Difference between revisions of "SMITH"
From LIMSWiki
Jump to navigationJump to searchShawndouglas (talk | contribs) (Created as needed.) |
Shawndouglas (talk | contribs) (Abandoned) |
||
| Line 9: | Line 9: | ||
| 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 | ||
| Line 22: | Line 22: | ||
}} | }} | ||
'''SMITH''' (Sequencing Machine Information Tracking and Handling) | '''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== | ||
| Line 28: | Line 28: | ||
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 | According to the associated journal article, the following were some of the features of SMITH<ref name="VencoSMITH" />: | ||
* Sample submission | * Sample submission | ||
| Line 50: | Line 52: | ||
==Hardware/software requirements== | ==Hardware/software requirements== | ||
According to the source code documentation, SMITH | According to the source code documentation, SMITH required the following for the source: | ||
* Maven (http://maven.apache.org/) | * Maven (http://maven.apache.org/) | ||
| Line 57: | Line 59: | ||
* Hibernate (http://hibernate.org/) | * Hibernate (http://hibernate.org/) | ||
The following | The following was required for installing the application: | ||
* Java 6 (or higher) (http://www.java.com/) | * Java 6 (or higher) (http://www.java.com/) | ||
| Line 66: | Line 68: | ||
==Videos, screenshots, and other media== | ==Videos, screenshots, and other media== | ||
* A demo of the software | * 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== | ||
| Line 83: | Line 85: | ||
<!---Place all category tags here--> | <!---Place all category tags here--> | ||
[[Category: | [[Category:Discontinued or abandoned software (open source)]] | ||
Latest revision as of 19:19, 6 May 2021
| Developer(s) | Yuriy Vaskin et al. |
|---|---|
| Initial release | September 2011 (1.0)[1] |
| Written in | Java |
| Operating system | Cross-platform |
| Type | Laboratory informatics software |
| License(s) | MIT License |
| Website | https://bitbucket.org/yuriy_vaskin/smith/overview |
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.[1]
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.[2]
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.[1]
As of May 2021, no code updates had been made since 2015. The project is presumed to be abandoned or discontinued.
Features
According to the associated journal article, the following were some of the features of SMITH[1]:
- 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."[1]
Hardware/software requirements
According to the source code documentation, SMITH required 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 was 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 was found at http://cru.genomics.iit.it/smith/. (Login: admin; Password: adminadmin)
Entities using SMITH
European Institute of Oncology; Italian Institute of Technology
Further reading
- Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko (2014). "SMITH: a LIMS for handling next-generation sequencing workflows". BMC Bioinformatics 15 (Suppl 14): S3. doi:10.1186/1471-2105-15-S14-S3. PMC PMC4255740. http://www.biomedcentral.com/1471-2105/15/S14/S3.
External links
References
- ↑ 1.0 1.1 1.2 1.3 1.4 Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko (2014). "SMITH: a LIMS for handling next-generation sequencing workflows". BMC Bioinformatics 15 (Suppl 14): S3. doi:10.1186/1471-2105-15-S14-S3. PMC PMC4255740. http://www.biomedcentral.com/1471-2105/15/S14/S3. Retrieved 04 November 2015.
- ↑ "SMITH - Commits - Initial Import". Bitbucket. 5 February 2014. https://bitbucket.org/yuriy_vaskin/smith/commits/46b82a77322e9bfad06701b89e8a1b5d1b496a4e. Retrieved 04 November 2015.
