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PPIevo – Protein-protein Interaction Prediction from PSSM based Evolutionary Information

 System Biology & Modeling 107 views Comments Off on PPIevo – Protein-protein Interaction Prediction from PSSM based Evolutionary Information
Aug 082019
 

PPIevo

:: DESCRIPTION

PPIevo is a software of protein-protein interaction prediction from PSSM based evolutionary information

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

PPIevo

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 PPIevo

:: MORE INFORMATION

Citation:

Genomics. 2013 Oct;102(4):237-42. doi: 10.1016/j.ygeno.2013.05.006. Epub 2013 Jun 6.
PPIevo: protein-protein interaction prediction from PSSM based evolutionary information.
Zahiri J1, Yaghoubi O, Mohammad-Noori M, Ebrahimpour R, Masoudi-Nejad A.

BioMet Toolbox 2.0 – Genome-wide analysis of Metabolism and Omics data

 Bioinformatics Platform 293 views Comments Off on BioMet Toolbox 2.0 – Genome-wide analysis of Metabolism and Omics data
Nov 222018
 

BioMet Toolbox 2.0

:: DESCRIPTION

The BioMet ToolBox is a web-based resource for exploiting the capabilites of metabolic networks described in genome scale models using flux analysis and random sampling, powered by RAVEN, gene set analysis and basic microarray analysis using PIANO, thereby providing an integrated analysis to identify coregulated subnetwork structures within the metabolic network and also for identifying statistically significant gene sets enabling biological interpretation.

:: DEVELOPER

Systems & Synthetic Biology – SYSBIO, Chalmers University of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.
Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, V?remo L, Nookaew I, Nielsen J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W175-81. doi: 10.1093/nar/gku371.

BioInfoServ 6.0 – Bioinformatic Platform

 Bioinformatics Platform 361 views Comments Off on BioInfoServ 6.0 – Bioinformatic Platform
Nov 222018
 

BioInfoServ 6.0

:: DESCRIPTION

The ideal Operation System, BioInfoServOS, which is a specially customised system for scientists handling and analysing biological data, but also for easy use of daily official business handing, has been distributed.

::DEVELOPER

BioInfoServ team

:: SCREENSHOTS

BioInfoServOS

:: REQUIREMENTS

  • DVD ROM

:: DOWNLOAD

  BioInfoServ

:: MORE INFORMATION

CRImage 1.30.0 – Tumour Image analysis

 Image Analysis 218 views Comments Off on CRImage 1.30.0 – Tumour Image analysis
Nov 222018
 

CRImage 1.30.0

:: DESCRIPTION

CRImage provides image analysis tools for segmentation, classification, and downstream analysis of tumour section images.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

  CRImage

:: MORE INFORMATION

Citation

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling
Y. Yuan, H. Failmezger, O.M. Rueda, H.R. Ali, S. Gräf, S-F. Chin, R.F. Schwarz, C Curtis, M.J. Dunning, H. Bardwell, N. Johnson, S. Doyle, G. Turashvili, E. Provenzano, S. Aparicio, C. Caldas, F. Markowetz
Science Translational Medicine, 4, 157ra142 (2012)

Staden 2.0.0b11 – DNA Sequence Assembly , Editing and Analysis

 Bioinformatics Platform 926 views Comments Off on Staden 2.0.0b11 – DNA Sequence Assembly , Editing and Analysis
Nov 222018
 

Staden 2.0.0b11

:: DESCRIPTION

Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) .

::DEVELOPER

Staden Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Staden

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 15;26(14):1699-703. doi: 10.1093/bioinformatics/btq268. Epub 2010 May 30.
Gap5–editing the billion fragment sequence assembly.
Bonfield JK1, Whitwham A.

