Tag: Workflow System

MOIRAI 20140528 – Compact Workflow System for CAGE Analysis

MOIRAI 20140528

:: DESCRIPTION

MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

::  REQUIREMENTS

  • Linux
  • web2.0 client/server
  • Java
  • c++ server infrastructure

:: DOWNLOAD

 MOIRAI

:: MORE INFORMATION

Citation

MOIRAI: a compact workflow system for CAGE analysis.
Hasegawa A, Daub C, Carninci P, Hayashizaki Y, Lassmann T.
BMC Bioinformatics. 2014 May 16;15(1):144. doi: 10.1186/1471-2105-15-144.

BioPartsDB – DNA Synthesis Workflow System for Synthetic Biology

BioPartsDB

:: DESCRIPTION

BioPartsDB is an open-source, modular tool for DNA synthesis workflow and parts registration, ready to be used in most scenarios, such as molecular biology laboratories or iGem teams.

::DEVELOPER

BioPartsDB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BioPartsDB

:: MORE INFORMATION

Citation

BioPartsDB: a synthetic biology workflow web-application for education and research.
Stracquadanio G, Yang K, Boeke JD, Bader JS.
Bioinformatics. 2016 Jul 13. pii: btw394.

QuickNGS 1.2.4 – Next-Generation Sequencing Workflow System

QuickNGS 1.2.4

:: DESCRIPTION

QuickNGS is a software for efficient high-throughput data analysis of Next-Generation Sequencing data.

::DEVELOPER

the CECAD Research Center at the University of Cologne, Germany.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL server, Apache web server on separate machine

:: DOWNLOAD

 QuickNGS

:: MORE INFORMATION

Citation

QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation.
Wagle P, Nikolić M, Frommolt P.
BMC Genomics. 2015 Jul 1;16:487. doi: 10.1186/s12864-015-1695-x.

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).