Category: Bioinformatics Platform

SMS 2 – Sequence Manipulation Suite

SMS 2

:: DESCRIPTION

SMS (Sequence Manipulation Suite) is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.

::DEVELOPER

Stothard Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Internet Browser
  • java

:: DOWNLOAD

SMS

:: MORE INFORMATION

Citation

Stothard P (2000)
The Sequence Manipulation Suite: JavaScript programs for analyzing and formatting protein and DNA sequences.
Biotechniques 28:1102-1104.

Genamics Expression 1.1 – DNA and Protein Sequence Analysis

Genamics Expression 1.1

:: DESCRIPTION

Genamics Expression is a revolutionary new Windows application for DNA and protein sequence analysis. Utilising a novel interface, Expression makes complex computational analyses of sequence information incredibly simple. The coupling of creative innovations with the very latest computing technology defines Expression as the new gold standard in computational sequence analysis.

::DEVELOPER

Genamics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Genamics Expression

:: MORE INFORMATION

If you are not a registered user of Expression, the software will expire 30 days after installation.

BioCocoa 2.2.2 – Cocoa Framework for Bioinformatics

BioCocoa 2.2.2

:: DESCRIPTION

BioCocoa is an open source Cocoa framework for bioinformatics written in Objective-C. We intend to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. Cocoa is a great framework for rapid application development and it is therefore often used to create innovative bioscientific apps. To speed up development even more, BioCocoa wants to offer reusable Cocoa classes that are specific for molecular biology and biofinformatics. At this time, BioCocoa offers model classes for biological sequences, controller classes for alignment, sequence manipulation and I/O, interfacing with ENTREZ and view classes that let you easily display and work with sequences in your own applications.

::DEVELOPER

BioCocoa Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

BioCocoa

:: MORE INFORMATION

BioWeka 0.6.1 – Weka Framework for Bioinformatics

BioWeka 0.6.1

:: DESCRIPTION

BioWeka‘s aim is to add bioinformatics functionalities such as e.g. alignments to the popular machine learning framework  Weka (Waikato Environment for Knowledge Analysis). BioWeka introduce various input formats for bioinformatics data and bioinformatics methods like alignments to Weka. This allows users to easily combine them with Weka’s classification, clustering, validation and visualization facilities on a single platform and therefore reduces the overhead of converting data between different data formats as well as the need to write custom evaluation procedures that can deal with many different programs. We encourage users to participate in this project by adding their own components and data formats to BioWeka.

::DEVELOPER

Institut für Informatik, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

BioWeka

:: MORE INFORMATION

Citation

Jan E. Gewehr, Martin Szugat and Ralf Zimmer
BioWeka—extending the Weka framework for bioinformatics
Bioinformatics (2007) 23 (5): 651-653

DNALinux VD – A Linux Solution for Bioinformatics

DNALinux VD

:: DESCRIPTION

DNALinux VD (DNALinux Virtual Desktop) is a Virtual Machine with bioinformatic software preinstalled.The main advantage of this approach is that a virtualized environment doesn’t affect a installed system. With a virtual machine a Linux system can be run under a Windows system, provided that the virtual machine player is installed.

::DEVELOPER

Genes Digitales and Quilmes National University, Argentina.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

DNALinux VD

:: MORE INFORMATION

Citation:

Bassi, Sebastian and Gonzalez, Virginia.
DNALinux Virtual Desktop Edition
Nature Precedings

SeWeR 3.0 – Sequence Analysis using Web Resources

SeWeR 3.0

:: DESCRIPTION

SeWeR (Sequence analysis using Web Resources) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser.

::DEVELOPER

Malay Kumar Basu , Centre for Cellular and Molecular Biology,  India

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

SeWeR

:: MORE INFORMATION

Citaiton

Basu M K (2001)
SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services.
Bioinformatics. 17(6): 577-578.

BioGridRunner 2002 – Bioinformatics Data Grid Application

BioGridRunner 2002

:: DESCRIPTION

BioGridRunner is a distributed computing application for bioinformatics, incorporating directory services (data and software), grid computing methods (security, authentication, data transport and remote jobs), and gene sequence and genomic data processing methods.

::DEVELOPER

Don Gilbert at Indiana University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

BioGridRunner

:: MORE INFORMATION

This is an experimental program. No warranty is made for its operations. It includes methods which view and manipulate files, on your computer and others. The author believes it is safe for testing, but cannot promise use will not damage your files or data inadvertantly.