LIMSWiki - User contributions [en]

SeqWare

2022-11-23T22:26:11Z

Morgantaschuk: Corrected website links

{{Infobox software
| name = SeqWare
| title = SeqWare
| logo = [[File:Seqware_logo.png‎|200px]]
| screenshot = 
| caption =
| collapsible =
| author =
| developer = [http://seqware.github.com/partners/ SeqWare development team]
| released = {{Start date|2009|12|11}} (0.3.0)<ref name="SWStart">{{cite web |url=http://code.google.com/p/seqware/source/browse/trunk/seqware-queryengine/backend/dist/?r=601 |title=trunk/seqware-queryengine/backend/dist/ - SeqWare |publisher=Google Project Hosting |accessdate=02 October 2012}}</ref>
| discontinued = Yes
| frequently updated = yes
| programming language = Java
| operating system = Cross-platform
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = GNU General Public License v3
| website = [http://seqware.github.io/ seqware.github.io]
}}

'''SeqWare''' was a free open-source suite of software tools designed to act as a framework for building analysis workflows using the analysis tools you choose to implement. The software was targeted primarily at entities needing to analyze massive genomics datasets, especially those generated from next-generation sequencing (NGS) platforms.

==Product history==

Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web |url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf |format=PDF |title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production |author=Marx, Vivien |publisher=BioInform - Genomeweb LLC |date=5 February 2010 |accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web |url=http://seqware.github.com/about/ |title=SeqWare - About |publisher=GitHub, Inc. |accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web |url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page |title=SeqWare - Main Page |publisher=SourceForge |date=24 September 2012 |accessdate=02 October 2012}}</ref>

As of May 2021, no work has been performed on the project for over five years. The project is presumably abandoned.

The following table shows the dates of releases up to 0.12.1. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:

{|
| style="vertical-align:top;" |
{| class="wikitable"
|- valign="top"
!Version
!Release date
|- valign="top"
|0.12.1
|Unknown<ref name="BIGeek">{{cite web |url=https://boconnor.is-a-geek.com/pmwiki/index.php?n=Main.HomePage?logdate=201206 |title=BOConnor's Wiki - Research Blog |publisher=Brian O'Connor |accessdate=02 October 2012}}</ref>
|- valign="top"
|0.12.0
|Unknown<ref name="BIGeek" />
|- valign="top"
|0.11.4
|11 May 2012<ref name="BISFMain" />
|- valign="top"
|0.11.2
|Unknown<ref name="BIDatabase" />
|- valign="top"
|0.10.2
|Unknown<ref name="BIDatabase" />
|- valign="top"
|0.10.1
|Unknown<ref name="BIDatabase" />
|- valign="top"
|0.10.0
|12 January 2012<ref name="BISFMain" />
|- valign="top"
|0.9.1
|Unknown<ref name="BIDatabase">{{cite web |url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Setup_SeqWare_MetaDB#Upgrading_your_Database_Version |title=Setup SeqWare MetaDB - Upgrading your Database Version |publisher=SourceForge |date=10 July 2012 |accessdate=02 October 2012}}</ref>
|- valign="top"
|0.9.0
|Unknown<ref name="BIDatabase" />
|- valign="top"
|0.8.0
|Unknown<ref name="BIDatabase" />
|}
| style="vertical-align:top; padding-right:10px;" |
{| class="wikitable"
|- valign="top"
!Version
!Release date
|- valign="top"
|0.7.0
|03 May 2010<ref name="BIMeetNotes1">{{cite web |url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=20100426 |title=SeqWare - 20100426 |publisher=SourceForge |date=26 April 2010 |accessdate=02 October 2012}}</ref>
|- valign="top"
|0.6.1
|24 February 2010<ref name="SWStart" />
|- valign="top"
|0.6.0
|19 February 2010<ref name="SWStart" />
|- valign="top"
|0.5.0
|18 February 2010<ref name="SWStart" />
|- valign="top"
|0.4.0
|14 January 2010<ref name="SWStart" />
|- valign="top"
|0.3.0
|11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
|0.2.0
|11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
|0.1.2
|11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
|0.1.1
|11 December 2009 (public)<ref name="SWStart" />
|}
|}

==Features==

Features of SeqWare included<ref name="SWAbout" />:

*a database for storing metadata
*sample management
*data analysis and retrieval
*worflow management
*extensibility
*query

==Hardware/software requirements==

Requirements for proper installation of SeqWare included:

*a 64-bit Linux environment
*VirtualBox (if willing to run a local VM on Windows or MacOS)

More information about installation can be found on [https://seqware.github.io/docs/2-installation/ the GitHub site].

==Videos, screenshots, and other media==

Screenshots were provided in the [http://seqware.github.io/docs/3-getting-started/user-tutorial/ user tutorial] as well as much of the current [http://seqware.github.io/docs/ documentation].

