KaleidaGraph - Data Analysis Management software

KaleidaGraph contains the comprehensive toolset you need to get your graphing and data analysis done quickly and easily. Period. No costly "bells and whistles" that you rarely use. No complicated software that costs you valuable time and takes you away from your science. Just exceptional, accurate graphing and analysis at a remarkable price.

Details

KaleidaGraph contains the comprehensive toolset you need to get your graphing and data analysis done quickly and easily. Period. No costly "bells and whistles" that you rarely use. No complicated software that costs you valuable time and takes you away from your science. Just exceptional, accurate graphing and analysis at a remarkable price.

Flexible Data Entry.
Begin your analysis by either opening a data file or entering data using the keyboard. Excel files may be opened directly. Tab, space, and other delimited text files use a very flexible import facility.

Fast and Versatile Graphing Choices.
Create plots quickly and easily using entire data columns or just a selection of your data. Data can be spread across multiple files and seamlessly integrated into one powerful graph to best explain your work. Plot types include: Line, Scatter (X-Y), Double-X, Double-Y, Histogram, Box, Percentile, Horizontal Bar, Stack Bar, Column, Stack Column, Polar, Pie, Summary Column, Double Y Bar, Double Y Column, Dot and Function (enter a formula).

Complete Control over Every Plot Option.
To customize every detail of your plot, simply click directly on each plot element, and a make the logical choices to best illustrate your data. You can modify the axis limits, text labels, tick marks, legend, line thickness, marker shapes & sizes, and more.

Templates.
When you create a graph you like, save it as a template so you can use it with repetitive data sets for a consistent presentation.

Powerful Data Analysis and Manipulation.
Easy-to-use commands for analyzing your data include a variety of basic statistics, Student t-test, ANOVA, and Wilcoxon. Use the Formula entry window to manipulate your data using over 100 algebraic equations and statistical functions from convenient menus.

Error Bars.
Add error bars to your plot where the error can be specified in a data column or can be calculated by KaleidaGraph.

Precise Curve Fitting.
Apply a variety of curve fits to your plot. We supply 9 generic fits, including Least Squares (Linear) Regression and Smoothing fits, plus a library of over 100 industry-specific formulas. Utilize one of these predefined fits or enter your own equation for your data. All fits are calculated with incredible speed and accuracy.

Effortless Printing and Plot Export.
Use KaleidaGraph's page layout window to create multigraph presentations. Choose simple features that rearrange and resize your graphs. Then add text, colored backgrounds, and graphics as needed to achieve a professional result. Easily export graphs to PowerPoint, the web, or a favorite application using popular file formats. 

Software Link: KaleidaGraph - Data Analysis Management software

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GPMAWTM - Protein Mass Analysis Software

GPMAWTM General Protein Mass Analysis for Windows
Mass spectrometric analysis of proteins and peptides and more.

The GPMAW program is primarily intended as a tool for mass spectrometric analysis of proteins and peptides. However, a number of other bioinformatics tools have been included, so the use of the program extends far beyond simple mass analysis.

The program runs on all 32-bit versions of Windows since Windows 2000 (i.e. 2000, XP, Vista, Win7). It will also run on current 64-bit versions, but has not been thoroughly tested on these platforms. It can also run on Mac systems with a Windows emulator, but full compatibility is not guaranteed.

Except for the MS/MS Search, the program does not need a strong processor or fast hard disk but can run on any system. Running the MS/MS Search you need a screen with SVGA+ resolution, otherwise you may even run it on a netbook.


GPMAW™ General Protein Mass Analysis Program content

Sequence handling
Import of sequences from a number of different formats with direct database search in Entrez and in local databases (FastA format and Swiss-Prot). Sequences can be saved in local files (databases) for future reference.

From the sequence window a large number of actions can be performed. Sequences can be exported in FastA format (either singly or all sequences at once) for easy transfer to other programs.

Mass analysis
The protein can be cleaved by automatic methods (e.g. a flexible nomenclature for defining enzyme actions) or manually. The peptides are displayed with a number of parameters (various mass values - mono, ave, charges - Bull&Breese index, HPLC index, pI, charge) and can be further worked upon (e.g. cross-linked, new cleavage).

Peptide mass searches can be performed on any local database in FastA format.

Bioinformatics
A number of graphs can be displayed, hydrophobicity, dot-plot, secondary structure prediction. BLAST searches can be performed on local databases.


GPMAW™ General Protein Mass Analysis Program Features

Sequence window
The sequence window is the default view of a sequence. From here you can call most of other sequence related functions (either through the menu, the toolbar, or the pop-up menu).

The display can be configured in various ways, 1- or 3-letter display, average mass/monoisotopic mass, fixed residue width, sidebar with sequence information, show disulfide bridges etc. By highlighting part of the sequence you can easily obtain the mass of the given section. For easy navigation you can color specific residues (three different colors and underlining are available).

Most of the settings can easily be pre-set.

The sequence window is the parent window from which a large number of derived daughter windows can be created:

Peptide window
Ms/ms window
Mass search, composition search
Available graphs
Hydrophobicity
Secondary structure
Charge vs. pH
Dot-plot
Alpha-helical wheel
Peptide window
The peptide window is normally called from the sequence window through the automatic digest commend. However, there are alternative methods like manual or semi-automatic cleavage.

The peptide window lists all the peptides that will be generated from the given protein along with a large number of physical-chemical parameters (charge single/multiple/negative, peptide number, location, HPLC index, theoretical pI, Bull & Breese index, sequence - 1/3-letter etc.).

Peptides can be generated with partial cleavages, modified termini, modified residues (even partial modifications are supported in a limited way). Specific residues may be colored for easier referencing.

