title: VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations.
abstract: The control and elimination of Plasmodium vivax will require a better understanding of its transmission dynamics, through the application of genotyping and population genetics analyses. This paper describes VivaxGEN (http://vivaxgen.menzies.edu.au), a web-based platform that has been developed to support P. vivax short tandem repeat data sharing and comparative analyses.
  
  
  
  The VivaxGEN platform provides a repository for raw data generated by capillary electrophoresis (FSA files), with fragment analysis and standardized allele calling tools. The query system of the platform enables users to filter, select and differentiate samples and alleles based on their specified criteria. Key population genetic analyses are supported including measures of population differentiation (FST), expected heterozygosity (HE), linkage disequilibrium (IAS), neighbor-joining analysis and Principal Coordinate Analysis. Datasets can also be formatted and exported for application in commonly used population genetic software including GENEPOP, Arlequin and STRUCTURE. To date, data from 10 countries, including 5 publicly available data sets have been shared with VivaxGEN.
  
  
  
  VivaxGEN is well placed to facilitate regional overviews of P. vivax transmission dynamics in different endemic settings and capable to be adapted for similar genetic studies of P. falciparum and other organisms.
authors.affiliation: Eijkman Institute for Molecular Biology, Jakarta Pusat, Indonesia.|Agency for Assessment and Application of Technology, Jakarta Pusat, Indonesia.
authors.forename: Hidayat
authors.initials: H
authors.lastname: Trimarsanto
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
authors.forename: Ernest D
authors.initials: ED
authors.lastname: Benavente
authors.affiliation: Eijkman Institute for Molecular Biology, Jakarta Pusat, Indonesia.|The Ministry of Research, Technology and Higher Education, Jakarta Pusat, Indonesia.
authors.forename: Rintis
authors.initials: R
authors.lastname: Noviyanti
authors.affiliation: Eijkman Institute for Molecular Biology, Jakarta Pusat, Indonesia.|The Ministry of Research, Technology and Higher Education, Jakarta Pusat, Indonesia.
authors.forename: Retno Ayu Setya
authors.initials: RA
authors.lastname: Utami
authors.affiliation: Eijkman Institute for Molecular Biology, Jakarta Pusat, Indonesia.|The Ministry of Research, Technology and Higher Education, Jakarta Pusat, Indonesia.
authors.forename: Leily
authors.initials: L
authors.lastname: Trianty
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia.
authors.forename: Zuleima
authors.initials: Z
authors.lastname: Pava
authors.affiliation: College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia.|Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
authors.forename: Sisay
authors.initials: S
authors.lastname: Getachew
authors.affiliation: Division of Malaria and Parasitic Diseases, National Institute of Health, Korea CDC, Osong, Republic of Korea.
authors.forename: Jung-Yeon
authors.initials: JY
authors.lastname: Kim
authors.affiliation: Division of Malaria and Parasitic Diseases, National Institute of Health, Korea CDC, Osong, Republic of Korea.|Department of Parasitology and Tropical Medicine, Kyungpook National University School of Medicine, Daegu, Republic of Korea.
authors.forename: Youn-Kyoung
authors.initials: YK
authors.lastname: Goo
authors.affiliation: Royal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan.
authors.forename: Sonam
authors.initials: S
authors.lastname: Wangchuck
authors.affiliation: Medical College of Soochow University, Suzhou, Jiangsu, People's Republic of China.|Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, People's Republic of China.
authors.forename: Yaobao
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu, People's Republic of China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Gao
authors.affiliation: Drug Resistance and Diagnostics, Army Malaria Institute, Brisbane, Australia.
authors.forename: Simone
authors.initials: S
authors.lastname: Dowd
authors.affiliation: Drug Resistance and Diagnostics, Army Malaria Institute, Brisbane, Australia.|The AMI Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
authors.forename: Qin
authors.initials: Q
authors.lastname: Cheng
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.|Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom.
authors.forename: Taane G
authors.initials: TG
authors.lastname: Clark
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia.|Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: Ric N
authors.initials: RN
authors.lastname: Price
authors.affiliation: Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia.
authors.forename: Sarah
authors.identifier: 0000-0002-4638-536X
authors.initials: S
authors.lastname: Auburn
mesh_terms: D022126:Access to Information; D000483:Alleles; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D033181:Information Dissemination; D016247:Information Storage and Retrieval; D020407:Internet; D015810:Linkage Disequilibrium; D016778:Malaria, Falciparum / Q000453:epidemiology / Q000469:parasitology / Q000635:transmission; D018895:Microsatellite Repeats; D010963:Plasmodium falciparum / Q000235:genetics; D010966:Plasmodium vivax / Q000235:genetics*; D012984:Software; D013223:Statistics as Topic / Q000379:methods*