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A Mathematics Coursebook: Basic Data handling for Science & Medicine Windows
This prototype tutorial module, written using Asymetrix Toolbook, is designed to improve the basic understanding of elementary mathematical concepts applied to the graphical representation of numerical data. It is for use by first year biological science and medical undergraduates. The tutorial contains static text and graphics and is combined with many interactive features such as equations which rearrange themselves step by step or graphs of equations which redraw when their parameters are adjusted. The tutorial covers the following topics: graphing experimental data; understanding linear equations and graphs; exponents and rearranging equations containing exponents; algorithms; exponential growth and decay; linear transformation of numerical data.
Web Site Home Web Site: BioNet

ABI to FASTA free converter Windows
This free tool will batch convert all (selected) ABI files to FASTA files. All you need to do is to locate your ABI chromatogram files and press the CONVERT button. With this automatic converter you can convert hundreds or thousands of ABI chromatogram files in seconds. All with A SINGLE PUSH OF A BUTTON! ---------- No installation process is required.
Web Site Home Web Site: DNA Baser Contig Assembler

ALP Windows
Automated Linkage Preprocessor. Determines sizes of microsatellite fragments separated on an A.L.F. Sequencer (Pharmacia Biotech), removes stutter, performs genotyping and Mendelian checks, and formats data for Lathrop's Linkage Program Package.
Web Site Home Web Site: MRC Human Genetics Unit

Anemona Mac  Windows
ANEMONA.XLT is an EXCEL template for calculation of enzyme kinetic parameters by non-linear regression. Details in A. Hernández and M. T. Ruiz (1998) An EXCEL template for calculation of enzyme kinetic parameters by non-linear regression. Bioinformatics 14(2):227-228. Requires SOLVER ADD-IN installed in your copy of EXCEL.
Download  (198 kb, 06-Oct-1997)

Axum Windows
A technical data analysis and graphing program which provides 2D and 3D graphs.
Web Site Home Web Site: MathSoft, Inc.

BLAST 2.0 Internet Browser  MS-DOS
A tool used to identify any potential homologies of a given DNA or protein sequence with those stored in GenBank.
Web Site Home Web Site: NCBI

BioMapper Internet Browser  Windows
Web Site Home Web Site: BIOGIS Biodiversity, Geo and Metadata Management Solutions

BioNumerics Windows
One universal bioinformatics solution to store and analyze all your biological data. Powerful databasing, integrated networking and a wide range of analysis, visualization and decision-making tools, including data mining, querying, clustering, identification, statistics, and much more. With applications for bacteriology, virology and mycology including features for surveillance networks for bacterial (Salmonella, E. coli & Shigella, Campylobacter spp., Listeria monocytogenes, Vibrio cholerae, Vibrio parahaemolyticus, Yersinia pestis, etc.) and viral pathogens (norovirus).
Web Site Home Web Site: Applied Maths

BioOffice Internet Browser  Windows
BioOffice from BIOGIS Consulting is a tool for input, mapping, spatial analysis and exchange of biological distribution data and collections. This application for professional biodiversity data management is used at many natural history museums and universities in Europe and also in international projects.
Web Site Home Web Site: BioOffice Biodiversity Data Management Solutions

CLC Protein Workbench Linux  Mac  Windows
CLC Protein Workbench 1.5 provides a wide range of advanced protein sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Advanced and integrated 3D molecular viewer - 2 types of alignments - Phylogenetics - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Protein family analysis (PFAM) - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, Swiss-Prot, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLUTO Linux  Unix  Windows
CLUTO is a software package for clustering high dimensional datasets and for analyzing the characteristics of the various clusters. CLUTO is well-suited for clustering data sets arising in many diverse application areas including information retrieval, customer purchasing transactions, science, and biology. CLUTO implements various partitional and agglomerative clustering algorithms that treat the clustering problem as an optimization process which seeks to maximize or minimize a particular clustering criterion function defined over the entire clustering solution. CLUTO also provides tools for analyzing the discovered clusters to understand the relations between the objects assigned to each cluster and the relations between the different clusters. In particular, CLUTO can identify the features that best describe and/or discriminate each cluster. These set of features can be used to gain a better understanding of the set of objects assigned to each cluster and to provide concise summaries about the cluster's contents. Moreover, CLUTO provides visualization capabilities that can be used to see the relationships between the clusters, objects, and features.
Web Site Home Web Site: CLUTO

ClickIt Graph Windows
ClickIt Graph is a user friendly full featured data graphics package that offers over 23 different graph types for business, engineering and science presentations. ClickIt Graph supports two and three-dimensional graph types including line, linear-logarithmic, logarithmic-linear, logarithmic-logarithmic, scatter, 3D scatter, bar, 3D bar, pie, 3D pie, 3D tape, 3D surface, polar, area, 3D area, box-whisker, bubble, candlestick, open-high-low-close, high-low-close, gantt, and data bound line. ClickIt Graph supports linear regression, polynomial, logarithmic, exponential, power, inverse power and spline curve fitting. Best fit, mean, maximum, minimum and standard deviation lines are available for scatter and line graph types.
Web Site Home Web Site: Intuitive Logic

