SMITH - Revision history

Shawndouglas: Abandoned

2021-05-06T19:19:45Z

Abandoned

← Older revision		Revision as of 19:19, 6 May 2021
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	\| developer = Yuriy Vaskin et al.		\| developer = Yuriy Vaskin et al.
	\| released = {{Start date\|2011\|09}} (1.0)<ref name="VencoSMITH">{{cite journal \|url=http://www.biomedcentral.com/1471-2105/15/S14/S3 \|title=SMITH: a LIMS for handling next-generation sequencing workflows \|journal=BMC Bioinformatics \|author=Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko \|volume=15 \|issue=Suppl 14 \|page=S3 \|year=2014 \|doi=10.1186/1471-2105-15-S14-S3 \|pmc=PMC4255740 \|accessdate=04 November 2015}}</ref>		\| released = {{Start date\|2011\|09}} (1.0)<ref name="VencoSMITH">{{cite journal \|url=http://www.biomedcentral.com/1471-2105/15/S14/S3 \|title=SMITH: a LIMS for handling next-generation sequencing workflows \|journal=BMC Bioinformatics \|author=Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko \|volume=15 \|issue=Suppl 14 \|page=S3 \|year=2014 \|doi=10.1186/1471-2105-15-S14-S3 \|pmc=PMC4255740 \|accessdate=04 November 2015}}</ref>
	\| discontinued =		\| discontinued = Yes
	\| frequently updated = yes<!-- Release version update? Don't edit this page, just click on the version number! -->		\| frequently updated = yes<!-- Release version update? Don't edit this page, just click on the version number! -->
	\| programming language = Java		\| programming language = Java
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	}}		}}

	'''SMITH''' (Sequencing Machine Information Tracking and Handling) is free open-source [[laboratory information management system]] (LIMS) software for sequencing applications, originally designed for the Italian Institute of Technology and the European Institute of Oncology.<ref name="VencoSMITH" />		'''SMITH''' (Sequencing Machine Information Tracking and Handling) was free open-source [[laboratory information management system]] (LIMS) software for sequencing applications, originally designed for the Italian Institute of Technology and the European Institute of Oncology.<ref name="VencoSMITH" />

	==Product history==		==Product history==
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	The development team reported in 2014 that SMITH had been used at IIT and EIO to process more than 4000 samples sequenced on 170 flow cells.<ref name="VencoSMITH" />		The development team reported in 2014 that SMITH had been used at IIT and EIO to process more than 4000 samples sequenced on 170 flow cells.<ref name="VencoSMITH" />

			As of May 2021, no code updates had been made since 2015. The project is presumed to be abandoned or discontinued.

	==Features==		==Features==

	According to the associated journal article, the following ~~are~~ some of the features of SMITH<ref name="VencoSMITH" />:		According to the associated journal article, the following were some of the features of SMITH<ref name="VencoSMITH" />:

	* Sample submission		* Sample submission
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	==Hardware/software requirements==		==Hardware/software requirements==

	According to the source code documentation, SMITH ~~requires~~ the following for the source:		According to the source code documentation, SMITH required the following for the source:

	* Maven (http://maven.apache.org/)		* Maven (http://maven.apache.org/)
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	* Hibernate (http://hibernate.org/)		* Hibernate (http://hibernate.org/)

	The following is required for installing the application:		The following was required for installing the application:

	* Java 6 (or higher) (http://www.java.com/)		* Java 6 (or higher) (http://www.java.com/)
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	==Videos, screenshots, and other media==		==Videos, screenshots, and other media==

	* A demo of the software ~~can be~~ found at [http://cru.genomics.iit.it/smith/ http://cru.genomics.iit.it/smith/]. (Login: admin; Password: adminadmin)		* A demo of the software was found at [http://cru.genomics.iit.it/smith/ http://cru.genomics.iit.it/smith/]. (Login: admin; Password: adminadmin)

	==Entities using SMITH==		==Entities using SMITH==
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	<!---Place all category tags here-->		<!---Place all category tags here-->
	[[Category:~~Laboratory informatics~~ software ~~(open source)]]~~		[[Category:Discontinued or abandoned software (open source)]]
	~~[[Category:Laboratory information management systems~~ (open source)]]

Shawndouglas: Created as needed.

