PMID- 21569484
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20110714
LR  - 20211020
IS  - 1751-0473 (Electronic)
IS  - 1751-0473 (Linking)
VI  - 6
DP  - 2011 May 13
TI  - LimsPortal and BonsaiLIMS: development of a lab information management system for 
      translational medicine.
PG  - 9
LID - 10.1186/1751-0473-6-9 [doi]
AB  - BACKGROUND: Laboratory Information Management Systems (LIMS) are an increasingly 
      important part of modern laboratory infrastructure. As typically very 
      sophisticated software products, LIMS often require considerable resources to 
      select, deploy and maintain. Larger organisations may have access to specialist 
      IT support to assist with requirements elicitation and software customisation, 
      however smaller groups will often have limited IT support to perform the kind of 
      iterative development that can resolve the difficulties that biologists often 
      have when specifying requirements. Translational medicine aims to accelerate the 
      process of treatment discovery by bringing together multiple disciplines to 
      discover new approaches to treating disease, or novel applications of existing 
      treatments. The diverse set of disciplines and complexity of processing 
      procedures involved, especially with the use of high throughput technologies, 
      bring difficulties in customizing a generic LIMS to provide a single system for 
      managing sample related data within a translational medicine research setting, 
      especially where limited IT support is available. RESULTS: We have designed and 
      developed a LIMS, BonsaiLIMS, around a very simple data model that can be easily 
      implemented using a variety of technologies, and can be easily extended as 
      specific requirements dictate. A reference implementation using Oracle 11 g 
      database and the Python framework, Django is presented. CONCLUSIONS: By focusing 
      on a minimal feature set and a modular design we have been able to deploy the 
      BonsaiLIMS system very quickly. The benefits to our institute have been the 
      avoidance of the prolonged implementation timescales, budget overruns, scope 
      creep, off-specifications and user fatigue issues that typify many enterprise 
      software implementations. The transition away from using local, uncontrolled 
      records in spreadsheet and paper formats to a centrally held, secured and 
      backed-up database brings the immediate benefits of improved data visibility, 
      audit and overall data quality. The open-source availability of this software 
      allows others to rapidly implement a LIMS which in itself might sufficiently 
      address user requirements. In situations where this software does not meet 
      requirements, it can serve to elicit more accurate specifications from end-users 
      for a more heavyweight LIMS by acting as a demonstrable prototype.
FAU - Bath, Timothy G
AU  - Bath TG
AD  - Translational Medicine Research Collaboration Institute, Pfizer Inc, Ninewells 
      Hospital, Dundee, DD1 9SY, UK. d.crowther@dundee.ac.uk.
FAU - Bozdag, Selcuk
AU  - Bozdag S
FAU - Afzal, Vackar
AU  - Afzal V
FAU - Crowther, Daniel
AU  - Crowther D
LA  - eng
PT  - Journal Article
DEP - 20110513
PL  - England
TA  - Source Code Biol Med
JT  - Source code for biology and medicine
JID - 101276533
PMC - PMC3113716
EDAT- 2011/05/17 06:00
MHDA- 2011/05/17 06:01
PMCR- 2011/05/13
CRDT- 2011/05/17 06:00
PHST- 2010/09/28 00:00 [received]
PHST- 2011/05/13 00:00 [accepted]
PHST- 2011/05/17 06:00 [entrez]
PHST- 2011/05/17 06:00 [pubmed]
PHST- 2011/05/17 06:01 [medline]
PHST- 2011/05/13 00:00 [pmc-release]
AID - 1751-0473-6-9 [pii]
AID - 10.1186/1751-0473-6-9 [doi]
PST - epublish
SO  - Source Code Biol Med. 2011 May 13;6:9. doi: 10.1186/1751-0473-6-9.