Difference between revisions of "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}} | ||
==External links== | ==External links== | ||
*[https://github.com/maxplanck-ie/parkour2 Parkour] on GitHub | *[https://github.com/maxplanck-ie/parkour2 Parkour] on GitHub | ||
Latest revision as of 21:50, 26 October 2022
| Developer(s) | Max Planck Institute of Immunobiology and Epigenetics |
|---|---|
| Initial release | January 23, 2020[1] |
| Stable release |
23.11.22 (November 22, 2023) [±] |
| 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
- 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.
External links
- Parkour on GitHub
- Old deprecated code
References
- ↑ 1.0 1.1 "Parkour 0.1.0". GitHub, Inc. 23 January 2020. https://github.com/maxplanck-ie/parkour/releases. Retrieved 26 October 2022.
- ↑ 2.0 2.1 "Parkour2". GitHub, Inc. https://github.com/maxplanck-ie/parkour2. Retrieved 26 October 2022.
- ↑ "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.
- ↑ "Initial commit". GitHub, Inc. 23 May 2016. https://github.com/maxplanck-ie/parkour/commit/af242ce014b1fb141ab395b34d581646d7a55e88. Retrieved 26 October 2022.
- ↑ 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.
- ↑ "First commit". GitHub, Inc. 13 June 2022. https://github.com/maxplanck-ie/parkour2/commit/e74191a7d0ea4b50ca1bef35f07b03fc4bf81bc4. Retrieved 26 October 2022.
- ↑ 7.0 7.1 "Parkour2 - Releases". GitHub, Inc. https://github.com/maxplanck-ie/parkour2/releases. Retrieved 26 October 2022.
