
 
| voice_rec          =  
==Entities using MISO==
| external_monitor  =  
| messaging          =
| multilingual      =
| network            = Y <ref name="manual" />
| web_client        = Y <ref name="manual" />
| online_help        = Y <ref name="manual" />
| saas_model        =  
| usage_cost        =  
| industries        = sequencing genomics
}}
|-
|}
|}


* Earlham Institute
* Ontario Institute for Cancer Research


==Media and news==
==Further reading==


* July 2012: ISMB 2012 presentation<ref name="ismb2012_presentation">{{cite web|url=https://f1000research.com/slides/1092117|title=MISO: An open-source LIMS for next-generation sequencing centres|author=Robert Davey|accessdate=7 May 2019}}</ref> and poster<ref name="ismb2012_poster">{{cite web |url=https://f1000research.com/posters/1092116 |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>. MISO: An open-source LIMS for next-generation sequencing centres.
* {{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}}
* July 2016 : BOSC 2016 presentation<ref name="bosc2016_vid">{{cite url|url=https://www.youtube.com/watch?v=znrRsPip5D0|title=MISO LIMS: HTS Management by Earlham Institute and Ontario Institute for Cancer Research|author=Masella, Andre; Taschuk, Morgan; Armstrong, Heather; Cooke, Dillan; Debat, Tony; Davey, Robert; Salt, Chris|date=2016 |publisher=YouTube|accessdate=7 May 2019}}</ref><ref name="bosc2016_slides">{{cite web|url=https://f1000research.com/slides/5-1608|title=Enhancements to MISO: an open-source community-driven LIMS|publisher=F1000Research|author=Masella, Andre; Taschuk, Morgan; Armstrong, Heather; Cooke, Dillan; Debat, Tony; Davey, Robert; Salt, Chris}}</ref> Enhancements to MISO: an open-source community-driven LIMS
* {{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 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==

Revision as of 17:19, 8 May 2019

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

2.10.1  (December 14, 2023; 4 months ago (2023-12-14))

[±]
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. 
Retrieved from "https://www.limswiki.org/index.php?title=MISO&oldid=35581"