Tag: Bioinformatics

BioWarehouse 4.6 – Database Integration for Bioinformatics

BioWarehouse 4.6

:: DESCRIPTION

BioWarehouse is a database interoperation environment that supports data mining and integration of multiple databases including the UniProt, BioCyc, NCBI Taxonomy, Genbank, CMR, ENZYME, Gene Ontology, and KEGG databases.

::DEVELOPER

BioWarehouse Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows /MacOsX
  • MySQL

:: DOWNLOAD

 BioWarehouse

:: MORE INFORMATION

Citation

Thomas J Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta, David WJ Stringer-Calvert, Jessica D Tenenbaum3 and Peter D Karp
BioWarehouse: a bioinformatics database warehouse toolkit
BMC Bioinformatics 2006, 7:170

Darwin 2.1 – Programming Environment for Bioinformatics

Darwin 2.1

:: DESCRIPTION

Darwin (Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences) is a programming environment with its own, modern language and a growing library of functions for sequence management and analysis, statistics, numerics, graphics, parallel execution and more.

::DEVELOPER

CBRG – Computational Biochemistry Research Group ,Institut für Wissenschaftliches Rechnen at the ETH Zurich.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

  Darwin

:: MORE INFORMATION

Citation

G. H. Gonnet, M. T. Hallett, C. Korostensky, and L. Bernardin
Darwin v. 2.0: an interpreted computer language for the biosciences
Bioinformatics 2000 16: 101-103.

BioSLAX 7.5 – BioInformatics LiveCD Suite

BioSLAX 7.5

:: DESCRIPTION

BioSLAX is a new live CD/DVD suite of bioinformatics tools that has been released by the resource team of the BioInformatics Center (BIC), National University of Singapore (NUS). Bootable from any PC, this CD/DVD runs the compressed SLACKWARE flavour of the LINUX operating system also known as SLAX.

::DEVELOPER

the BioInformatics Center (BIC), National University of Singapore

:: SCREENSHOTS

:: REQUIREMENTS

  • bootable CD-ROM drive

:: DOWNLOAD

 BioSLAX

:: MORE INFORMATION

VLinux 2.0 alpha 2 – Linux Workbench for Bioinformatics

VLinux 2.0 alpha 2

:: DESCRIPTION

VLinux is a Linux distribution and appliance for students and researchers in Bioinformatics. It is based on the well known openSUSE Linux distribution and is built using Novell’s Suse Studio.

::DEVELOPER

Vimalkumar Velayudhan

:: SCREENSHOTS

:: REQUIREMENTS

  • bootable CD-ROM drive

:: DOWNLOAD

 VLinux

:: MORE INFORMATION

VigyaanCD 1.0 – Workbench for Bioinformatics

VigyaanCD 1.0

:: DESCRIPTION

Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry. It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling software.

At present the following ready to use software comes on VigyaanCD: Arka/GP, Artemis, Bioperl, BLAST (NCBI-tools), ClustalW/ClustalX, Cn3D, EMBOSS tools, Garlic, Glimmer, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, Jmol, MPQC, MUMer, NJPlot, Open Babel, Octave, PSI3, PyMOL, Ramachandran plot viewer, Rasmol, Raster3D, Seaview, TINKER, XDrawChem, Xmgr and Xfig. GNU C/C++/Fortran compilers and additional Linux tools (such as ps2pdf) are also available.

::DEVELOPER

Pratul K. Agarwal

:: SCREENSHOTS

:: REQUIREMENTS

  • live Linux CD

:: DOWNLOAD

 VigyaanCD

:: MORE INFORMATION

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

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.

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