BioNumerics explained
BioNumerics is a bioinformatics desktop software application that manages microbiological data. It is developed by Applied Maths NV, a bioMérieux company.
History
BioNumerics was first released in 1998. PulseNet, a network run by the Centers for Disease Control and Prevention (CDC), uses BioNumerics to compare pulsed field gel electrophoresis (PFGE) patterns and whole genome sequences from different bacterial strains.[1] [2] CaliciNet, an outbreak surveillance network for noroviruses, is another example of a network which uses BioNumerics to submit norovirus sequences and basic epidemiologic information to a central database.[3]
Features
The basis of BioNumerics is a database consisting of entries. The entries correspond to the individual organisms or samples under study and are characterized by a unique key and by a number of user-defined information fields. Each entry in a database may be characterized by one or more experiments that can be linked easily to the entry.[4] In BioNumerics, experiments are divided in seven classes: fingerprints, spectra, characters, sequences, sequence read sets, trend data and matrices.
Examples of BioNumerics applications are whole genome Multi Locus Sequence Typing (wgMLST), whole genome Single Nucleotide Polymorphisms (wgSNP), genome comparison, identification based on MALDI-TOF Mass Spectrometry, PFGE typing, Amplified Fragment Length Polymorphism (AFLP) typing, sequence-based typing of viruses, antibiotic resistance profiling and functional genotyping.[5] [6] [7]
External links
Notes and References
- http://www.pulsenetinternational.org/protocols/Pages/bionumerics.aspx BioNumerics protocols used by Pulsenet
- Hunter SB, Vauterin P, Lambert-Fair MA, Van Duyne MS, Kubota K, Graves L, Wrigley D, Barrett T, Ribot E . 6 . Establishment of a universal size standard strain for use with the PulseNet standardized pulsed-field gel electrophoresis protocols: converting the national databases to the new size standard . Journal of Clinical Microbiology . 43 . 3 . 1045–50 . March 2005 . 15750058 . 1081233 . 10.1128/JCM.43.3.1045-1050.2005 .
- Vega E, Barclay L, Gregoricus N, Williams K, Lee D, Vinjé J . Novel surveillance network for norovirus gastroenteritis outbreaks, United States . Emerging Infectious Diseases . 17 . 8 . 1389–95 . August 2011 . 21801614 . 3381557 . 10.3201/eid1708.101837 .
- Vauterin L, Vauterin P. Integrated databasing and analysis. In: Molecular Identification, Systematics, and Population Structure of Prokaryotes (ed. Erko Stackebrandt). Springer, 2006.
- Schouls LM, Spalburg EC, van Luit M, Huijsdens XW, Pluister GN, van Santen-Verheuvel MG, van der Heide HG, Grundmann H, Heck ME, de Neeling AJ . 6 . Multiple-locus variable number tandem repeat analysis of Staphylococcus aureus: comparison with pulsed-field gel electrophoresis and spa-typing . PLOS ONE . 4 . 4 . e5082 . 2009-04-03 . 19343175 . 2661140 . 10.1371/journal.pone.0005082 . 2009PLoSO...4.5082S . free .
- Web site: 2012-07-14. Polyphasic study of wine Lactobacillus strains: taxonomic implications. 2021-04-15. archive.ph. 2012-07-14. https://archive.today/20120714025130/http://ijs.sgmjournals.org/content/55/1/197.full. live.
- Gröschel MI, Meehan CJ, Barilar I, Diricks M, Gonzaga A, Steglich M, Conchillo-Solé O, Scherer IC, Mamat U, Luz CF, De Bruyne K . 6 . 2019-08-28. The global phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. bioRxiv. en. 748954. 10.1101/748954. free.
