AMEN 1.5.5 – Molecular Systems Biology Data Analysis

AMEN 1.5.5

:: DESCRIPTION

AMEN (Annotation, Mapping, Expression and Network) is a stand-alone, unified suite of tools to manage, explore and combine biological multifaceted high-throughput data such as annotation, chromosomal location, expression and interaction data.

::DEVELOPER

Frédéric Chalmel and Michael Primig

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  AMEN

:: MORE INFORMATION

Citation:

Frédéric Chalmel and Michael Primig
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
BMC Bioinformatics 2008, 9:86doi:10.1186/1471-2105-9-86

BMT – Bioinformatics Mini Toolbox

BMT

:: DESCRIPTION

BMT is combination of seven tools including FastqTrimmer, Gene Prediction, DNA Analysis, Translation, Protein analysis and Pairwise and Multiple alignment.

::DEVELOPER

Muhammad Nasir Iqbal

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

BMT

:: MORE INFORMATION

Citation

Iqbal MN, Rasheed MA, Awais M, Chammam W, Kanwal S, Khan SU, Saddick S, Tlili I.
BMT: Bioinformatics mini toolbox for comprehensive DNA and protein analysis.
Genomics. 2020 Nov;112(6):4561-4566. doi: 10.1016/j.ygeno.2020.08.010. Epub 2020 Aug 10. PMID: 32791200.

STINGRAY 20140221 – The System for Integrate Genomic Resources and Analyses

STINGRAY 20140221

:: DESCRIPTION

STINGRAY is a user-friendly web-based system designed to analyse genomic data in the context of a pipeline.

::DEVELOPER

STINGRAY team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl,
  • Bioperl
  • CGI
  • Apache
  • MySQL

:: DOWNLOAD

 STINGRAY

 :: MORE INFORMATION

Citation:

STINGRAY: system for integrated genomic resources and analysis.
Wagner G, Jardim R, Tschoeke DA, Loureiro DR, Oca?a KA, Ribeiro AC, Emmel VE, Probst CM, Pitaluga AN, Grisard EC, Cavalcanti MC, Campos ML, Mattoso M, Dávila AM.
BMC Res Notes. 2014 Mar 7;7:132. doi: 10.1186/1756-0500-7-132.

StrBio 1.3 – Java Classes for Computational Structural Biology

StrBio 1.3

:: DESCRIPTION

StrBio library is a set of Java classes useful for development of software for computational structural biology research. The StrBio library includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.

::DEVELOPER

John-Marc Chandonia

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 StrBio

:: MORE INFORMATION

Citation:

Chandonia, JM. 2007.
StrBioLib: a Java library for development of custom computational structural biology applications.
Bioinformatics, May 30, doi: 10.1093/bioinformatics/btm269.

Logol – Pattern matching language and tools

Logol

:: DESCRIPTION

Logol is a language used to describe some patterns in a DNA/RNA/Protein sequence

::DEVELOPER

GenOuest

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Logol

:: MORE INFORMATION

Citation

Catherine Belleannée, Olivier Sallou, Jacques Nicolas.
Expressive Pattern Matching with Logol.
Application to the Modelling of -1 Ribosomal Frameshift events. JOBIM 2012- 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp. 5-14.

TREVA 1 – Bioinformatics Pipelines for Targeted Resequencing and Whole-exome Sequencing

TREVA

:: DESCRIPTION

TREVA (Targeted REsequencing Virtual Appliance) is a user-friendly virtual appliance, containing complex bioinformatics pipelines that can be installed and setup with minimal efforts. TREVA pipelines support a series of analyses commonly required for targeted resequencing and whole exome sequencing data, including: single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses.

::DEVELOPER

TREVA team

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

:: DOWNLOAD

 TREVA

:: MORE INFORMATION

Citation:

Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment.
Li J, Doyle MA, Saeed I, Wong SQ, Mar V, Goode DL, Caramia F, Doig K, Ryland GL, Thompson ER, Hunter SM, Halgamuge SK, Ellul J, Dobrovic A, Campbell IG, Papenfuss AT, McArthur GA, Tothill RW.
PLoS One. 2014 Apr 21;9(4):e95217. doi: 10.1371/journal.pone.0095217.

CLIP-Explorer – Web Server for CLIP-Seq data analysis

CLIP-Explorer

:: DESCRIPTION

Galaxy CLIP-Explorer is a webserver to process, analyse and visualise CLIP-Seq data.

::DEVELOPER

the Freiburg Galaxy Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Heyl F, Maticzka D, Uhl M, Backofen R.
Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.
Gigascience. 2020 Nov 11;9(11):giaa108. doi: 10.1093/gigascience/giaa108. PMID: 33179042; PMCID: PMC7657819.

ORCA – Genomics Research Container Architecture

ORCA

:: DESCRIPTION

ORCA is a platform for bioinformatics analysis. It is suited for those wishing to conduct self-serve analysis using their own existing data. Hundreds of bioinformatics tools from Brewsci/bio are installed in the ORCA Docker image using Linuxbrew.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

ORCA

:: MORE INFORMATION

Citation

Jackman SD, Mozgacheva T, Chen S, O’Huiginn B, Bailey L, Birol I, Jones SJM.
ORCA: a comprehensive bioinformatics container environment for education and research.
Bioinformatics. 2019 Nov 1;35(21):4448-4450. doi: 10.1093/bioinformatics/btz278. PMID: 31004474; PMCID: PMC6821186.

TAGOPSIN 1.3 – Collating Taxa-specific Gene and Protein Functional and Structural Information

TAGOPSIN 1.3

:: DESCRIPTION

TAGOPSIN (TAxonomy, Gene, Ontology, Protein, Structure INtegrated) retrieves select data from NCBI Taxonomy, NCBI Nucleotide, UniProtKB, Gene Ontology, Pfam, EBI SIFTS and RCSB PDB, and assembles them in the database management system PostgreSQL. TAGOPSIN is an organism-centred data warehousing tool that works with prokaryotic and eukaryotic organisms as well as viruses.

::DEVELOPER

TAGOPSIN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Java
  • PostgreSQL

:: DOWNLOAD

TAGOPSIN

:: MORE INFORMATION

Citation

Bundhoo E, Ghoorah AW, Jaufeerally-Fakim Y.
TAGOPSIN: collating taxa-specific gene and protein functional and structural information.
BMC Bioinformatics. 2021 Oct 23;22(1):517. doi: 10.1186/s12859-021-04429-5. PMID: 34688246; PMCID: PMC8541804.

Bioclojure – Functional Library for the Manipulation of Biological Sequences

Bioclojure

:: DESCRIPTION

BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large datasets.

::DEVELOPER

Bioclojure team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 BioClojure

:: MORE INFORMATION

Citation

Bioclojure: a functional library for the manipulation of biological sequences.
Plieskatt J, Rinaldi G, Brindley PJ, Jia X, Potriquet J, Bethony J, Mulvenna J.
Bioinformatics. 2014 May 2. pii: btu311

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