The actual parameters presented can be configured by the user.

Sorting and reverse sorting can take place on any column by clicking on the header.

Through the toolbar and/or the pop-up menu (right mouse click) you can access a large number of additional functions related either to the digest (like the simulated HPLC reversed phase chromatogram) or to the currently selected peptide (ms/ms cleavage, peptide information, charge vs. pH graph).

User Defined pI Values
How are these pKa values then used by GPMAW? For the modifications, it is quite simple, as the pKa values are taken into the calculations of pI and charge whenever they are defined in a sequence (i.e. whenever a residue is modified with the relevant modification).

However, for the mass file GPMAW has a user-defined table, as GPMAW has four different tables.

The first and third are values taken from the literature (references in the on-line help and the manual). The second option is based on the values for free amino acid residues. The fourth and last option is based on the definitions in the currently selected mass file and has to be checked in order to use these values.

Software Link : GPMAWTM General Protein Mass Analysis Software

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Origin - Data Analysis Management software

Origin is a software application with tools for data analysis, publication-quality graphing, and programming.

Data Analysis
Origin contains powerful tools for all of your analytic needs, including peak analysis, curve fitting, statistics, and signal processing. To make data analysis more efficient, Origin supports many common formats for importing data, and exporting results. Multi-sheet workbooks and an integrated Project Explorer help you organize your Origin projects. Streamline your workflow by saving workbooks as analysis templates for repeat use.

Graphing
With over 70 built-in graph types, Origin makes it easy to create and customize publication quality graphs to suit your needs. Many popular contour, 2D, and 3D graph types are supported, as are specialty graphs such as windrose, stock (OHLC), ternary (including ternary-contour), 2D vector and 3D vector, and several statistical plots.

Programming
Origin includes two built-in programming languages: Origin C, a C-based compiled language, and a scripting language called LabTalk™. Use them to automate graphing and analysis. Origin comes with an Integrated Development Environment (IDE), Code Builder , that makes it easy to write and debug your own code. Origin is also an Automation Server for users of VB, C++, C# and LabVIEW™.

Detailed Pricing

$550 for academic users $1,095 for commercial users 

Software Link: Origin - Data Analysis Management software

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MATLAB - Data Analysis Management software

MATLAB® is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages, such as C, C++, and Fortran.

You can use MATLAB in a wide range of applications, including signal and image processing, communications, control design, test and measurement, financial modeling and analysis, and computational biology. Add-on toolboxes (collections of special-purpose MATLAB functions) extend the MATLAB environment to solve particular classes of problems in these application areas.

MATLAB provides a number of features for documenting and sharing your work. You can integrate your MATLAB code with other languages and applications, and distribute your MATLAB algorithms and applications.

Key Features:

• High-level language for technical computing
• Development environment for managing code, files, and data
• Interactive tools for iterative exploration, design, and problem solving
• Mathematical functions for linear algebra, statistics, Fourier analysis, filtering, optimization, and numerical integration
• 2-D and 3-D graphics functions for visualizing data
• Tools for building custom graphical user interfaces
• Functions for integrating MATLAB based algorithms with external applications and languages, such as C, C++, Fortran, Java, COM, and Microsoft Excel 

Software link : MATLAB - Data Analysis Management software

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GraphPad InStat - Biostatistics Software

Most statistics programs are designed by statisticians, for statisticians. These programs are feature-packed and powerful, but can overwhelm scientists with thick manuals, obscure statistical jargon and high prices. GraphPad InStat is different. InStat is designed by a scientist for scientists.

Five reasons why you should choose InStat:
InStat guides you step by step
InStat conquers the learning curve by escorting you through statistical analyses. You'll master the program in just a few minutes - really.

Clear analysis choices with explanations
You don't have to know the name of the test you need. InStat helps you pick an appropriate test by asking questions about your data. If you are unsure, consult the extensive help screens, which explain the statistical reasoning in plain language.

Easy to understand results
InStat does not assume that you are a statistics whiz. It presents results in simple paragraphs, with a minimum of statistical jargon. InStat's help screens review the use of each test and explain every portion of the results.

Unique analysis checklists
With other statistics software, it is too easy to get the right answer to the wrong question. That's why InStat provides a unique analysis checklist. Double-check that your data have not violated any assumptions of the test, and that you have picked a test that matches your experimental design and really answers the question you had in mind.

A bargain
Most other statistics programs cost several hundred dollars, but we've made InStat affordable for everyone. InStat costs only $149 for single copies and $79 for upgrades. Buy InStat right now.

Software Link: GraphPad InStat -  Biostatistics Software

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CLC Bioinformatics Database

CLC Bioinformatics Database is a smart and efficient way of managing sequence data in a 3-tier client/server architecture: a server containing one or more databases coupled with CLC workbenches as clients.

Components of the solution
• A database management system of choice; Microsoft SQL Server, Oracle, PostgreSQL, or MySQL.
• CLC Workbenches (clients) for interacting with the database.
• Thin client for administration and setup. -Upload and download of data.
• CLC Database Middleware to ensure scalability and performance.

Centralized sequence data management
In many bioinformatics organizations, the data is a virtual mess, since data is spread out on several computers in various formats and versions. Even employees' personal computers contain essential company data. The main advantages of the CLC Bioinformatics Database is centralization of data, storage, and management. Centralized data in combination with restricted user access makes it possible to be in control of the data and to share information in different groups across the organization. Centralized management of sequence data has been proven vital to increase the general knowledge level in an organization and increase productivity

Software Link:  CLC Bioinformatics Database

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