Category: Bioinformatics Platform

Pygr 0.82 – Python Graph Database Framework for Bioinformatics

Pygr 0.82

:: DESCRIPTION

pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use

Pygr is open source software to develop graph database interfaces for the popular Python language  to make it easy to do powerful sequence and comparative genomics analyses, even with extremely large multi-genome data sets. pygr includes:

  • Code for interacting with sequence databases, search methods such as BLAST, repeat-masking, megablast, etc.;
  • Querying and working with sequence annotation databases and sequence alignment datasets;
  • A data namespace for accessing a given resource with seamless data relationship management.
  • Easy data sharing that includes transparent access over network protocols.
  • High performance graph representation and query of interval-based data.

::DEVELOPER

Chris Lee, Dept. of Chemistry & Biochemistry,UCLA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/Mac OsX
  • Python

:: DOWNLOAD

Pygr

:: MORE INFORMATION

Ergatis v2r18 – A Workflow System for Bioinformatics

Ergatis v2r18

:: DESCRIPTION

Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data.

::DEVELOPER

The Institute for Genome Sciences (IGS)

:: SCREENSHOTS

Ergatis

:: REQUIREMENTS

  • Workflow Engine
  • Sun Grid Engine
  • Web server
  • Perl

:: DOWNLOAD

 Ergatis

:: MORE INFORMATION

Citation

Orvis J, Crabtree J, Galens K, Gussman A, Inman JM, Lee E, Nampally S, Riley D, Sundaram JP, Felix V, Whitty B, Mahurkar A, Wortman J, White O, Angiuoli SV.
Ergatis: A web interface and scalable software system for bioinformatics workflows.
Bioinformatics. 2010 Jun 15;26(12).

Sirius PSB 2.3.3 – Generic System for Analysis of Biological Sequences

Sirius PSB 2.3.3

:: DESCRIPTION

Sirius PSB  (Sirius Prediction System Builder) is a software to carry out sequence (DNA or protein) analysis. Main operations: 1) Building a classifier 2) Deploying a classifer 3) Search for proteins similar to query proteins 4) Preliminary and post prediction analysis (Visualization)

::DEVELOPER

Sirius PSB Team

:: SCREENSHOTS

SiriusPSB

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 Sirius PSB

:: MORE INFORMATION

Citation:

Koh CH, Lin S, Jedd G, Wong L:
Sirius PSB: A Generic System for Analysis of Biological Sequences.
Journal of Bioinformatics and Computational Biology, 7(6): 973-990, December 2009.

BioC++ 0.3 – C++ Computational Libraries for Bioinformatics

BioC++ 0.3

:: DESCRIPTION

The BioC++ project provides an accessible and comprehensive framework of C/C++ tools and libraries for computational biology.

::DEVELOPER

Hongyu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 BioC++

:: MORE INFORMATION

CloudBioLinux – Genome Analysis for Cloud Computing platforms

CloudBioLinux

:: DESCRIPTION

CloudBioLinux offers genome analysis resources for cloud computing platforms such as Amazon EC2. The software is a build and deployment system which installs a large selection of Bioinformatics and machine learning libraries on a bare virtual machine (VM) image, freshly installed PC, or in the Cloud.

::DEVELOPER

CloudBioLinux Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CloudBioLinux

:: MORE INFORMATION

Citation

Curr Protoc Bioinformatics. 2012 Jun;Chapter 11:Unit11.9.
Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.
Afgan E, Chapman B, Jadan M, Franke V, Taylor J.

BioHPC 1Rev293 – Computational Biology Application Suite for High Performance Computing

BioHPC 1Rev293

:: DESCRIPTION

BioHPC is a suite of applications modified and adapted for efficient use in an HPC (High Performance Computing)environment with ASP.NET interface allowing both easy access and use, as well as easy administration of users, applications, data and other features.

::DEVELOPER

Computational Biology Service Unit

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET 3.5 Runtime
  • Microsoft SQL Express Advanced

:: DOWNLOAD

  BioHPC

:: MORE INFORMATION

ARCT 0.9 – Comparative Genomics of Aging

ARCT 0.9

:: DESCRIPTION

ARCT (Ageing Research Computational Tools) is a toolkit of Perl modules aimed at bioinformatics, genomics, and gerontology, partly based on the BioPerl package.The aim of ARCT is to allow the comparative genomics of aging. ARCT is a collection of data-mining tools, algorithms, parsers,wrappers, spiders and web applications, etc.

::DEVELOPER

João Pedro de Magalhães. @ Human Ageing Genomic Resources

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  ARCT

:: MORE INFORMATION

Citation

Aging Cell. 2009 Feb;8(1):65-72. Epub 2008 Nov 5.
The Human Ageing Genomic Resources: online databases and tools for biogerontologists.
de Magalhães JP, Budovsky A, Lehmann G, Costa J, Li Y, Fraifeld V, Church GM.

AiO 8 – Integrate Oligo ordering/Data Base and DNA/Protein programs

AiO 8

:: DESCRIPTION

AiO  (All in One) is a program for Windows, that combines typical DNA/protein features such as plasmid map drawing, finding of ORFs, translate, backtranslate, primer design and virtual cloning. AiO uses databases that allow the management of oligonucleotides, oligonucleotide-manufacturers, restriction enzymes, structural DNA and program users in a multi-user/multi-group environment

::DEVELOPER

Dr. Christiaan Karreman

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  AiO

:: MORE INFORMATION

Citation

Bioinformatics. 2002 Jun;18(6):884-5.
AiO, combining DNA/protein programs and oligo-management.
Karreman C.

SOAP 3 – Short Oligonucleotide Analysis Package

SOAP 3

:: DESCRIPTION

SOAP (Short Oligonucleotide Analysis Package) has been in evolution from a single alignment tool to a tool package that provides full solution to next generation sequencing data analysis

::DEVELOPER

BGI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SOAP

:: MORE INFORMATION

Citation:

Li et al. (2009)
SOAP2: an improved ultrafast tool for short read alignment.
BIOINFORMATICS, doi:10.1093/bioinformatics/btp336