Tag: Workflow

Jflow 1.2 – A Workflow Management System for Web Applications

Jflow 1.2

:: DESCRIPTION

Jflow is a JavaScript based workflow management system, composed of Jquery plugins which can easily be embedded in any WEB application and a Python library providing all requested features to setup, run and monitor workflows.

::DEVELOPER

Jflow team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JavaScript
  • Python

:: DOWNLOAD

 Jflow

:: MORE INFORMATION

Citation

Jflow: a workflow management system for web applications.
Mariette J, Escudié F, Bardou P, Nabihoudine I, Noirot C, Trotard MS, Gaspin C, Klopp C.
Bioinformatics. 2015 Oct 10. pii: btv589

SNPflow 1.3.5 – SNP Workflow Manager

SNPflow 1.3.5

:: DESCRIPTION

SNPflow is a freely available web application to automatically check the quality of SNP data employing the ABI 7900 HT-platform (e.g. TaqMan, KASPar Assays) or the Sequenom iPLEX platform: Single raw output files of plates are automatically merged and converted to genotype lists.

::DEVELOPER

GenEpi – Division of Genetic Epidemiology Innsbruck

:: SCREENSHOTS

SNPflow

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 SNPflow

:: MORE INFORMATION

Citation

SNPflow: a lightweight application for the processing, storing and automatic quality checking of genotyping assays.
Weissensteiner H, Haun M, Schönherr S, Neuner M, Forer L, Specht G, Kloss-Brandstätter A, Kronenberg F, Coassin S.
PLoS One. 2013;8(3):e59508. doi: 10.1371/journal.pone.0059508.

Snakemake 6.4.1 – Scalable Bioinformatics Workflow Engine

Snakemake 6.4.1

:: DESCRIPTION

Snakemake is a workflow engine and language. It aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style.

::DEVELOPER

Johannes Köster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Snakemake

:: MORE INFORMATION

Citation

Snakemake–a scalable bioinformatics workflow engine.
Köster J, Rahmann S.
Bioinformatics. 2012 Oct 1;28(19):2520-2.

RseqFlow 2.2 – RNA-seq Data Analysis Workflow

RseqFlow 2.2

:: DESCRIPTION

RseqFlow is a workflow which can implement a set of RNA-Seq analysis, such as performing quality control (QC) for sequencing data, generating signal tracks of mapped reads, calculating expression levels, and identifying differentially expressed genes. The workflow allows users to express multi-step RNA-Seq analysis by just providing sequencing RNA-Seq datasets and typing a few commands in an easy-to-use environment.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Virtual Machine

:: DOWNLOAD

 RseqFlow

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Sep 15;27(18):2598-600. Epub 2011 Jul 27.
RseqFlow: workflows for RNA-Seq data analysis.
Wang Y, Mehta G, Mayani R, Lu J, Souaiaia T, Chen Y, Clark A, Yoon HJ, Wan L, Evgrafov OV, Knowles JA, Deelman E, Chen T.

draw+sneakpeek – DNA Resequencing Analysis Workflow

draw+sneakpeek

:: DESCRIPTION

DRAW and SneakPeek are two computer programs that we use for analyzing whole-genome and whole-exome DNA-seq experiments.

DRAW stands for DNA Resequencing Analysis Workflow. DRAW automates the entire process of mapping sequence reads, various quality control steps and calling variants.

SneakPeek is a web-based diagnostic tool for reviewing quality metrics generated by our DNA Resequencing Analysis Workflow (DRAW).

