title: LabKey Server NAb: a tool for analyzing, visualizing and sharing results from neutralizing antibody assays.
abstract: BACKGROUND
  Multiple types of assays allow sensitive detection of virus-specific neutralizing antibodies. For example, the extent of antibody neutralization of HIV-1, SIV and SHIV can be measured in the TZM-bl cell line through the degree of luciferase reporter gene expression after infection. In the past, neutralization curves and titers for this standard assay have been calculated using an Excel macro. Updating all instances of such a macro with new techniques can be unwieldy and introduce non-uniformity across multi-lab teams. Using Excel also poses challenges in centrally storing, sharing and associating raw data files and results.
  
  
  RESULTS
  We present LabKey Server's NAb tool for organizing, analyzing and securely sharing data, files and results for neutralizing antibody (NAb) assays, including the luciferase-based TZM-bl NAb assay. The customizable tool supports high-throughput experiments and includes a graphical plate template designer, allowing researchers to quickly adapt calculations to new plate layouts. The tool calculates the percent neutralization for each serum dilution based on luminescence measurements, fits a range of neutralization curves to titration results and uses these curves to estimate the neutralizing antibody titers for benchmark dilutions. Results, curve visualizations and raw data files are stored in a database and shared through a secure, web-based interface. NAb results can be integrated with other data sources based on sample identifiers. It is simple to make results public after publication by updating folder security settings.
  
  
  CONCLUSIONS
  Standardized tools for analyzing, archiving and sharing assay results can improve the reproducibility, comparability and reliability of results obtained across many labs. LabKey Server and its NAb tool are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. Many members of the HIV research community can also access the LabKey Server NAb tool without installing the software by using the Atlas Science Portal (https://atlas.scharp.org). Atlas is an installation of LabKey Server.
authors: LabKey Software, Seattle, Washington 98102, USA.
authors: Britt
authors: B
authors: Piehler
authors: Elizabeth K
authors: EK
authors: Nelson
authors: Josh
authors: J
authors: Eckels
authors: Sarah
authors: S
authors: Ramsay
authors: Karl
authors: K
authors: Lum
authors: Blake
authors: B
authors: Wood
authors: Kelli M
authors: KM
authors: Greene
authors: Hongmei
authors: H
authors: Gao
authors: Michael S
authors: MS
authors: Seaman
authors: David C
authors: DC
authors: Montefiori
authors: Mark
authors: M
authors: Igra
references: J Virol. 2002 Jul;76(13):6480-6
references: 12050360
references: J Virol. 2006 Dec;80(23):11776-90
references: 16971434
references: J Virol. 2008 Jan;82(1):115-25
references: 17942537
references: BMC Bioinformatics. 2011 Mar 09;12:71
references: 21385461
references: J Proteome Res. 2006 Jan;5(1):112-21
references: 16396501
references: J Virol. 2010 Feb;84(3):1439-52
references: 19939925
references: Anal Biochem. 2005 Aug 1;343(1):54-65
references: 15953581
references: J Virol. 2005 Aug;79(16):10108-25
references: 16051804
references: Virology. 1999 Feb 15;254(2):235-44
references: 9986790
references: J Clin Microbiol. 2003 Nov;41(11):5046-52
references: 14605137
references: PLoS Med. 2005 Feb;2(2):e25
references: 15740411
references: J Immunol Methods. 2008 Jul 31;336(2):113-8
references: 18511063
references: Curr Protoc Immunol. 2005 Jan;Chapter 12:Unit 12.11
references: 18432938