Parkour - Revision history

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	==Further reading==		==Further reading==
	* {{Cite journal \|last=Anatskiy \|first=E \|last2=Ryan \|first2=D P \|last3=Grüning \|first3=B A \|last4=Arrigoni \|first4=L \|last5=Manke \|first5=T \|last6=Bönisch \|first6=U \|date=2019-04-15 \|editor-last=Valencia \|editor-first=Alfonso \|title=Parkour LIMS: high-quality sample preparation in next generation sequencing \|url=https://academic.oup.com/bioinformatics/article/35/8/1422/5102872 \|journal=Bioinformatics \|language=en \|volume=35 \|issue=8 \|pages=1422–1424 \|doi=10.1093/bioinformatics/bty820 \|issn=1367-4803}}		* {{Cite journal \|last=Anatskiy \|first=E \|last2=Ryan \|first2=D P \|last3=Grüning \|first3=B A \|last4=Arrigoni \|first4=L \|last5=Manke \|first5=T \|last6=Bönisch \|first6=U \|date=2019-04-15 \|editor-last=Valencia \|editor-first=Alfonso \|title=Parkour LIMS: high-quality sample preparation in next generation sequencing \|url=https://academic.oup.com/bioinformatics/article/35/8/1422/5102872 \|journal=Bioinformatics \|language=en \|volume=35 \|issue=8 \|pages=1422–1424 \|doi=10.1093/bioinformatics/bty820 \|issn=1367-4803}}

	==External links==		==External links==
	*[https://github.com/maxplanck-ie/parkour2 Parkour] on GitHub		*[https://github.com/maxplanck-ie/parkour2 Parkour] on GitHub

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2022-10-26T21:45:28Z

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← Older revision		Revision as of 21:45, 26 October 2022
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	==Product history==		==Product history==
	In May 2016<ref name="ParkourFirst">{{cite web \|url=https://github.com/maxplanck-ie/parkour/commit/af242ce014b1fb141ab395b34d581646d7a55e88 \|title=Initial commit \|publisher=GitHub, Inc \|date=23 May 2016 \|accessdate=26 October 2022}}</ref>, after finding commercial options expensive or lacking in required features, researchers at the Max Planck Institute of Immunobiology and Epigenetics and the University of Freiburg began work on developing a [[laboratory information management system]] (LIMS) for not only [[next-generation sequencing]] [[Sample (material)\|sample]] management and preparation but also for documenting experimental procedures and standardizing experimental [[metadata]].<ref name="AnatskiyPark19">{{Cite journal \|last=Anatskiy \|first=E \|last2=Ryan \|first2=D P \|last3=Grüning \|first3=B A \|last4=Arrigoni \|first4=L \|last5=Manke \|first5=T \|last6=Bönisch \|first6=U \|date=2019-04-15 \|editor-last=Valencia \|editor-first=Alfonso \|title=Parkour LIMS: high-quality sample preparation in next generation sequencing \|url=https://academic.oup.com/bioinformatics/article/35/8/1422/5102872 \|journal=Bioinformatics \|language=en \|volume=35 \|issue=8 \|pages=1422–1424 \|doi=10.1093/bioinformatics/bty820 \|issn=1367-4803}}</ref> Once the software reached a strong enough development stage, they published an article about their LIMS in the journal ''Bioinformatics'' in September 2018, making the software available on GitHub.<ref name="AnatskiyPark19" /> In January 2020, a stable first release, as 0.1.0, appeared on GitHub after more than a year of institutional use.<ref name="Parkour0.1.0" />		In May 2016<ref name="ParkourFirst">{{cite web \|url=https://github.com/maxplanck-ie/parkour/commit/af242ce014b1fb141ab395b34d581646d7a55e88 \|title=Initial commit \|publisher=GitHub, Inc \|date=23 May 2016 \|accessdate=26 October 2022}}</ref>, after finding commercial options expensive or lacking in required features, researchers at the Max Planck Institute of Immunobiology and Epigenetics and the University of Freiburg began work on developing a [[laboratory information management system]] (LIMS) for not only [[next-generation sequencing]] [[Sample (material)\|sample]] management and preparation but also for documenting experimental procedures and standardizing experimental [[metadata]].<ref name="AnatskiyPark19">{{Cite journal \|last=Anatskiy \|first=E \|last2=Ryan \|first2=D P \|last3=Grüning \|first3=B A \|last4=Arrigoni \|first4=L \|last5=Manke \|first5=T \|last6=Bönisch \|first6=U \|date=2019-04-15 \|editor-last=Valencia \|editor-first=Alfonso \|title=Parkour LIMS: high-quality sample preparation in next generation sequencing \|url=https://academic.oup.com/bioinformatics/article/35/8/1422/5102872 \|journal=Bioinformatics \|language=en \|volume=35 \|issue=8 \|pages=1422–1424 \|doi=10.1093/bioinformatics/bty820 \|issn=1367-4803}}</ref> Once the software reached a strong enough development stage, they published an article about their LIMS in the journal ''Bioinformatics'' in September 2018, making the software available on GitHub.<ref name="AnatskiyPark19" /> In January 2020, a stable first release, as 0.1.0, appeared on GitHub after more than a year of institutional use.<ref name="Parkour0.1.0" />

