Difference between revisions of "Parkour"

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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==
Line 40: Line 59:


==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}}


Revision as of 21:45, 26 October 2022

Parkour
Developer(s) Max Planck Institute of Immunobiology and Epigenetics
Initial release January 23, 2020 (2020-01-23)[1]
Stable release

23.11.22  (November 22, 2023; 5 months ago (2023-11-22))

[±]
Written in JavaScript[2]
Operating system Cross-platform
Type Laboratory informatics software
License(s) GNU General Public License v3.0[3]
Website 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 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."[2]

Product history

In May 2016[4], 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 management and preparation but also for documenting experimental procedures and standardizing experimental metadata.[5] 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.[5] In January 2020, a stable first release, as 0.1.0, appeared on GitHub after more than a year of institutional use.[1]

An updated version of Parkour—referred to as Parkour2—was added to GitHub in June 2022[6], with a first stable release appearing on August 12, 2022, as 0.3.4.[7]

Features

A collection of features are not clearly stated, but a few things can be discerned from the user manual:

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

Hardware/software requirements

The software requires[7]:

  • 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

Entities using Parkour

Max Planck Institute of Immunobiology and Epigenetics

Further reading


External links

References

  1. ↑ 1.0 1.1 "Parkour 0.1.0". GitHub, Inc. 23 January 2020. https://github.com/maxplanck-ie/parkour/releases. Retrieved 26 October 2022. 
  2. ↑ 2.0 2.1 "Parkour2". GitHub, Inc. https://github.com/maxplanck-ie/parkour2. Retrieved 26 October 2022. 
  3. ↑ "parkour2/parkour_app/static/main-hub/ext/LICENSE". GitHub, Inc. https://github.com/maxplanck-ie/parkour2/blob/022f5e3b36a8939e07b4bbc9520cbec93a6b9df8/parkour_app/static/main-hub/ext/LICENSE. Retrieved 26 October 2022. 
  4. ↑ "Initial commit". GitHub, Inc. 23 May 2016. https://github.com/maxplanck-ie/parkour/commit/af242ce014b1fb141ab395b34d581646d7a55e88. Retrieved 26 October 2022. 
  5. ↑ 5.0 5.1 Anatskiy, E; Ryan, D P; Grüning, B A; Arrigoni, L; Manke, T; Bönisch, U (15 April 2019). Valencia, Alfonso. ed. "Parkour LIMS: high-quality sample preparation in next generation sequencing" (in en). Bioinformatics 35 (8): 1422–1424. doi:10.1093/bioinformatics/bty820. ISSN 1367-4803. https://academic.oup.com/bioinformatics/article/35/8/1422/5102872. 
  6. ↑ "First commit". GitHub, Inc. 13 June 2022. https://github.com/maxplanck-ie/parkour2/commit/e74191a7d0ea4b50ca1bef35f07b03fc4bf81bc4. Retrieved 26 October 2022. 
  7. ↑ 7.0 7.1 "Parkour2 - Releases". GitHub, Inc. https://github.com/maxplanck-ie/parkour2/releases. Retrieved 26 October 2022. 
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