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Difference between revisions of "MISO"

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| caption                =  
| caption                =  
| collapsible            =  
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| author                = Earlham Institute
| author                =  
| developer              = Earlham Institute, Ontario Institute for Cancer Research
| developer              = The Genome Analysis Centre
| 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>
| 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>
| 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! -->
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| 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://github.com/miso-lims/miso-lims github.com/miso-lims/miso-lims]
| website                = [https://miso-lims.github.io/miso-lims/ https://miso-lims.github.io/miso-lims/]
}}
}}


'''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 [[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>.  


==Product history==
==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).<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>
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>.


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>
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>.
 
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==


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. 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>.


* user-centric authentication
{|
* extensive laboratory tracking
| STYLE="vertical-align:top;"|
* barcode and print support
{| class="wikitable collapsible" style="border-style:none;" background="#ffffff" border="0" cellpadding="0" cellspacing="0"
* taxonomy lookup
|-
* monitoring and reporting of analytical processes
  ! colspan="2"| Product: [https://miso-lims.github.io/miso-lims/ MISO LIMS]
* data visualization
|-
* user and group management
  | style="background-color:white; border-style:none;"| {{Databox LIMSfeature
* notifications
| sample_login_man  = Y <ref name="manual" />
* automated data/metadata submissions
| sample_track      = Y <ref name="manual" />
* broadened metadata support (reference genomes, tissues, stains, libraries, QC types, boxes and containers, arrays, etc.)
| sample_batch      = Y <ref name="manual" />
* broadened sample and library management (including support for library dilutions)
| task_event_sched  =
* project management (including support for worksets, pools, orders, sequence runs, arrays, etc.)
| manual_entry      = Y <ref name="manual" />
* inventory management
| multiple_view      = Y <ref name="manual" />
* instrument management
| data_analysis      =
* document management
| data_sharing      = Y <ref name="manual" />
* workflow management
| custom_fields      = Y <ref name="manual" />
* alerts
| query              = Y <ref name="manual" />
* extensibility
| 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        =


==Hardware/software requirements==
| reg_compliance    =  
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.
| 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  =


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


==Videos, screenshots, and other media==
| admin_manage      = Y <ref name="manual" />
 
| modular            =  
The [http://miso-lims.github.io/miso-lims/usr/user-manual-table-of-contents.html user manual] is also full of useful information.
| instrument_inter  = Y <ref name="manual" />
 
| mobile_device      =
==Entities using MISO==
| alarms_alerts      =
| work_timetrack    =
| voice_rec          =
| 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


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


* {{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}}
* 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=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}}
* 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


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

Revision as of 21:36, 7 May 2019

MISO
Developer(s) The Genome Analysis Centre
Initial release May 31, 2012 (2012-05-31) (0.1.6)[1]
Stable release

1.51.1  (December 15, 2022; 2 years ago (2022-12-15))

[±]
Preview release none [±]
Written in Java
Operating system platform-independent
Type Laboratory informatics software
License(s) GNU Public License v3.0[1]
Website https://miso-lims.github.io/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[2].

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 [3][4][5].

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[6]. The teams at Earlham and OICR worked out a development plan to better support multiple institutes with the same code base[7].

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[8].

Product: MISO LIMS
Sample, inventory, and data management
Sample login and management?Y [8]
Sample tracking?Y [8]
Sample and/or result batching?Y [8]
Task and event scheduling?
Option for manual result entry?Y [8]
Multiple data viewing methods?Y [8]
Data and trend analysis?
Data and equipment sharing?Y [8]
Customizable fields and/or interface?Y [8]
Query capability?Y [8]
Import data?Y [8]
Internal file or data linking?Y [8]
External file or data linking?Y [8]
ELN support or integration?
Export data to MS Excel?Y [8]
Raw data management?Y [8]
Data warehouse?
Deadline control?
Production control?
Project and/or task management?
Inventory management?Y [8]
Document creation and/or management?Y [8]
Case management?
Workflow management?
Specification management?
Customer and supplier management?Y [8]
Billing management?
Quality, security, and compliance
Regulatory compliance?
QA / QC functions?Y [8]
Performance evaluation?
Audit trail?Y [8]
Chain of custody?Y [8]
Configurable roles and security?Y [8]
Data normalization?
Data validation?Y [8]
Data encryption?
Version control?
Automatic data backup?
Environmental monitoring?
Reporting, barcoding, and printing
Custom reporting?
Report printing?
Label support?Y [8]
Barcode support?Y [8]
Export to PDF?
Export to MS Word?
Export to HTML and/or XML?
Fax integration?
Email integration?
Base functionality
Administrator management?Y [8]
Modular?
Instrument interfacing and management?Y [8]
Mobile device integration?
Alarms and/or alerts?
Work-related time tracking?
Voice recognition system?
External monitoring?
Messaging?
Multilingual?
Network-capable?Y [8]
Web client or portal?Y [8]
Online or integrated help?Y [8]
Software as a service delivery model?
Usage-based cost?
Industries served
sequencing genomics


Media and news

  • July 2012: ISMB 2012 presentation[9] and poster[10]. MISO: An open-source LIMS for next-generation sequencing centres.
  • July 2016 : BOSC 2016 presentation[11][12] Enhancements to MISO: an open-source community-driven LIMS

External links

References

  1. ↑ 1.0 1.1 "MISO 0.1.6RC User Manual" (pdf). The Genome Analysis Centre. 2012. pp. 2–3. https://web.archive.org/web/20160429075804/http://www.tgac.ac.uk/misofiles/MISO-01.6.RC-User_Manual.pdf. Retrieved 30 September 2012. 
  2. ↑ {{cite web |url=https://github.com/miso-lims/miso-lims%7Ctitle=miso-lims/miso-lims : MISO: An open-source LIMS for NGS sequencing centres|accessdate=7 May 2019
  3. ↑ ""Release 0.1.6 on Github"". 26 July 2012. https://github.com/miso-lims/miso-lims/releases/tag/0.1.6. Retrieved 7 May 2019. 
  4. ↑ 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 7 May 2019. 
  5. ↑ "TGAC launches MISO: A free open source LIMS for NGS". The Genome Analysis Centre. 23 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. 
  6. ↑ "Contributors to miso-lims/miso-lims". https://github.com/miso-lims/miso-lims/graphs/contributors?from=2014-04-26&to=2016-06-17&type=c. Retrieved 7 May 2019. 
  7. ↑ "International collaboration cooks up powerful new software: MISO". https://news.oicr.on.ca/2017/02/international-collaboration-cooks-up-powerful-new-software-miso/. 
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 8.19 8.20 8.21 8.22 8.23 8.24 8.25 8.26 8.27 8.28 ""MISO: User Manual"". https://miso-lims.github.io/miso-lims/usr/user-manual-table-of-contents.html. Retrieved 7 May 2019. 
  9. ↑ Robert Davey. "MISO: An open-source LIMS for next-generation sequencing centres". https://f1000research.com/slides/1092117. Retrieved 7 May 2019. 
  10. ↑ 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. https://f1000research.com/posters/1092116. Retrieved 30 September 2012. 
  11. ↑ Template:Cite url
  12. ↑ Masella, Andre; Taschuk, Morgan; Armstrong, Heather; Cooke, Dillan; Debat, Tony; Davey, Robert; Salt, Chris. "Enhancements to MISO: an open-source community-driven LIMS". F1000Research. https://f1000research.com/slides/5-1608. 
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