==Entities using SeqWare==

Current users included<ref name="SWPart">{{cite web |url=http://seqware.github.com/partners/ |title=SeqWare - Partners |publisher=Brian O’Connor |accessdate=02 October 2012}}</ref>:

Lineberger Comprehensive Cancer Center, Nimbus Informatics

==Further reading==

* {{cite journal |journal=BMC Bioinformatics |year=2010 |volume=11 |issue=Suppl. 12 |pages=S2 |title=SeqWare Query Engine: storing and searching sequence data in the cloud |author=O'Connor, Brian D.; Merriman, Barry; Nelson, Stanley F. |url=http://www.biomedcentral.com/1471-2105/11/S12/S2 |doi=10.1186/1471-2105-11-S12-S2}}

* {{cite web |url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf |format=PDF |title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production |author=Marx, Vivien |publisher=BioInform - Genomeweb LLC |date=5 February 2010 |accessdate=02 October 2012}}

==External links==

*[http://code.google.com/p/seqware/ SeqWare on Google Projects] (deprecated)
*[https://github.com/SeqWare/seqware SeqWare GitHub repository] (current)

==References==
<references />


[[Category:Discontinued or abandoned software (open source)]]

SeqWare

2022-05-19T14:36:35Z

Morgantaschuk: Remove Ontario Institute for Cancer Research from current institutions using SeqWare

{{Infobox software
| name = SeqWare
| title = SeqWare
| logo = [[File:Seqware_logo.png‎|200px]]
| screenshot = 
| caption =
| collapsible =
| author =
| developer = [http://seqware.github.com/partners/ SeqWare development team]
| released = {{Start date|2009|12|11}} (0.3.0)<ref name="SWStart">{{cite web |url=http://code.google.com/p/seqware/source/browse/trunk/seqware-queryengine/backend/dist/?r=601 |title=trunk/seqware-queryengine/backend/dist/ - SeqWare |publisher=Google Project Hosting |accessdate=02 October 2012}}</ref>
| discontinued = Yes
| frequently updated = yes
| programming language = Java
| operating system = Cross-platform
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = GNU General Public License v3
| website = [http://seqware.github.com/ seqware.github.com]
}}

'''SeqWare''' was a free open-source suite of software tools designed to act as a framework for building analysis workflows using the analysis tools you choose to implement. The software was targeted primarily at entities needing to analyze massive genomics datasets, especially those generated from next-generation sequencing (NGS) platforms.

==Product history==

Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles.<ref name="BIStory">{{cite web |url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf |format=PDF |title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production |author=Marx, Vivien |publisher=BioInform - Genomeweb LLC |date=5 February 2010 |accessdate=02 October 2012}}</ref><ref name="SWAbout">{{cite web |url=http://seqware.github.com/about/ |title=SeqWare - About |publisher=GitHub, Inc. |accessdate=02 October 2012}}</ref> Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site.<ref name="SWStart" /> In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core."<ref name="BIStory" /> SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities."<ref name="BIStory" /> Work progressed steadily, including a 2012 switch from SourceForge to GitHub.<ref name="BISFMain">{{cite web |url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page |title=SeqWare - Main Page |publisher=SourceForge |date=24 September 2012 |accessdate=02 October 2012}}</ref>

As of May 2021, the seqware.io website is dead, and no work has been performed on the project for over five years. The project is presumably abandoned.

The following table shows the dates of releases up to 0.12.1. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the [http://seqware.github.io/release-notes/ release notes]:

{|
| style="vertical-align:top;" |
{| class="wikitable"
|- valign="top"
!Version
!Release date
|- valign="top"
|0.12.1
|Unknown<ref name="BIGeek">{{cite web |url=https://boconnor.is-a-geek.com/pmwiki/index.php?n=Main.HomePage?logdate=201206 |title=BOConnor's Wiki - Research Blog |publisher=Brian O'Connor |accessdate=02 October 2012}}</ref>
|- valign="top"
|0.12.0
|Unknown<ref name="BIGeek" />
|- valign="top"
|0.11.4
|11 May 2012<ref name="BISFMain" />
|- valign="top"
|0.11.2
|Unknown<ref name="BIDatabase" />
|- valign="top"
|0.10.2
|Unknown<ref name="BIDatabase" />
|- valign="top"
|0.10.1
|Unknown<ref name="BIDatabase" />
|- valign="top"
|0.10.0
|12 January 2012<ref name="BISFMain" />
|- valign="top"
|0.9.1
|Unknown<ref name="BIDatabase">{{cite web |url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Setup_SeqWare_MetaDB#Upgrading_your_Database_Version |title=Setup SeqWare MetaDB - Upgrading your Database Version |publisher=SourceForge |date=10 July 2012 |accessdate=02 October 2012}}</ref>
|- valign="top"
|0.9.0
|Unknown<ref name="BIDatabase" />
|- valign="top"
|0.8.0
|Unknown<ref name="BIDatabase" />
|}
| style="vertical-align:top; padding-right:10px;" |
{| class="wikitable"
|- valign="top"
!Version
!Release date
|- valign="top"
|0.7.0
|03 May 2010<ref name="BIMeetNotes1">{{cite web |url=http://sourceforge.net/apps/mediawiki/seqware/index.php?title=20100426 |title=SeqWare - 20100426 |publisher=SourceForge |date=26 April 2010 |accessdate=02 October 2012}}</ref>
|- valign="top"
|0.6.1
|24 February 2010<ref name="SWStart" />
|- valign="top"
|0.6.0
|19 February 2010<ref name="SWStart" />
|- valign="top"
|0.5.0
|18 February 2010<ref name="SWStart" />
|- valign="top"
|0.4.0
|14 January 2010<ref name="SWStart" />
|- valign="top"
|0.3.0
|11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
|0.2.0
|11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
|0.1.2
|11 December 2009 (public)<ref name="SWStart" />
|- valign="top"
|0.1.1
|11 December 2009 (public)<ref name="SWStart" />
|}
|}

==Features==

Features of SeqWare included<ref name="SWAbout" />:

*a database for storing metadata
*sample management
*data analysis and retrieval
*worflow management
*extensibility
*query

==Hardware/software requirements==

Requirements for proper installation of SeqWare included:

*a 64-bit Linux environment
*VirtualBox (if willing to run a local VM on Windows or MacOS)

More information about installation can be found on [http://seqware.github.com/docs/2-installation/ the GitHub site].

==Videos, screenshots, and other media==

Screenshots were provided in the [http://seqware.github.com/docs/3-getting-started/user-tutorial/ user tutorial] as well as much of the current [http://seqware.github.com/docs/ documentation].

==Entities using SeqWare==

Current users included<ref name="SWPart">{{cite web |url=http://seqware.github.com/partners/ |title=SeqWare - Partners |publisher=Brian O’Connor |accessdate=02 October 2012}}</ref>:

Lineberger Comprehensive Cancer Center, Nimbus Informatics

==Further reading==

* {{cite journal |journal=BMC Bioinformatics |year=2010 |volume=11 |issue=Suppl. 12 |pages=S2 |title=SeqWare Query Engine: storing and searching sequence data in the cloud |author=O'Connor, Brian D.; Merriman, Barry; Nelson, Stanley F. |url=http://www.biomedcentral.com/1471-2105/11/S12/S2 |doi=10.1186/1471-2105-11-S12-S2}}

* {{cite web |url=http://pegasus.isi.edu/publications/ucla-pegasus.pdf |format=PDF |title=UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production |author=Marx, Vivien |publisher=BioInform - Genomeweb LLC |date=5 February 2010 |accessdate=02 October 2012}}

==External links==

*[http://code.google.com/p/seqware/ SeqWare on Google Projects] (deprecated)
*[https://github.com/SeqWare/seqware SeqWare GitHub repository] (current)

==References==
<references />


[[Category:Discontinued or abandoned software (open source)]]

User:Morgantaschuk

2019-05-08T17:21:19Z

Morgantaschuk: Created page with " == Morgan Taschuk == Senior Manager at Ontario Institute for Cancer Research, leading the MISO project."

== Morgan Taschuk ==

Senior Manager at Ontario Institute for Cancer Research, leading the [[MISO]] project.

MISO

2019-05-08T17:19:19Z

Morgantaschuk: corrected spelling, removed outdated features (no longer exist in MISO), added links to other sites

{{Infobox software
| name = MISO
| title = MISO
| logo = 
| screenshot = 
| caption =
| collapsible =
| author = Earlham Institute
| developer = Earlham Institute, Ontario Institute for Cancer Research
| 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 =
| frequently updated = yes
| programming language = Java
| operating system = platform-independent
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = GNU Public License v3.0<ref name="MISOStart" />
| website = [https://github.com/miso-lims/miso-lims 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).<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 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==

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
* 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 [http://miso-lims.github.io/miso-lims/usr/user-manual-table-of-contents.html 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 [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.

==Videos, screenshots, and other media==

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==

* Earlham Institute
* Ontario Institute for Cancer Research

==Further reading==

* {{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 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==

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

==References==
<references />


[[Category:Bioinformatics software (open source)]]
[[Category:Laboratory informatics software (open source)]]
[[Category:Laboratory information management systems (open source)]]

User talk:Morgantaschuk

2019-05-08T17:17:45Z

Morgantaschuk:

'''Welcome to ''LIMSWiki''!'''
We hope you will contribute much and well.
Please be mindful to make all contributions as accurate as possible.

