BioSim2 Program (Latest Version)
   With Windows XP at least, when downloading the biosim2-0-03.jar file, Windows tries to save it as
      biosim2-0-03.zip. If this happens to you, save it as ".jar" or rename it after saving it as ".jar".

   Please send us your suggestions for improvement

User's Manual (EPA Publication-pdf file)

Relevant Publications (email pinkhamc@norwich.edu for copies of these)

  Pinkham, C.F.A., and Pearson, J.G.  1976.  Applications of a new coefficient of similarity
         to pollution surveys. J. Water Pollut. Control Fed., 48, 717. (53)

   Pearson, J.G., and C.F.A. Pinkham.  1992.  Strategy for data analysis in environmental surveys emphasizing the index of biotic similarity and BIOSIM1. Water Environ. Res., 64:901-909. (52)

Recent Examples of Application of BioSim2

·              3/17/05,  J. Gareth Pearson, Brian P. Reid and Victor T. Chevalier, Demonstration of the Java version of the Pinkham-Pearson index for the comparison of community structure, 29^th Annual Meeting of the New England  Association of Environmental Biologists – EPA, Lake George, NY (Poster Presentation)
(Power Point Version)  (MS Word Version)

·              6/08/05, Fiske, Steven, & C.F.A. Pinkham, Use of BioSim2 to identify relationships between biotic and abiotic parameters for small, moderate gradient, Vermont streams, 11^th Annual Meeting of the North Atlantic Branch of the Society of Environmental Toxicology and Chemistry, Burlington, VT (Platform Presentation)
(Power Point Presentation with Notes-6 MB file)

·              3/30/06, Pinkham, C. F.A., BioSim2, 30^th Annual Meeting of the New England  Association of Environmental Biologists , Bethel, ME  (Workshop)
(Power Point Presentation with Notes-5 MB file)

·              3/14/07, Olsen, Darlene and C. F. A. Pinkham, Using BioSim2 to identify statistically-valid sectors of indicator taxa, 31st Annual Meeting of the New England  Association of Environmental Biologists , Mount Snow, VT (Platform Presentation)
(Power Point Presentation with Notes-6 MB file)

·              6/6/07, Olsen, Darlene,  C. F. A. Pinkham, J. G. Pearson, and B.P. Reid, The use of the Pinkham-Pearson Index for the comparison of community structure in BioSim2 to identify statistically-valid sectors of indicator taxa with sites, 55th Annual Meeting of the North American Benthological Society, Columbia, NC (Platform Presentation)
(Power Point Presentation with Notes-4 MB file)

·              6/4/08, C. F. A. Pinkham, Olsen, Darlene, J. G. Pearson, and B.P. Reid, The use of the Pinkham-Pearson Index for the comparison of community structure in BioSim2 to identify statistically-valid sectors of taxa, Streams Project Training Session, UVM (Platform Presentation)  This presentation includes the story of how and why  the Index was developed.
(Power Point Presentation with Notes-5 MB file)

Programs designed to facilitate your data analysis using the row and column dendrograms and the original data matrix rearranged in double-dendrogram order produced by BioSim2.
(Feel free to contact Carl Pinkham with any question.)

            Moving from the original data matrix rearranged in double dendrogram order produced by BioSim2 to a matrix with sectors delineated by lines using Excel (Excel file) and both the row dendrogram and column dendrogram and the row cophenetic correlation coefficient and the column cophenetic correlation coefficient.

            Scaling the original data matrix using Excel, with instructions and a sample data set (Excel file)
(Scaling is used when the original data set exists with different units as, e.g., would happen if you are comparing density values with physical parameters such as pH and temperature.)

            Statistical analysis of sectors, with an example with instructions and the run program (Excel file)

            Semiquantitative analysis of sectors using Excel, with instructions
Step 1 Summarizing sector values (Excel file)
Step 2 Coding all sectors for presentation/publication (Excel file)

If you wish to be notified of updates as soon as they happen, send email to: pinkhamc@norwich.edu
(As a minimum, please provide your name, title, address and work phone.)