ISkyLIMS - Revision history

Shawndouglas: Text replacement - "\[\[Illumina, Inc.(.*)" to "[[Vendor:Illumina, Inc.$1"

2024-03-29T16:14:08Z

Text replacement - "\[\[Illumina, Inc.(.*)" to "[[Vendor:Illumina, Inc.$1"

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	==Product history==		==Product history==
	iSkyLIMS was conceived as part of the masters project of Luis Chapado at the Autonomous University of Madrid in 2017 and 2018.<ref name="ChapadoCreacion18">{{cite web \|url=https://repositorio.uam.es/bitstream/handle/10486/682665/chapado_chorro_luisantonio_tfm.pdf?sequence=1&isAllowed=y \|format=PDF \|title=Creación de un LIMS para NextSeq \|author=Chapado Chorro, L.A. \|publisher=Universidad Autonomo de Madrid \|date=February 2018 \|accessdate=15 February 2019}}</ref> The core reason for developing the LIMS was, according to Chapado, the fact that no open-source options existed that could integrate readily with the NextSeq series of [[Illumina, Inc.\|Illumina]] sequencers, and the cost of adapting existing open-source options or buying proprietary options to meet the needs of the Carlos III Health Institute (ISCIII) was prohibitive.<ref name="ChapadoCreacion18" /> Shortly after Chapado's masters thesis was released, the software was presented at the European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) in April 2018<ref name="MonzoniSLPDF" />, and a beta 1.1.1 version of iSkyLIMS appeared on GitHub, in May 2018.<ref name="iSLStart1" /> As of December 2018, commits were still being made to the project.<ref name="iSL-GHHome" />		iSkyLIMS was conceived as part of the masters project of Luis Chapado at the Autonomous University of Madrid in 2017 and 2018.<ref name="ChapadoCreacion18">{{cite web \|url=https://repositorio.uam.es/bitstream/handle/10486/682665/chapado_chorro_luisantonio_tfm.pdf?sequence=1&isAllowed=y \|format=PDF \|title=Creación de un LIMS para NextSeq \|author=Chapado Chorro, L.A. \|publisher=Universidad Autonomo de Madrid \|date=February 2018 \|accessdate=15 February 2019}}</ref> The core reason for developing the LIMS was, according to Chapado, the fact that no open-source options existed that could integrate readily with the NextSeq series of [[Vendor:Illumina, Inc.\|Illumina]] sequencers, and the cost of adapting existing open-source options or buying proprietary options to meet the needs of the Carlos III Health Institute (ISCIII) was prohibitive.<ref name="ChapadoCreacion18" /> Shortly after Chapado's masters thesis was released, the software was presented at the European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) in April 2018<ref name="MonzoniSLPDF" />, and a beta 1.1.1 version of iSkyLIMS appeared on GitHub, in May 2018.<ref name="iSLStart1" /> As of December 2018, commits were still being made to the project.<ref name="iSL-GHHome" />

