PMID- 16914063
OWN - NLM
STAT- MEDLINE
DCOM- 20060925
LR  - 20181113
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 7
DP  - 2006 Aug 17
TI  - Laboratory Information Management Software for genotyping workflows: applications 
      in high throughput crop genotyping.
PG  - 383
AB  - BACKGROUND: With the advances in DNA sequencer-based technologies, it has become 
      possible to automate several steps of the genotyping process leading to increased 
      throughput. To efficiently handle the large amounts of genotypic data generated 
      and help with quality control, there is a strong need for a software system that 
      can help with the tracking of samples and capture and management of data at 
      different steps of the process. Such systems, while serving to manage the 
      workflow precisely, also encourage good laboratory practice by standardizing 
      protocols, recording and annotating data from every step of the workflow. 
      RESULTS: A laboratory information management system (LIMS) has been designed and 
      implemented at the International Crops Research Institute for the Semi-Arid 
      Tropics (ICRISAT) that meets the requirements of a moderately high throughput 
      molecular genotyping facility. The application is designed as modules and is 
      simple to learn and use. The application leads the user through each step of the 
      process from starting an experiment to the storing of output data from the 
      genotype detection step with auto-binning of alleles; thus ensuring that every 
      DNA sample is handled in an identical manner and all the necessary data are 
      captured. The application keeps track of DNA samples and generated data. Data 
      entry into the system is through the use of forms for file uploads. The LIMS 
      provides functions to trace back to the electrophoresis gel files or sample 
      source for any genotypic data and for repeating experiments. The LIMS is being 
      presently used for the capture of high throughput SSR (simple-sequence repeat) 
      genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal 
      (sorghum and millets) crops of importance in the semi-arid tropics. CONCLUSION: A 
      laboratory information management system is available that has been found useful 
      in the management of microsatellite genotype data in a moderately high throughput 
      genotyping laboratory. The application with source code is freely available for 
      academic users and can be downloaded from 
      http://www.icrisat.org/gt-bt/lims/lims.asp.
FAU - Jayashree, B
AU  - Jayashree B
AD  - Bioinformatics and Biometrics Unit, International Crops Research Institute for 
      the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Andhra Pradesh, India. 
      b.jayashree@cgiar.org
FAU - Reddy, Praveen T
AU  - Reddy PT
FAU - Leeladevi, Y
AU  - Leeladevi Y
FAU - Crouch, Jonathan H
AU  - Crouch JH
FAU - Mahalakshmi, V
AU  - Mahalakshmi V
FAU - Buhariwalla, Hutokshi K
AU  - Buhariwalla HK
FAU - Eshwar, K E
AU  - Eshwar KE
FAU - Mace, Emma
AU  - Mace E
FAU - Folksterma, Rolf
AU  - Folksterma R
FAU - Senthilvel, S
AU  - Senthilvel S
FAU - Varshney, Rajeev K
AU  - Varshney RK
FAU - Seetha, K
AU  - Seetha K
FAU - Rajalakshmi, R
AU  - Rajalakshmi R
FAU - Prasanth, V P
AU  - Prasanth VP
FAU - Chandra, Subhash
AU  - Chandra S
FAU - Swarupa, L
AU  - Swarupa L
FAU - Srikalyani, P
AU  - Srikalyani P
FAU - Hoisington, David A
AU  - Hoisington DA
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20060817
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
RN  - 0 (DNA, Plant)
SB  - IM
MH  - Algorithms
MH  - Base Sequence
MH  - Crops, Agricultural/*genetics
MH  - DNA, Plant/analysis/*genetics
MH  - *Database Management Systems
MH  - *Databases, Genetic
MH  - Genotype
MH  - Information Management/methods
MH  - Information Storage and Retrieval/*methods
MH  - Laboratories
MH  - Molecular Sequence Data
MH  - Sequence Analysis, DNA/*methods
MH  - *Software
MH  - User-Computer Interface
PMC - PMC1559653
EDAT- 2006/08/18 09:00
MHDA- 2006/09/26 09:00
PMCR- 2006/08/17
CRDT- 2006/08/18 09:00
PHST- 2006/05/19 00:00 [received]
PHST- 2006/08/17 00:00 [accepted]
PHST- 2006/08/18 09:00 [pubmed]
PHST- 2006/09/26 09:00 [medline]
PHST- 2006/08/18 09:00 [entrez]
PHST- 2006/08/17 00:00 [pmc-release]
AID - 1471-2105-7-383 [pii]
AID - 10.1186/1471-2105-7-383 [doi]
PST - epublish
SO  - BMC Bioinformatics. 2006 Aug 17;7:383. doi: 10.1186/1471-2105-7-383.