2015-11-04T19:54:10Z

Created as needed.

New page

{{Infobox software
| name = SMITH
| title = '''SMITH'''
| logo =
| screenshot = 
| caption =
| collapsible =
| author =
| developer = Yuriy Vaskin et al.
| released = {{Start date|2011|09}} (1.0)<ref name="VencoSMITH">{{cite journal |url=http://www.biomedcentral.com/1471-2105/15/S14/S3 |title=SMITH: a LIMS for handling next-generation sequencing workflows |journal=BMC Bioinformatics |author=Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko |volume=15 |issue=Suppl 14 |page=S3 |year=2014 |doi=10.1186/1471-2105-15-S14-S3 |pmc=PMC4255740 |accessdate=04 November 2015}}</ref>
| discontinued =
| frequently updated = yes
| programming language = Java
| operating system = Cross-platform
| platform =
| size =
| language =
| status =
| genre = [[Laboratory informatics]] software
| license = MIT License
| website = [https://bitbucket.org/yuriy_vaskin/smith/overview https://bitbucket.org/yuriy_vaskin/smith/overview]
}}

'''SMITH''' (Sequencing Machine Information Tracking and Handling) is free open-source [[laboratory information management system]] (LIMS) software for sequencing applications, originally designed for the Italian Institute of Technology and the European Institute of Oncology.<ref name="VencoSMITH" />

==Product history==
The first version of SMITH was deployed at the Italian Institute of Technology (IIT) and the European Institute of Oncology (EIO) in September 2011. On February 5, 2014, the developers ported the source code to Bitbucket and made it available under the MIT license.<ref name="BBSMITH1">{{cite web |url=https://bitbucket.org/yuriy_vaskin/smith/commits/46b82a77322e9bfad06701b89e8a1b5d1b496a4e |title=SMITH - Commits - Initial Import |publisher=Bitbucket |date=05 February 2014 |accessdate=04 November 2015}}</ref>

The development team reported in 2014 that SMITH had been used at IIT and EIO to process more than 4000 samples sequenced on 170 flow cells.<ref name="VencoSMITH" />

==Features==

According to the associated journal article, the following are some of the features of SMITH<ref name="VencoSMITH" />:

* Sample submission
* Sample annotation
* Sample analysis
* Sample tracking
* Project awareness
* Run folder monitoring
* Quality control
* Reagent storage
* Role-based access
* Virtual flow cells
* Index compatibility testing
* Email alerts

The team also noted the following: "Adaptation of SMITH for use with alternative sequencing platforms likely requires a limited set of changes in the script generator, which is tailor-made for Illumina sequencers in the current implementation."<ref name="VencoSMITH" />

==Hardware/software requirements==

According to the source code documentation, SMITH requires the following for the source:

* Maven (http://maven.apache.org/)
* NetBeans is a recommended IDE (https://netbeans.org/)
* PrimeFaces (http://primefaces.org/)
* Hibernate (http://hibernate.org/)

The following is required for installing the application:

* Java 6 (or higher) (http://www.java.com/)
* MySql server (http://www.mysql.com/)
* MySql Workbench for MySql manipulation (optional) ((http://www.mysql.com/))
* Glassfish (https://glassfish.java.net/)

==Videos, screenshots, and other media==

* A demo of the software can be found at [http://cru.genomics.iit.it/smith/ http://cru.genomics.iit.it/smith/]. (Login: admin; Password: adminadmin)

==Entities using SMITH==
European Institute of Oncology; Italian Institute of Technology

==Further reading==

* {{cite journal |url=http://www.biomedcentral.com/1471-2105/15/S14/S3 |title=SMITH: a LIMS for handling next-generation sequencing workflows |journal=BMC Bioinformatics |author=Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko |volume=15 |issue=Suppl 14 |page=S3 |year=2014 |doi=10.1186/1471-2105-15-S14-S3 |pmc=PMC4255740}}

==External links==

* [https://bitbucket.org/yuriy_vaskin/smith SMITH at Bitbucket]

==References==
<references />


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