Software for Microbiologyby Allen Bethea
In addition to microscopes and Petri dishes, computers are an important tool for microbiologists. Software for microbiology research includes tools used by other scientific and engineering disciplines as well as specialized applications for the study of bacteria and other micro-organisms. Many applications developed by government agencies, non-profit foundations or academic researchers are available as free software to download and use as your experiment or lab requires.
A physical or mental picture of the raw data you collect may help you better grasp its quality, significance and implications. Open source and commercial data visualization software is widely available for microbiology research. Create charts and graphs of your data using LibreOffice Calc, Microsoft's Excel or the Mondrian data-visualization system. Cell-O and RasMol applications help you create 2D and 3D-animated models of biologically-significant molecules like proteins and amino acids.
Large collections of microbiology data often yield more meaningful information once they have been numerically analyzed. MATLAB, Octave and SciPy software packages that perform mathematical refinement, analysis and modeling of scientists' data. Use these packages to do parameter estimating through curve fitting, epidemiological predictions, bacterial growth simulations and data noise or stochastic effect elimination. These application also perform statistical calculations, like analysis of variance or Chi-square tests.
Microbiology software applications also help you visualize and mine information from the sequence of nucleic acids that make up a micro-organism's DNA. The Open Bioinformatics Foundation provides free, open-source DNA sequencing and analysis applications like BioJava and Biopython that extract data from genome information banks, parse an organism's DNA code and compare it to other DNA samples. Additional genome analysis packages include Emboss, HMMER, Clustal Omega, Phylogeny Inference Package, or PHYLIP, and the Sequence Manipulation Suite, or SMS.
The rapid pace of scientific discovery in microbiology and changing government regulations makes it essential that microbiologists have ready access to the information that impacts their work. HUGO is a commercial software package that provides microbiologists with current information on tools, chemicals, equipment, culture media, safety requirements, new organisms, taxonomic changes and antibiotics. In addition, microbiologists working in food science can use the ComBase Browser Web application to access the food-related microbiological data provided by government agencies in the United Kingdom, Australia and the United States.
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