You will probably want to read the [[https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents|help pages]].
Don't hesitate to ask for assistance on the creation of your own page, as well as whatever else you would like to contribute.

We hope that '''LIMSWiki''' will become the go-to source for all your information needs regarding everything related to LIMS, whether it be a company, information on a specific industry topic, or even just a definition of a simple abbreviation!!
Stay ahead of the game, and be informed.

Again, welcome and have fun! [[User:Admin|Admin]] ([[User talk:Admin|talk]]) 16:26, 6 May 2019 (UTC)

==MISO edits==
Here on LIMSwiki, we treat our open-source software pages differently than we do our vendor pages. (You can browse our [[:Category:Open-source software|open-source software articles]] to verify this is the case.) I reverted your edits because they made the page look exactly like a vendor page, which isn't OK. Also, we don't remove valid history from articles. I'll go through the changes you made and see how I can integrate them into the article without removing the important core material. [[User:Shawndouglas|Shawn Douglas]] ([[User talk:Shawndouglas|talk]]) 16:40, 8 May 2019 (UTC)

Great, thanks. I couldn't find any information about how to construct pages on this wiki (beyond the basic help above), so I copied some of the most popular pages that referred to specific software, hence it looking like a vendor page. [[User:Morgantaschuk|Morgan Taschuk]] ([[User talk:Morgantaschuk|talk]]) 17:17, 8 May 2019 (UTC)

MISO

2019-05-07T21:39:27Z

Morgantaschuk:

{{Infobox software
| name = MISO
| title = MISO
| logo = 
| screenshot = 
| caption =
| collapsible =
| author =
| developer = 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>
| discontinued =
| frequently updated = yes
| programming language = Java
| operating system = platform-independent
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = GNU Public License v3.0<ref name="MISOStart" />
| website = [https://miso-lims.github.io/miso-lims/ 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<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>.

==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>.

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>.

==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>.

{|
| STYLE="vertical-align:top;"|
{| class="wikitable collapsible" style="border-style:none;" background="#ffffff" border="0" cellpadding="0" cellspacing="0"
|-
! colspan="2"| Product: [https://miso-lims.github.io/miso-lims/ MISO LIMS]
|-
| style="background-color:white; border-style:none;"| {{Databox LIMSfeature
| sample_login_man = Y <ref name="manual" />
| sample_track = Y <ref name="manual" />
| sample_batch = Y <ref name="manual" />
| task_event_sched =
| manual_entry = Y <ref name="manual" />
| multiple_view = Y <ref name="manual" />
| 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 =
| 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 =
| report_printing =
| 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" />
| modular =
| instrument_inter = Y <ref name="manual" />
| mobile_device =
| 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
}}
|-
|}
|}

==Media==

* 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.
* July 2016 : BOSC 2016 presentation<ref name="bosc2016_vid">{{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, 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==

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

==References==
<references />


[[Category:Bioinformatics software (open source)]]
[[Category:Laboratory informatics software (open source)]]
[[Category:Laboratory information management systems (open source)]]

MISO

2019-05-07T21:36:19Z

Morgantaschuk:

{{Infobox software
| name = MISO
| title = MISO
| logo = 
| screenshot = 
| caption =
| collapsible =
| author =
| developer = The Genome Analysis Centre
| 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 =
| frequently updated = yes
| programming language = Java
| operating system = platform-independent
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = GNU Public License v3.0<ref name="MISOStart" />
| website = [https://miso-lims.github.io/miso-lims/ 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<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>.

==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>.

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>.

==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>.

{|
| STYLE="vertical-align:top;"|
{| class="wikitable collapsible" style="border-style:none;" background="#ffffff" border="0" cellpadding="0" cellspacing="0"
|-
! colspan="2"| Product: [https://miso-lims.github.io/miso-lims/ MISO LIMS]
|-
| style="background-color:white; border-style:none;"| {{Databox LIMSfeature
| sample_login_man = Y <ref name="manual" />
| sample_track = Y <ref name="manual" />
| sample_batch = Y <ref name="manual" />
| task_event_sched =
| manual_entry = Y <ref name="manual" />
| multiple_view = Y <ref name="manual" />
| 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 =
| 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 =
| report_printing =
| 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" />
| modular =
| instrument_inter = Y <ref name="manual" />
| mobile_device =
| 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
}}
|-
|}
|}

==Media and news==

* 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.
* 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==

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

==References==
<references />


[[Category:Bioinformatics software (open source)]]
[[Category:Laboratory informatics software (open source)]]
[[Category:Laboratory information management systems (open source)]]