	==Features==		==Features==

Shawndouglas: Citation error

2019-02-16T00:21:01Z

Citation error

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	==Product history==		==Product history==
	iSkyLIMS was conceived as part of the masters project of Luis Chapado at the Autonomous University of Madrid in 2017 and 2018.<ref name="ChapadoCreacion18">{{cite web \|url=https://repositorio.uam.es/bitstream/handle/10486/682665/chapado_chorro_luisantonio_tfm.pdf?sequence=1&isAllowed=y \|format=PDF \|title=Creación de un LIMS para NextSeq \|author=Chapado Chorro, L.A. publisher=Universidad Autonomo de Madrid \|date=February 2018 \|accessdate=15 February 2019}}</ref> The core reason for developing the LIMS was, according to Chapado, the fact that no open-source options existed that could integrate readily with the NextSeq series of [[Illumina, Inc.\|Illumina]] sequencers, and the cost of adapting existing open-source options or buying proprietary options to meet the needs of the Carlos III Health Institute (ISCIII) was prohibitive.<ref name="ChapadoCreacion18" /> Shortly after Chapado's masters thesis was released, the software was presented at the European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) in April 2018<ref name="MonzoniSLPDF" />, and a beta 1.1.1 version of iSkyLIMS appeared on GitHub, in May 2018.<ref name="iSLStart1" /> As of December 2018, commits were still being made to the project.<ref name="iSL-GHHome" />		iSkyLIMS was conceived as part of the masters project of Luis Chapado at the Autonomous University of Madrid in 2017 and 2018.<ref name="ChapadoCreacion18">{{cite web \|url=https://repositorio.uam.es/bitstream/handle/10486/682665/chapado_chorro_luisantonio_tfm.pdf?sequence=1&isAllowed=y \|format=PDF \|title=Creación de un LIMS para NextSeq \|author=Chapado Chorro, L.A. \|publisher=Universidad Autonomo de Madrid \|date=February 2018 \|accessdate=15 February 2019}}</ref> The core reason for developing the LIMS was, according to Chapado, the fact that no open-source options existed that could integrate readily with the NextSeq series of [[Illumina, Inc.\|Illumina]] sequencers, and the cost of adapting existing open-source options or buying proprietary options to meet the needs of the Carlos III Health Institute (ISCIII) was prohibitive.<ref name="ChapadoCreacion18" /> Shortly after Chapado's masters thesis was released, the software was presented at the European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) in April 2018<ref name="MonzoniSLPDF" />, and a beta 1.1.1 version of iSkyLIMS appeared on GitHub, in May 2018.<ref name="iSLStart1" /> As of December 2018, commits were still being made to the project.<ref name="iSL-GHHome" />

	==Features==		==Features==

Shawndouglas: /* Further reading */ Fix

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	\| name = iSkyLIMS		\| name = iSkyLIMS
	\| title = iSkyLIMS		\| title = iSkyLIMS
	\| logo = [[~~Image:~~File:ISkyLIMS.png\|140px]]		\| logo = [[File:ISkyLIMS.png\|140px]]
	\| screenshot = <!-- [[File: ]] -->		\| screenshot = <!-- [[File: ]] -->
	\| caption =		\| caption =

Shawndouglas: Created as needed.

2019-02-16T00:17:57Z

Created as needed.

New page

{{lowercase title}}
{{Infobox software
| name = iSkyLIMS
| title = iSkyLIMS
| logo = [[Image:File:ISkyLIMS.png|140px]]
| screenshot = 
| caption =
| collapsible =
| author =
| developer = Luis Chapado, Sara Monson, ''et al.''
| released = {{Start date|2018|05|10}} (v1.1.1)<ref name="iSLStart1">{{cite web |url=https://github.com/BU-ISCIII/iSkyLIMS/releases/tag/v.1.1.1 |title=iSkyLIMS first beta version!! |author=Monzon, S. |publisher=GitHub, Inc. |date=10 May 2018 |accessdate=15 February 2019}}</ref>
| discontinued =
| frequently updated = yes
| programming language = Python and Django Framework<ref name="MonzoniSLPDF">{{cite web |url=https://www.escmid.org/escmid_publications/escmid_elibrary/material/?mid=64095 |format=PDF |title=iSkyLIMS, a friendly environment to facilitate the incorporation of massive sequencing to a genomics core facility |author=Chapado, L.; Monzon, S.; Sola-Campoy, A. et al. |publisher=European Society of Clinical Microbiology and Infectious Diseases |date=22 April 2018 |accessdate=15 February 2019}}</ref>
| operating system = Linux
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = GNU General Public License v3.0
| website = [https://github.com/BU-ISCIII/iSkyLIMS https://github.com/BU-ISCIII/iSkyLIMS]
}}
'''iSkyLIMS''' is a free, open-source [[laboratory information management system]] (LIMS) "for next generation sequencing [NGS] sample management, statistics and reports, and [[bioinformatics]] analysis service management."<ref name="iSL-GHHome">{{cite web |url=https://github.com/BU-ISCIII/iSkyLIMS |title=BU-ISCIII/iSkyLIMS |work=GitHub |accessdate=15 February 2019}}</ref> The software attempts to address managing the workflow of NGS laboratories, including library preparation and data production, while reducing errors and facilitating quality control.<ref name="iSL-GHHome" />