::DEVELOPER

 Wang Lab

:: SCREENSHOTS

SneakPeek

:: REQUIREMENTS

  • Amazon EC2 / Linux

:: DOWNLOAD

 draw+sneakpeek

:: MORE INFORMATION

Citation

Lin CF, Valladares O, Childress DM, Klevak E, Geller ET, Hwang YC, Tsai EA, Schellenberg GD, and Wang LS.
DRAW+SneakPeek: Analysis Workflow and Quality Metric Man-agement for DNA-Seq Experiments.
Bioinformatics (2013) 29 (19): 2498-2500. doi: 10.1093/bioinformatics/btt422

RAMPART 0.12.2 – A Workflow Management System for de novo Genome Assembly

RAMPART 0.12.2

:: DESCRIPTION

RAMPART is a de novo assembly pipeline that makes use of third party-tools and High Performance Computing resources. It can be used as a single interface to several popular assemblers, and can perform automated comparison and analysis of any generated assemblies.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • JRE

:: DOWNLOAD

 RAMPART

:: MORE INFORMATION

Citation

RAMPART: a workflow management system for de novo genome assembly.
Mapleson D, Drou N, Swarbreck D.
Bioinformatics. 2015 Jan 30. pii: btv056.

XiP 3.0 – Construction of Workflows

XiP 3.0

:: DESCRIPTION

XiP (eXtensible integrative Pipeline) is a flexible, editable and modular environment with a user-friendly interface that does not require previous programming skills to run,construct and edit workflows. XiP allows the construction of workflows by linking components written in both R and Java, the analysis of high-throughput data in grid engine systems and also the development of customized pipelines that can be encapsulated in a package and distributed.

::DEVELOPER

Nagasaki Lab

:: SCREENSHOTS

XiP

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 XiP

:: MORE INFORMATION

Citation

Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, Li C, Miyano S.
XiP: a computational environment to create, extend and share workflows.
Bioinformatics. 2013 Jan 1;29(1):137-9

Proteomatic 1.2.1 – Platform for creating MS/MS data Analysis Workflows using Scripts

Proteomatic 1.2.1

:: DESCRIPTION

Proteomatic is a free data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments. Functionality is provided via scripts, and these scripts can be chained together into a high-throughput data processing pipeline.

::DEVELOPER

Proteomatic team

:: SCREENSHOTS

Proteomatic

:: REQUIREMENTS

  • Windows/ MacOsX / Linux

:: DOWNLOAD

 Proteomatic

:: MORE INFORMATION

Citation

Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows
Specht M., Kuhlgert S., Fufezan C., Hippler M.
Bioinformatics (2011) 27(8): 1183-1184, doi: 10.1093/bioinformatics/btr081

PWIMS 2.3 – Proteomics Workflow and Information Management System

PWIMS 2.3

:: DESCRIPTION

PWIMS is an information management system designed as client-server tool for handling Proteomics Experiments. It has features for 2DGe image capturing, Protocol Management, Mass spec data integration, sample management etc.

::DEVELOPER

Bioinformatics Group, Roskamp Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • LAMPP (Linux-Apache-MySQL-Perl/PHP) environment

:: DOWNLOAD

 PWIMS

:: MORE INFORMATION

Citation

Venkatarajan Mathura, Deepak Kolippakkam, Sarah Wilson, Freya Geall, Hong Wang, Fiona Crawford, Michael Mullan., 2004
“PWIMS 1.0: Proteomics Workflow and Information Management System”,
Society of Neuroscience, 34th Annual Meeting.

CDK-Taverna 2.0.5.4 – Workflow Management System for Cheminformatics

CDK-Taverna 2.0.5.4

:: DESCRIPTION

CDK Taverna project based on the “Pipelining Technology” idea tries to address the advantages of software libraries and sophisticated information systems.The project combines two other open-source projects:

The Taverna workbench as a workflow container.
The Chemistry Development Kit (CDK) as a basic chemo-/bioinformatics library.

::DEVELOPER

CDK-Taverna Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

CDK-Taverna

:: MORE INFORMATION

Citation:

Kuhn T, Willighagen EL, Zielesny A, Steinbeck S:
CDK-Taverna: an open workflow environment for cheminformatics.
BMC Bioinformatics 2010, 11:159.