CoPlot Linux  MS-DOS  Unix  Windows
CoPlot is an extremely versatile program for creating publication-quality scientific graphs, maps, and technical drawings. CoPlot lets you change any attribute of any part of any graph or drawing object, so that you can get exactly the drawing that you want. CoPlot has many features for scientists: numerous types of graphs and ways of representing data, different axis types, an easy way to get multiple graphs on one drawing, a vast selection of special characters, horizontal and vertical error bars, etc. CoPlot can save drawings as .eps, .gif, .jpg, .pdf, .png, .svg, .wmf, and other file types. CoPlot can also be used to draw field maps, genetic maps, flow charts, apparatus diagrams, circuit diagrams, chemical structures, etc. CoPlot includes CoStat for data manipulation and statistics.
Web Site Home Web Site: CoHort Software

CoStat Linux  MS-DOS  Unix  Windows
CoStat is a statistical program which makes commonly used statistical procedures easily accessible. CoStat has a wide selection of procedures: descriptive statistics, GLM ANOVA, regression (including multiple regression and nonlinear regression), analysis of frequency data, non-parametric tests, etc. CoStat's spreadsheets can contain different types of data (floating point, integer, date, time, degrees, string, etc.) and can have any number of rows and columns.
Web Site Home Web Site: CoHort Software

ConvAn Windows
ConvAn (Convergence Analysis) is a novel software tool that helps user in friendly GUI to gather, compere, analyze and make prediction about optimization behavior in statistical way based on previously obtained results of optimization runs. The first version of ConvAn was released on 25.05.2011. ConvAn also advices the best method from internal data base for particular model parameter set, that can save time and effort by optimizing model in the most efficient way. ConvAn works on machines running Windows XP operating system or higher and Microsoft .NET Framework version 3.5 Service Pack 1 or higher. CovnAn is developed with funding sources of of a project of European Structural Fund Nr. 2009/0207/1DP/ "Latvian Interdisciplinary Interuniversity Scientific Group of Systems Biology"
Web Site Home Web Site: Biosystems group

CrossGraphs Mac  Unix  Windows
A software tool that helps the user visualize, understand, and report complex, multidimensional data in analysis databases and data warehouses.
Web Site Home Web Site: Belmont Research Inc.

Curves MS-DOS
The program performs the fit and the graphic display of linear, exponential, geometric and polynomial regression curves from two-dimensional data. It also performs mathematical manipulations of data producing graphic displays from the transformed data, as well as the calculation of several statistics for the different regression curves. Applications: interpolations, enzymeinetics, electrophoresis, etc.
Download  (87 kb, 14-Jun-1994)

DIG - Analysis, Reporting, Intelligence Linux  Unix  Windows
DIG is a Data Analysis, Reporting, Intelligence tool for data workers, labs, and webmasters. Use DIG to clean up duplicates, consolidate, trim, query, summarize large data set in Excel/Access, log files, Oracle, MySQL, lab or POS systems, or any databases. Comes with powerful Excel/Access add-ons, ad-hoc query & multi-dimensional analysis. Watch on-line demo, get a free 30-day trial, then pay $96/yr or $8/month.
Web Site Home Web Site: DigDB

DNA Counter Mac  Windows
This FREEWARE tool will show the proportions between nucleotides in a DNA sequence. You do not need to install it or unpack it. Just download the program and double click to run it. It does not need additional software/add-ons/Java or VBRun packages to run. To uninstall it just delete the program.
Web Site Home Web Site: DNA Counter

Nonlinear regression analysis of models that are the solution of a set of differential equations. Based on DNRP53 and used to fit regression models that are the solution of a set of differential equations; e.g. where the data consist of time courses but the model is in the form of rate equations. BASIC source code only.
Download  (10 kb, 11-May-1994)

Nonlinear regression analysis. A forerunner to DNRPEASY; in some ways more versatile, but without the graphics. This program is described in "Computers in Biology and Medicine" 14, 447-455 (1984). BASIC source code only.
Download  (20 kb, 20-Oct-1985)

DNRPEASY is a computer program which performs a nonlinear regression fit of selected equations to experimental or theoretical data. Statistical information about the fit is calculated, and fitted curve can be plotted (graphically) on the screen or copied to the printer.
Download  (433 kb, 27-May-1997)

Dagra Windows
Software to digitize data from graphs for further analysis, comparison with experimental results and design calculations. Add-in support for MathCAD, Matlab and Excel.
Web Site Home Web Site: Blue Leaf Software

DataFit Windows
DataFit performs nonlinear regression (curve fitting) with 2D/3D plotting capability. Easily perform regression analysis on data with 1 to 20 independent variables. You can define your own regression models, or choose from over 350 built in commonly used models. Solved models are sorted automatically according to goodness of fit. Results include plots of the regression models, q-q plots, scatter plots, fitted parameters with confidence intervals, input vs. estimated data, and goodness of fit statistics. Plots are customizable, including fonts, line styles, error bars, footnotes, contours, extrapolation, et. Data table export of regression models supports extrapolation, and you can also export source code in BASIC or C to use a model in a user written program. Intuitive interface and wide range of features makes it a tool efficiently used by both beginners and experts.
Web Site Home Web Site: Oakdale Engineering

Density from Distance Windows
DfD (Density from Distances) is a Windows 95/98 program that offers a range of analytical techniques commonly used by ecologists to stimate animal and plant density using plotless methods. This program can easily be used by both students and professional ecologists. The program includes a data simulation module that allows the accuracy and efficiency of the different methods to be assessed. This is particularly useful for ecological teaching because it allows students to quickly simulate and explore a range of methods within a familiar Windows setting.
Web Site Home Web Site: PISCES

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