Informatics Educational Institutions & Programs
|Developer(s)||Yuriy Vaskin et al.|
|Initial release||September 2011(1.0)|
|Type||Laboratory informatics software|
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.
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.
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.
According to the associated journal article, the following are some of the features of SMITH:
- 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."
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/. (Login: admin; Password: adminadmin)
Entities using SMITH
European Institute of Oncology; Italian Institute of Technology
- 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.
- 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. 05 February 2014. https://bitbucket.org/yuriy_vaskin/smith/commits/46b82a77322e9bfad06701b89e8a1b5d1b496a4e. Retrieved 04 November 2015.