PMID- 25159034
OWN - NLM
STAT- MEDLINE
DCOM- 20141108
LR  - 20211021
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 15
IP  - 1
DP  - 2014 Aug 27
TI  - MendeLIMS: a web-based laboratory information management system for clinical 
      genome sequencing.
PG  - 290
LID - 10.1186/1471-2105-15-290 [doi]
LID - 290
AB  - BACKGROUND: Large clinical genomics studies using next generation DNA sequencing 
      require the ability to select and track samples from a large population of 
      patients through many experimental steps. With the number of clinical genome 
      sequencing studies increasing, it is critical to maintain adequate laboratory 
      information management systems to manage the thousands of patient samples that 
      are subject to this type of genetic analysis. RESULTS: To meet the needs of 
      clinical population studies using genome sequencing, we developed a web-based 
      laboratory information management system (LIMS) with a flexible configuration 
      that is adaptable to continuously evolving experimental protocols of next 
      generation DNA sequencing technologies. Our system is referred to as MendeLIMS, 
      is easily implemented with open source tools and is also highly configurable and 
      extensible. MendeLIMS has been invaluable in the management of our clinical 
      genome sequencing studies. CONCLUSIONS: We maintain a publicly available 
      demonstration version of the application for evaluation purposes at 
      http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and 
      accesses data stored in SQL-compliant relational databases. Software is freely 
      available for non-commercial use at 
      http://dna-discovery.stanford.edu/software/mendelims/.
FAU - Grimes, Susan M
AU  - Grimes SM
FAU - Ji, Hanlee P
AU  - Ji HP
AD  - Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA. 
      genomics_ji@stanford.edu.
LA  - eng
GR  - RC2HG005570/HG/NHGRI NIH HHS/United States
GR  - P01 HG000205/HG/NHGRI NIH HHS/United States
GR  - HHMI/Howard Hughes Medical Institute/United States
GR  - 2P01HG000205/HG/NHGRI NIH HHS/United States
GR  - DK56339/DK/NIDDK NIH HHS/United States
GR  - P30 DK056339/DK/NIDDK NIH HHS/United States
GR  - RC2 HG005570/HG/NHGRI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20140827
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
SB  - IM
MH  - *Clinical Laboratory Techniques
MH  - Databases, Genetic
MH  - Gene Library
MH  - Genetic Testing
MH  - Genomics/*methods
MH  - Health Information Management/*methods
MH  - High-Throughput Nucleotide Sequencing
MH  - Humans
MH  - *Internet
MH  - Medical Informatics/*methods
MH  - Sequence Analysis, DNA/*methods
MH  - *Software
MH  - User-Computer Interface
PMC - PMC4155081
EDAT- 2014/08/28 06:00
MHDA- 2014/11/09 06:00
PMCR- 2014/08/27
CRDT- 2014/08/28 06:00
PHST- 2013/06/11 00:00 [received]
PHST- 2014/08/18 00:00 [accepted]
PHST- 2014/08/28 06:00 [entrez]
PHST- 2014/08/28 06:00 [pubmed]
PHST- 2014/11/09 06:00 [medline]
PHST- 2014/08/27 00:00 [pmc-release]
AID - 1471-2105-15-290 [pii]
AID - 6555 [pii]
AID - 10.1186/1471-2105-15-290 [doi]
PST - epublish
SO  - BMC Bioinformatics. 2014 Aug 27;15(1):290. doi: 10.1186/1471-2105-15-290.