PMID- 25471934
OWN - NLM
STAT- MEDLINE
DCOM- 20150401
LR  - 20181202
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 15 Suppl 14
IP  - Suppl 14
DP  - 2014
TI  - SMITH: a LIMS for handling next-generation sequencing workflows.
PG  - S3
LID - 10.1186/1471-2105-15-S14-S3 [doi]
AB  - BACKGROUND: Life-science laboratories make increasing use of Next Generation 
      Sequencing (NGS) for studying bio-macromolecules and their interactions. 
      Array-based methods for measuring gene expression or protein-DNA interactions are 
      being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by 
      specialized facilities that have to keep track of sequencing requests, trace 
      samples, ensure quality and make data available according to predefined 
      privileges. An integrated tool helps to troubleshoot problems, to maintain a high 
      quality standard, to reduce time and costs. Commercial and non-commercial tools 
      called LIMS (Laboratory Information Management Systems) are available for this 
      purpose. However, they often come at prohibitive cost and/or lack the flexibility 
      and scalability needed to adjust seamlessly to the frequently changing protocols 
      employed. In order to manage the flow of sequencing data produced at the Genomic 
      Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing 
      Machine Information Tracking and Handling). METHODS: SMITH is a web application 
      with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic 
      Science and database experts from the Politecnico of Milan in the context of a 
      Genomic Data Model Project developed SMITH. The data base schema stores all the 
      information of an NGS experiment, including the descriptions of all protocols and 
      algorithms used in the process. Notably, an attribute-value table allows 
      associating an unconstrained textual description to each sample and all the data 
      produced afterwards. This method permits the creation of metadata that can be 
      used to search the database for specific files as well as for statistical 
      analyses. RESULTS: SMITH runs automatically and limits direct human interaction 
      mainly to administrative tasks. SMITH data-delivery procedures were standardized 
      making it easier for biologists and analysts to navigate the data. Automation 
      also helps saving time. The workflows are available through an API provided by 
      the workflow management system. The parameters and input data are passed to the 
      workflow engine that performs de-multiplexing, quality control, alignments, etc. 
      CONCLUSIONS: SMITH standardizes, automates, and speeds up sequencing workflows. 
      Annotation of data with key-value pairs facilitates meta-analysis.
FAU - Venco, Francesco
AU  - Venco F
FAU - Vaskin, Yuriy
AU  - Vaskin Y
FAU - Ceol, Arnaud
AU  - Ceol A
FAU - Muller, Heiko
AU  - Muller H
LA  - eng
PT  - Journal Article
DEP - 20141127
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
SB  - IM
MH  - Algorithms
MH  - Automation
MH  - Genomics
MH  - High-Throughput Nucleotide Sequencing/instrumentation/methods
MH  - Sequence Analysis, DNA/instrumentation/*methods
MH  - *Software
MH  - Workflow
PMC - PMC4255740
EDAT- 2014/12/05 06:00
MHDA- 2015/04/02 06:00
PMCR- 2014/11/27
CRDT- 2014/12/05 06:00
PHST- 2014/12/05 06:00 [entrez]
PHST- 2014/12/05 06:00 [pubmed]
PHST- 2015/04/02 06:00 [medline]
PHST- 2014/11/27 00:00 [pmc-release]
AID - 1471-2105-15-S14-S3 [pii]
AID - 10.1186/1471-2105-15-S14-S3 [doi]
PST - ppublish
SO  - BMC Bioinformatics. 2014;15 Suppl 14(Suppl 14):S3. doi: 
      10.1186/1471-2105-15-S14-S3. Epub 2014 Nov 27.