			An updated version of Parkour—referred to as Parkour2—was added to GitHub in June 2022<ref name="Parkour2First">{{cite web \|url=https://github.com/maxplanck-ie/parkour2/commit/e74191a7d0ea4b50ca1bef35f07b03fc4bf81bc4 \|title=First commit \|publisher=GitHub, Inc \|date=13 June 2022 \|accessdate=26 October 2022}}</ref>, with a first stable release appearing on August 12, 2022, as 0.3.4.<ref name="Parkour2Releases">{{cite web \|url=https://github.com/maxplanck-ie/parkour2/releases \|title=Parkour2 - Releases \|publisher=GitHub, Inc \|accessdate=26 October 2022}}</ref>

	==Features==		==Features==
			A collection of features are not clearly stated, but a few things can be discerned from the [https://github.com/maxplanck-ie/parkour2/wiki/Introduction user manual]:

			* request management
			* sample and library management
			* sample preparation
			* sample pooling
			* flowcell management
			* index generation
			* invoicing
			* user management
			* statistics

	==Hardware/software requirements==		==Hardware/software requirements==
			The software requires<ref name="Parkour2Releases" />:

			* Docker
			* Python 3.8+
			* Django 3.2+
			* [[PostgreSQL]] 14.3+
			* NGINX 1.23+
			* Python dependencies like numpy 1.23+, psycopg2-binary 2.8.6+, pandas 1.4.3+, and gunicorn 20.1+

	==Videos, screenshots, and other media==		==Videos, screenshots, and other media==
			* [https://github.com/maxplanck-ie/parkour2/wiki Parkour wiki and user manual]

	==Entities using Parkour==		==Entities using Parkour==
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	==Further reading==		==Further reading==

	* {{Cite journal \|last=Anatskiy \|first=E \|last2=Ryan \|first2=D P \|last3=Grüning \|first3=B A \|last4=Arrigoni \|first4=L \|last5=Manke \|first5=T \|last6=Bönisch \|first6=U \|date=2019-04-15 \|editor-last=Valencia \|editor-first=Alfonso \|title=Parkour LIMS: high-quality sample preparation in next generation sequencing \|url=https://academic.oup.com/bioinformatics/article/35/8/1422/5102872 \|journal=Bioinformatics \|language=en \|volume=35 \|issue=8 \|pages=1422–1424 \|doi=10.1093/bioinformatics/bty820 \|issn=1367-4803}}		* {{Cite journal \|last=Anatskiy \|first=E \|last2=Ryan \|first2=D P \|last3=Grüning \|first3=B A \|last4=Arrigoni \|first4=L \|last5=Manke \|first5=T \|last6=Bönisch \|first6=U \|date=2019-04-15 \|editor-last=Valencia \|editor-first=Alfonso \|title=Parkour LIMS: high-quality sample preparation in next generation sequencing \|url=https://academic.oup.com/bioinformatics/article/35/8/1422/5102872 \|journal=Bioinformatics \|language=en \|volume=35 \|issue=8 \|pages=1422–1424 \|doi=10.1093/bioinformatics/bty820 \|issn=1367-4803}}