==Product history==
iSkyLIMS was conceived as part of the masters project of Luis Chapado at the Autonomous University of Madrid in 2017 and 2018.<ref name="ChapadoCreacion18">{{cite web |url=https://repositorio.uam.es/bitstream/handle/10486/682665/chapado_chorro_luisantonio_tfm.pdf?sequence=1&isAllowed=y |format=PDF |title=Creación de un LIMS para NextSeq |author=Chapado Chorro, L.A. publisher=Universidad Autonomo de Madrid |date=February 2018 |accessdate=15 February 2019}}</ref> The core reason for developing the LIMS was, according to Chapado, the fact that no open-source options existed that could integrate readily with the NextSeq series of [[Illumina, Inc.|Illumina]] sequencers, and the cost of adapting existing open-source options or buying proprietary options to meet the needs of the Carlos III Health Institute (ISCIII) was prohibitive.<ref name="ChapadoCreacion18" /> Shortly after Chapado's masters thesis was released, the software was presented at the European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) in April 2018<ref name="MonzoniSLPDF" />, and a beta 1.1.1 version of iSkyLIMS appeared on GitHub, in May 2018.<ref name="iSLStart1" /> As of December 2018, commits were still being made to the project.<ref name="iSL-GHHome" />

==Features==
Features of iSkyLIMS include<ref name="iSLWikiIntro">{{cite web |url=https://github.com/BU-ISCIII/iSkyLIMS/wiki/Introduction |title=Usage: Introduction |work=iSkyLIMS Wiki |publisher=GitHub, Inc |date=26 July 2018 |accessdate=15 February 2019}}</ref>:

* genomic sample management
* genomic sample identification and tracking
* genomic data queries and analysis
* quality management
* reporting
* wet- and dry-lab management

==Hardware/software requirements==
The original developers have experience installing the software on CentOS 6.9, though it presumably can be installed on other Linux pacakges. Apache 2.2, Django 2.0, and Python 3.6.1 are all used by iSkyLIMS.

==Videos, screenshots, and other media==
* [https://github.com/BU-ISCIII/iSkyLIMS/wiki iSkyLims wiki], with installation and usage instructions

==Entities using iSkyLIMS==
Carlos III Health Institute

==Further reading==
* {{cite web |url=https://www.escmid.org/escmid_publications/escmid_elibrary/material/?mid=64095 |format=PDF |title=iSkyLIMS, a friendly environment to facilitate the incorporation of massive sequencing to a genomics core facility |author=Chapado, L.; Monzon, S.; Sola-Campoy, A. et al. |publisher=European Society of Clinical Microbiology and Infectious Diseases |date=22 April 2018}}

* {{cite web |url=https://repositorio.uam.es/bitstream/handle/10486/682665/chapado_chorro_luisantonio_tfm.pdf?sequence=1&isAllowed=y |format=PDF |title=Creación de un LIMS para NextSeq |author=Chapado Chorro, L.A. publisher=Universidad Autonomo de Madrid |date=February 2018}} (in Spanish)

==External links==

==References==
<references />


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

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	* {{cite web \|url=https://www.escmid.org/escmid_publications/escmid_elibrary/material/?mid=64095 \|format=PDF \|title=iSkyLIMS, a friendly environment to facilitate the incorporation of massive sequencing to a genomics core facility \|author=Chapado, L.; Monzon, S.; Sola-Campoy, A. et al. \|publisher=European Society of Clinical Microbiology and Infectious Diseases \|date=22 April 2018}}		* {{cite web \|url=https://www.escmid.org/escmid_publications/escmid_elibrary/material/?mid=64095 \|format=PDF \|title=iSkyLIMS, a friendly environment to facilitate the incorporation of massive sequencing to a genomics core facility \|author=Chapado, L.; Monzon, S.; Sola-Campoy, A. et al. \|publisher=European Society of Clinical Microbiology and Infectious Diseases \|date=22 April 2018}}

	* {{cite web \|url=https://repositorio.uam.es/bitstream/handle/10486/682665/chapado_chorro_luisantonio_tfm.pdf?sequence=1&isAllowed=y \|format=PDF \|title=Creación de un LIMS para NextSeq \|author=Chapado Chorro, L.A. publisher=Universidad Autonomo de Madrid \|date=February 2018}} (in Spanish)		* {{cite web \|url=https://repositorio.uam.es/bitstream/handle/10486/682665/chapado_chorro_luisantonio_tfm.pdf?sequence=1&isAllowed=y \|format=PDF \|title=Creación de un LIMS para NextSeq \|author=Chapado Chorro, L.A. \|publisher=Universidad Autonomo de Madrid \|date=February 2018}} (in Spanish)

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