Category: Bioinformatics Platform

Confero 0.1 – Integrated Contrast and Gene Set Platform

Confero 0.1

:: DESCRIPTION

Confero is a contrast data and gene set platform for downstream analysis and biological interpretation of omics data.

::DEVELOPER

Confero team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java
  • Perl
  • MySQL Server

:: DOWNLOAD

 Confero

:: MORE INFORMATION

Citaton

BMC Genomics. 2013 Jul 29;14:514. doi: 10.1186/1471-2164-14-514.
Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.
Hermida L1, Poussin C, Stadler MB, Gubian S, Sewer A, Gaidatzis D, Hotz HR, Martin F, Belcastro V, Cano S, Peitsch MC, Hoeng J.

CloudDOE 2.2.0 – MapReduce-based Bioinformatics Environment

CloudDOE 2.2.0

:: DESCRIPTION

CloudDOE is a software package with user-friendly graphic interface to deploy, operate and extend a MapReduce-based bioinformatics environment, which is denoted as the CloudDOE Cloud

::DEVELOPER

CloudDOE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 CloudDOE

:: MORE INFORMATION

Citation

CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.
Chung WC, Chen CC, Ho JM, Lin CY, Hsu WL, Wang YC, Lee DT, Lai F, Huang CW, Chang YJ.
PLoS One. 2014 Jun 4;9(6):e98146. doi: 10.1371/journal.pone.0098146.

EBiAn – Easy Bioinformatics Analysis

EBiAn

:: DESCRIPTION

EBiAn package can perform the main analysis and manipulation of DNA, RNA, proteins and peptides sequences.

::DEVELOPER

Luiz Carlos Bertucci Barbosa (luiz_cbb@hotmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 EBiAn

:: MORE INFORMATION

Citation

Easy Bioinformatics Analysis (EBiAn): a package for manipulating and analysis of short biological sequences.
Bertucci Barbosa LC, Garrido SS, Garcia A, Delfino DB, Gon?alves RD, Marchetto R.
Bioinformation. 2010 Jul 6;5(2):46-8.

RSAT 2015 – Regulatory Sequence Analysis Tools

RSAT 2015

:: DESCRIPTION

RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences.

::DEVELOPER

RSAT TEam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

RSAT 2015: Regulatory Sequence Analysis Tools.
Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J.
Nucleic Acids Res. 2015 Apr 22. pii: gkv362.

Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J. (2011)
RSAT 2011: regulatory sequence analysis tools.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W86-91

Taiji 1.3.0 – Multi-omics Bioinformatics Pipeline

Taiji 1.3.0

:: DESCRIPTION

The Taiji software is an integrative multi-omics data analysis framework. It can be used as a standalone pipeline to analyze ATAC-seq, RNA-seq, single cell ATAC-seq or Drop-seq data. However, the uniqueness and the power of Taiji really lie in its ability to integrate diverse datasets and use these information in a clever way to construct regulatory network and identify candidate driver genes.

::DEVELOPER

Wei Wang’s group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

Taiji

:: MORE INFORMATION

Citation

Zhang K, Wang M, Zhao Y, Wang W.
Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development.
Sci Adv. 2019 Mar 27;5(3):eaav3262. doi: 10.1126/sciadv.aav3262. PMID: 30944857; PMCID: PMC6436936.

ChemoPy 1.0 – Python package for Computational Biology and Chemoinformatics

ChemoPy 1.0

:: DESCRIPTION

ChemoPy is an open-source python package called chemoinformatics in python for calculating the commonly used structural and physicochemical features.

::DEVELOPER

ChemoPy team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • Python

:: DOWNLOAD

 ChemoPy

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Apr 15;29(8):1092-4. doi: 10.1093/bioinformatics/btt105. Epub 2013 Mar 14.
ChemoPy: freely available python package for computational biology and chemoinformatics.
Cao DS, Xu QS, Hu QN, Liang YZ.

birgHPCC 1.0 – Creating Compute Unified Device Architecture (CUDA) Computing Cluster for Bioinformatics

birgHPCC 1.0

:: DESCRIPTION

birgHPCC (Bioinformatic Research Group High Performance CUDA Computing) is a free Linux Live DVD distribution based on PelicanHPC and birgHPC.birgHPCC is capable of creating and configuring a compute unified device architecture (CUDA) computing cluster, hence the extra “C” in the name.

::DEVELOPER

birgHPCC team

:: SCREENSHOTS

birgHPCC

:: REQUIREMENTS

  • bootable DVD / USB

:: DOWNLOAD

  birgHPCC

:: MORE INFORMATION

birgHPC 1.2.1 – Creating instant Computing Clusters for Bioinformatics

birgHPC 1.2.1

:: DESCRIPTION

birgHPC (Bioinformatic Research Group High Performance Computing) is a free Linux Live CD distribution based on PelicanHPC and Debian Live.birgHPC features automated cluster configuration on PCs in the same network specifically for bioinformatics and molecular dynamics.

::DEVELOPER

birgHPC team

:: SCREENSHOTS

birgHPC

:: REQUIREMENTS

  • bootable DVD / USB

:: DOWNLOAD

 birgHPC

:: MORE INFORMATION

Citation

Teong Han Chew, Kwee Hong Joyce-Tan, Farizuwana Akma and Mohd Shahir Shamsir.
birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics.
Bioinformatics. Volume 27, Issue 9. pp 1320-1321.

SB.OS 1.4.1 – Systems Biology Operational Software DVD ISO Image

SB.OS 1.4.1

:: DESCRIPTION

SB.OS is a live bootable DVD based on Ubuntu Linux that comes with a comprehensive list of Systems Biology Software. Text and video documentation material, as well as an offline copy of the BioModels.net database, are included.

List of Systems Biology Software is as below:

  • CellDesigner 4.0.1 (including plugin SBMLsqueezer 1.3)
  • COPASI 4.5.30
  • Cytoscape 2.6.3 (including plugin BiNoM)
  • Edinburgh Pathway Editor 1.3.0
  • ISATools 1.1
  • libSBML 3.4.1
  • modelMage 1.0beta
  • OpenAlea
  • SBML2LaTeX 0.9.8
  • SBML-PET 2.3.5
  • SBMLeditor 1.3.4
  • SystemsBiologyWorkbench 2.7.10
  • semanticSBML 1.0.11
  • STSE
  • Taverna 2.1
  • vanted 1.8
  • TiDE 1.2.1
  • Xppaut 6.0

Systems Biology Models

  • BioModels Database
  • Yeast consensus model version 2.0

Convenience Tools

  • gtk-recordMyDesktop
  • XML Copy Editor 1.2.0.6

Python

  • epydoc
  • NumArray
  • NumPy
  • Python 2.5, IPython
  • PyX
  • Soappy
  • SciPy

::DEVELOPER

SB.OS Team

:: SCREENSHOTS

:: REQUIREMENTS

  • bootable DVD

:: DOWNLOAD

SB.OS

:: MORE INFORMATION

ARB 6.0.6 – Sequence Database Handling and data analysis

ARB 6.0.6

:: DESCRIPTION

The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria.

::DEVELOPER

Prof. Dr. Wolfgang Liebl

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 ARB

:: MORE INFORMATION

Citation:

Wolfgang Ludwig, et al.
ARB: a software environment for sequence data.
Nucleic Acids Research. 2004. 32(4):1363-1371.