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2022-10-26T21:19:56Z

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{{Infobox software
| name = Parkour
| title = Parkour
| logo =
| screenshot = 
| caption =
| collapsible =
| author =
| developer = [https://www.ie-freiburg.mpg.de/ Max Planck Institute of Immunobiology and Epigenetics]
| released = {{Start date|2020|01|23}}<ref name="Parkour0.1.0">{{cite web |url=https://github.com/maxplanck-ie/parkour/releases |title=Parkour 0.1.0 |publisher=GitHub, Inc |date=23 January 2020 |accessdate=26 October 2022}}</ref>
| discontinued =
| frequently updated = yes
| programming language = JavaScript<ref name="Parkour2">{{cite web |url=https://github.com/maxplanck-ie/parkour2 |title=Parkour2 |publisher=GitHub, Inc |accessdate=26 October 2022}}</ref>
| operating system = Cross-platform
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = GNU General Public License v3.0<ref name="P2License">{{cite web |url=https://github.com/maxplanck-ie/parkour2/blob/022f5e3b36a8939e07b4bbc9520cbec93a6b9df8/parkour_app/static/main-hub/ext/LICENSE |title=parkour2/parkour_app/static/main-hub/ext/LICENSE |publisher=GitHub, Inc |accessdate=26 October 2022}}</ref>
| website = [https://github.com/maxplanck-ie/parkour2 github.com/maxplanck-ie/parkour2]
}}

'''Parkour''' is a free open-source [[laboratory information management system]] (LIMS) released under the GNU General Public License v3.0. The software is tailored to meeting the needs of high-throughput [[sequencing]] [[Laboratory|laboratories]]. The developers at the Max Planck Institute of Immunobiology and Epigenetics state it was "designed to coordinate laboratory work by clearly structuring tasks and facilitate high-quality sample preparation."<ref name="Parkour2" />

==Product history==
In May 2016<ref name="ParkourFirst">{{cite web |url=https://github.com/maxplanck-ie/parkour/commit/af242ce014b1fb141ab395b34d581646d7a55e88 |title=Initial commit |publisher=GitHub, Inc |date=23 May 2016 |accessdate=26 October 2022}}</ref>, after finding commercial options expensive or lacking in required features, researchers at the Max Planck Institute of Immunobiology and Epigenetics and the University of Freiburg began work on developing a [[laboratory information management system]] (LIMS) for not only [[next-generation sequencing]] [[Sample (material)|sample]] management and preparation but also for documenting experimental procedures and standardizing experimental [[metadata]].<ref name="AnatskiyPark19">{{Cite journal |last=Anatskiy |first=E |last2=Ryan |first2=D P |last3=Grüning |first3=B A |last4=Arrigoni |first4=L |last5=Manke |first5=T |last6=Bönisch |first6=U |date=2019-04-15 |editor-last=Valencia |editor-first=Alfonso |title=Parkour LIMS: high-quality sample preparation in next generation sequencing |url=https://academic.oup.com/bioinformatics/article/35/8/1422/5102872 |journal=Bioinformatics |language=en |volume=35 |issue=8 |pages=1422–1424 |doi=10.1093/bioinformatics/bty820 |issn=1367-4803}}</ref> Once the software reached a strong enough development stage, they published an article about their LIMS in the journal ''Bioinformatics'' in September 2018, making the software available on GitHub.<ref name="AnatskiyPark19" /> In January 2020, a stable first release, as 0.1.0, appeared on GitHub after more than a year of institutional use.<ref name="Parkour0.1.0" />

==Features==

==Hardware/software requirements==

==Videos, screenshots, and other media==

==Entities using Parkour==
Max Planck Institute of Immunobiology and Epigenetics

==Further reading==

* {{Cite journal |last=Anatskiy |first=E |last2=Ryan |first2=D P |last3=Grüning |first3=B A |last4=Arrigoni |first4=L |last5=Manke |first5=T |last6=Bönisch |first6=U |date=2019-04-15 |editor-last=Valencia |editor-first=Alfonso |title=Parkour LIMS: high-quality sample preparation in next generation sequencing |url=https://academic.oup.com/bioinformatics/article/35/8/1422/5102872 |journal=Bioinformatics |language=en |volume=35 |issue=8 |pages=1422–1424 |doi=10.1093/bioinformatics/bty820 |issn=1367-4803}}

==External links==
*[https://github.com/maxplanck-ie/parkour2 Parkour] on GitHub
*[https://github.com/maxplanck-ie/parkour/ Old deprecated code]

==References==
<references />


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