Rodger Staden, David P. Judge and James K. Bonfield.
Analysing Sequences Using the Staden Package and EMBOSS.
Introduction to Bioinformatics. A Theoretical and Practical Approach. Eds. Stephen A. Krawetz and David D. Womble. Human Press Inc., Totawa, NJ 07512 (2003)

Galaxy 18.09 – Evolutionary and Data Processing Module Development

 Bioinformatics Platform 573 views Comments Off on Galaxy 18.09 – Evolutionary and Data Processing Module Development
Nov 222018
 

Galaxy 18.09

:: DESCRIPTION

Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.

::DEVELOPER

Galaxy Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Python

:: DOWNLOAD

 Galaxy

:: MORE INFORMATION

Citation

Genome Res. 2009 Nov;19(11):2144-53. Epub 2009 Oct 9.
Windshield splatter analysis with the Galaxy metagenomic pipeline.
Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; Galaxy Team.

BioLite 1.0.0 – Bioinformatics Framework with automated Tracking of Diagnostics and Provenance

 Bioinformatics Platform 177 views Comments Off on BioLite 1.0.0 – Bioinformatics Framework with automated Tracking of Diagnostics and Provenance
Nov 222018
 

BioLite 1.0.0

:: DESCRIPTION

BioLite is a bioinformatics framework written in Python/C++ that automates the collection and reporting of diagnostics, tracks provenance, and provides lightweight tools for building out customized analysis pipelines.

::DEVELOPER

The Dunn Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python/C++

:: DOWNLOAD

 BioLite

:: MORE INFORMATION

Citation

Howison M, Sinnott-Armstrong NA, Dunn CW. 2012.
BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance.
In Proceedings of the 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP ’12), 14-15 June 2012, Boston, MA, USA.

Agalma 1.0.0 – A Transcriptome Assembly and Phylogenetic Analysis Environment

 Phylogenetic Analysis 152 views Comments Off on Agalma 1.0.0 – A Transcriptome Assembly and Phylogenetic Analysis Environment
Nov 222018
 

Agalma 1.0.0

:: DESCRIPTION

Agalma is an automated tool that constructs matrices for phylogenomic analyses.  It builds alignments of homologous genes and preliminary species trees from genomic and transcriptome data.

::DEVELOPER

The Dunn Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Agalma

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Nov 19;14:330. doi: 10.1186/1471-2105-14-330.
Agalma: an automated phylogenomics workflow.
Dunn CW1, Howison M, Zapata F.

Bio++ 2.4.1 – C++ Libraries for Bioinformatics

 Bioinformatics Platform 1,135 views Comments Off on Bio++ 2.4.1 – C++ Libraries for Bioinformatics
Nov 222018
 

Bio++ 2.4.1

:: DESCRIPTION

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is fully Object Oriented and is designed to be both easy to use and computer efficient.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Bio++

:: MORE INFORMATION

Citation:

Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, Galtier N, Belkhir K.
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.
BMC Bioinformatics. 2006 Apr 4;7:188.

SeqWare 1.1.1 – Tool Set to work with Next Generation Genome Sequencers

 Bioinformatics Platform 487 views Comments Off on SeqWare 1.1.1 – Tool Set to work with Next Generation Genome Sequencers
Nov 222018
 

SeqWare 1.1.1

:: DESCRIPTION

SeqWare currently provides four tools specifically designed to support massively parallel sequencing technologies (Illumina, ABI SOLiD, 454). The first is a LIMS web application (SeqWare LIMS) to manage samples, record computational events, and present results back to end users. The second component is a pipeline (SeqWare Pipeline) which consists of many different programs useful for processing and annotating sequence data. These can be combined with other tools (BFAST, BWA, SAMtools, etc) and strung together to form more complex workflows to support many experiment types. Third, a query tool (SeqWare Query Engine) is available to database and query variants and other events inferred from sequence data. Finally, SeqWare MetaDB provides a common database to store metadata used by all components. All four tools can be used together or separately.

::DEVELOPER

SeqWare Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  SeqWare

:: MORE INFORMATION

Citation

Brian D O’Connor, Barry Merriman and Stanley F Nelson
SeqWare Query Engine: storing and searching sequence data in the cloud
BMC Bioinformatics 2010, 11(Suppl 12):S2