ASAP 1.1.7 – Automated Sequence data Processing on Computer Clusters

ASAP 1.1.7

:: DESCRIPTION

ASAP (Advanced Sequence Automated Pipeline)is an open source pipeline designed to assist users in managing various jobs associated with processing HiSeq data on a cluster or in serial. . The software was designed to alleviate these issues by providing a modular system to allow users with different needs to process their data with a minimal amount of effort. In addition to minimizing human involvement, ASAP is designed to work on the researcher’s local computer cluster, if one is available

::DEVELOPER

Chun Li

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ASAP

:: MORE INFORMATION

Citation

BMC Res Notes. 2013 Jan 4;6:5. doi: 10.1186/1756-0500-6-5.
ASAP: an environment for automated preprocessing of sequencing data.
Torstenson ES1, Li B, Li C.

ArrayExpressHTS 1.42.0 – RNA-seq data Processing and Quality Assessment

ArrayExpressHTS 1.42.0

:: DESCRIPTION

ArrayExpressHTS is an R and Bioconductor RNA-seq processing pipeline that highly utilizes distributed computing for data processing and quality assessment of High-Throughput Sequencing experiments and datasets

::DEVELOPER

EBI.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

  ArrayExpressHTS

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Mar 15;27(6):867-9. doi: 10.1093/bioinformatics/btr012. Epub 2011 Jan 13.
A pipeline for RNA-seq data processing and quality assessment.
Goncalves A, Tikhonov A, Brazma A, Kapushesky M.

RPASuite v0.02 – RNA Processing Analysis Suite

RPASuite v0.02

:: DESCRIPTION

RPASuite is a computational pipeline to identify differentially and coherently processed transcripts using RNA-seq data obtained from multiple tissue or cell lines.

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RPASuite

:: MORE INFORMATION

Citation

Pundhir S and Gorodkin J. (2015)
Differential and coherent processing patterns from small RNAs.
Sci Rep. 5:12062

BioMAJ 3.0.20 – Workflow Engine Dedicated to Data Synchronization and Processing

BioMAJ 3.0.20

:: DESCRIPTION

BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated to data synchronization and processing. The Software automates the update cycle and the supervision of the locally mirrored databank repository.

::DEVELOPER

BioMAJ TEam

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac / Linux
  • Java
  • ant >= 1.7.0.

:: DOWNLOAD

 BioMAJ

:: MORE INFORMATION

Citation

Olivier Filangi at el. 2008
BioMAJ: A flexible framework for databanks synchronization and processing
Bioinformatics 2008 24(16):1823-1825;

SePIA – RNA Sequence Processing, Integration, and Analysis

SePIA

:: DESCRIPTION

SePIA is a comprehensive RNA Sequencing workflow standardizing Processing, Integration, and Analysis of large-scale sequencing data. It provides a systematic, pipeline architecture to manage, individually analyze, and integrate both small-RNA and RNA data.

::DEVELOPER

Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SePIA

:: MORE INFORMATION

Citation

SePIA: RNA and small RNA sequence processing, integration, and analysis.
Icay K, Chen P, Cervera A, Rantanen V, Lehtonen R, Hautaniemi S.
BioData Min. 2016 May 20;9:20. doi: 10.1186/s13040-016-0099-z

MVP/MVP-Fit 2.0 – Macromolecular Visualization and Processing

MVP/MVP-Fit 2.0

:: DESCRIPTION

MVP (Macromolecular Visualization and Processing) is mainly for the illustration and processing of structure-related information which is useful in structure prediction.

MVP-Fit can flexibly move only one domain of the whole model during the fitting process and still keep all the geometric restraints of bond lengths, bond angles and steric clashes for the model.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows
:: DOWNLOAD

 MVPMVP-Fit

:: MORE INFORMATION

Citation

D Xu, Y Zhang,
MVP-Fit: A Convenient Tool for Flexible Fitting of Protein Domain Structures with Cryo-Electron Microscopy Density Map ,
(2011, in preparation).

BioC 1.1 – A Minimalist Approach to Interoperability for Biomedical Text Processing

BioC 1.1

:: DESCRIPTION

BioC is a simple XML format to share text documents and annotations. It allows a large number of different annotations to be represented. We provide simple code to hold this data, read it and write it back to XML files, and perform some sample processing.

::DEVELOPER

BioC Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java / C++

:: DOWNLOAD

 BioC 

:: MORE INFORMATION

Citation

Database (Oxford). 2013 Sep 18;2013:bat064. doi: 10.1093/database/bat064. Print 2013.
BioC: a minimalist approach to interoperability for biomedical text processing.
Comeau DC, Islamaj Doğan R, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ.

BetaMol v0.92d – Molecular Modeling, Analysis, and Processing software

BetaMol v0.92d

:: DESCRIPTION

BetaMol is a molecular modeling, analysis, and processing software completely based on the theory of the Voronoi diagram, the quasi-triangulation, and the Beta-complex.

::DEVELOPER

Voronoi Diagram Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BetaMol

:: MORE INFORMATION

Citation

Youngsong Cho, Jae-Kwan Kim, Joonghyun Ryu, Chung-In Won, Chong-Min Kim, Donguk Kim, and Deok-Soo Kim,
BetaMol: a molecular modeling, analysis and visualization software based on the beta-complex and the quasi-triangulation,
Journal of Advanced Mechanical Design, Systems, and Manufacturing, Vol.6, Issue 3, pp. 389-403, 2012

RobiNA 1.2.4 – Open Source Microarray and RNA-Seq Processing

RobiNA 1.2.4

:: DESCRIPTION

RobiNA is an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface. RobiNA accepts raw FastQ files, SAM/BAM alignment files and counts tables as input. It supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state-of-the art biostatistical methods developed in the R/Bioconductor projects. In-line help and a step-by-step manual guide users through the analysis.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 RobiNA

:: MORE INFORMATION

Citation

Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. (2012)
RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7.

JADOPPT – Java based AutoDock Preparing and Processing Tool

JADOPPT

:: DESCRIPTION

JADOPPT is a tool for automatically preparing and processing multiple AutoDock results, thus allowing their simultaneous analysis and comparison.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux /MacOs
  • Java

:: DOWNLOAD

JADOPPT

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):583-585. doi: 10.1093/bioinformatics/btw677.
JADOPPT: java based AutoDock preparing and processing tool.
García-Pérez C, Peláez R, Therón R, Luis López-Pérez J.