title: Analysis of ex vivo drug response data of Plasmodium clinical isolates: the pros and cons of different computer programs and online platforms.
abstract: BACKGROUND
  In vitro drug susceptibility testing of malaria parasites remains an important component of surveillance for anti-malarial drug resistance. The half-maximal inhibition of growth (IC50) is the most commonly reported parameter expressing drug susceptibility, derived by a variety of statistical approaches, each with its own advantages and disadvantages.
  
  
  METHODS
  In this study, licensed computer programs WinNonlin and GraphPad Prism 6.0, and the open access programs HN-NonLin, Antimalarial ICEstimator (ICE), and In Vitro Analysis and Reporting Tool (IVART) were tested for their ease of use and ability to estimate reliable IC50 values from raw drug response data from 31 Plasmodium falciparum and 29 P. vivax clinical isolates tested with five anti-malarial agents: chloroquine, amodiaquine, piperaquine, mefloquine, and artesunate.
  
  
  RESULTS
  The IC50 and slope estimates were similar across all statistical packages for all drugs tested in both species. There was good correlation of results derived from alternative statistical programs and non-linear mixed-effects modelling (NONMEM) which models all isolate data simultaneously. The user-friendliness varied between packages. While HN-NonLin and IVART allow users to enter the data in 96-well format, IVART and GraphPad Prism 6.0 are capable to analyse multiple isolates and drugs in parallel. WinNonlin, GraphPad Prism 6.0, IVART, and ICE provide alerts for non-fitting data and incorrect data entry, facilitating data interpretation. Data analysis using WinNonlin or ICE took the longest computationally, whilst the offline ability of GraphPad Prism 6.0 to analyse multiple isolates and drugs simultaneously made it the fastest among the programs tested.
  
  
  CONCLUSIONS
  IC50 estimates obtained from the programs tested were comparable. In view of processing time and ease of analysis, GraphPad Prism 6.0 or IVART are best suited for routine and large-scale drug susceptibility testing.
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT, 0811, Australia. Grennady.Wirjanata@menzies.edu.au.
authors.forename: Grennady
authors.initials: G
authors.lastname: Wirjanata
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT, 0811, Australia. Irene.Handayuni@menzies.edu.au.
authors.forename: Irene
authors.initials: I
authors.lastname: Handayuni
authors.affiliation: Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia. sophiez@unimelb.edu.au.
authors.forename: Sophie G
authors.initials: SG
authors.lastname: Zaloumis
authors.affiliation: Papuan Health and Community Development Foundation (PHCDF), Timika, Papua, Indonesia. ferryanto_cs@yahoo.com.
authors.forename: Ferryanto
authors.initials: F
authors.lastname: Chalfein
authors.affiliation: Papuan Health and Community Development Foundation (PHCDF), Timika, Papua, Indonesia. prayogatimika@gmail.com.
authors.forename: Pak
authors.initials: P
authors.lastname: Prayoga
authors.affiliation: Papuan Health and Community Development Foundation (PHCDF), Timika, Papua, Indonesia. ennykenangalem@yahoo.com.|District Health Authority, Timika, Papua, Indonesia. ennykenangalem@yahoo.com.
authors.forename: Enny
authors.initials: E
authors.lastname: Kenangalem
authors.affiliation: Papuan Health and Community Development Foundation (PHCDF), Timika, Papua, Indonesia. didot2266@yahoo.com.|District Health Authority, Timika, Papua, Indonesia. didot2266@yahoo.com.|Department of Paediatrics, Faculty of Medicine, Gadjah Mada University, Yogyakarta, Indonesia. didot2266@yahoo.com.
authors.forename: Jeanne Rini
authors.initials: JR
authors.lastname: Poespoprodjo
authors.affiliation: Eijkman Institute for Molecular Biology, Jl. Diponegoro 69, 10430, Jakarta, Indonesia. rintis@eijkman.go.id.
authors.forename: Rintis
authors.initials: R
authors.lastname: Noviyanti
authors.affiliation: Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia. julieas@unimelb.edu.au.
authors.forename: Julie A
authors.initials: JA
authors.lastname: Simpson
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT, 0811, Australia. ricprice99@googlemail.com.|Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK. ricprice99@googlemail.com.
authors.forename: Ric N
authors.initials: RN
authors.lastname: Price
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT, 0811, Australia. jutta.marfurt@menzies.edu.au.
authors.forename: Jutta
authors.initials: J
authors.lastname: Marfurt
mesh_terms: D000962:Antimalarials / Q000494:pharmacology*; D019295:Computational Biology; D003198:Computer Simulation; D004351:Drug Resistance / Q000187:drug effects; D006801:Humans; D020128:Inhibitory Concentration 50; D020407:Internet; D016778:Malaria, Falciparum / Q000469:parasitology; D016780:Malaria, Vivax / Q000469:parasitology; D021261:Parasitic Sensitivity Tests / Q000379:methods*; D010963:Plasmodium falciparum / Q000187:drug effects*; D010966:Plasmodium vivax / Q000187:drug effects*; D012984:Software
chemical_list: D000962:Antimalarials