Tag: Browser

Webina 1.0.3 – A JavaScript/WebAssembly library that runs Vina in a browser

Webina 1.0.3

:: DESCRIPTION

Webina is a JavaScript/WebAssembly library that runs AutoDock Vina entirely in a web browser. The docking calculations take place on the user’s own computer rather than a remote server.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

Webina

:: MORE INFORMATION

Citation

Webina: An Open-Source Library and Web App that Runs AutoDock Vina Entirely in the Web Browser
Yuri Kochnev, Erich Hellemann, Kevin C. Cassidy, View ORCID ProfileJacob D. Durrant
doi: https://doi.org/10.1101/2019.12.18.881789

ProteinVR 1.0.7 – Browser-based, virtual-reality visualization of Molecular Structures

ProteinVR 1.0.7

:: DESCRIPTION

ProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

ProteinVR

:: MORE INFORMATION

 

AGB – Ancestral Genome Browser

AGB

:: DESCRIPTION

AGB is a website which provides the ancestral organisms genomic information. It builds on genetic resources of existent living things.

::DEVELOPER

Bioinformatics Laboratory, Konkuk University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Lee D, Lee J, Hong WY, Jang E, and Kim J,
AGB (Ancestral Genome Browser): A Web Interface for Browsing Reconstructed Ancestral Genomes,
Journal of KIISE, 42(12):1584-1589, 2015

VarB 1.4 – Population Genomic Variation Browser

VarB 1.4

:: DESCRIPTION

Varb is a variant display and analysis tool for VCF files. The basic inputs are a reference genome (fasta format), variants (VCF) and annotation (GFF format) files. In real-time, the software filters variants and updates calculated population genetic matrics

::DEVELOPER

PathogenSeq

:: SCREENSHOTS

VarB

:: REQUIREMENTS

  • Linux / Windows
  • QT

:: DOWNLOAD

 VarB

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2983-5. doi: 10.1093/bioinformatics/bts557. Epub 2012 Sep 13.
VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data.
Preston MD1, Manske M, Horner N, Assefa S, Campino S, Auburn S, Zongo I, Ouedraogo JB, Nosten F, Anderson T, Clark TG.

GenPlay 1.1.0 – Genome Analyzer and Browser

GenPlay 1.1.0

:: DESCRIPTION

GenPlay is an analyzer and browser for high-throughput data . GenPlay recognizes a wide variety of common genomic data formats from microarray- or sequencing-based platforms and offers a library of operations (normalization, binning, smoothing) to process raw data into visualizable tracks.

::DEVELOPER

Eric Bouhassira, Nicolas Fourel and Julien Lajugie

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  GenPlay

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Aug 31. pii: btu588.
GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.
Lajugie J, Fourel N, Bouhassira EE

Bioinformatics. 2011 Jul 15;27(14):1889-93.
GenPlay, a multipurpose genome analyzer and browser.
Lajugie J, Bouhassira EE.

YGOB v7 – Yeast Gene Order Browser

YGOB v7

:: DESCRIPTION

YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes.

::DEVELOPER

the Wolfe Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genome Res. 2005 Oct;15(10):1456-61. Epub 2005 Sep 16.
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species.
Byrne KP1, Wolfe KH.

Krona 2.8 – Hierarchical Data Browser

Krona 2.8

:: DESCRIPTION

Krona allows the hierarchical results of metagenomic classifications to be explored visually in a web browser. Charts are created by KronaTools, which supports many metagenomic tools and generic file formats. Once charts are created, they can be viewed on any platform with a recent version of any major browser.

::DEVELOPER

Krona team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 Krona

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Sep 30;12:385. doi: 10.1186/1471-2105-12-385.
Interactive metagenomic visualization in a Web browser.
Ondov BD, Bergman NH, Phillippy AM.

PGB 1.1 – Personal Genome Browser

PGB 1.1

:: DESCRIPTION

The PGB is developed to provide comprehensive functional annotation and visualization for individual genomes

::DEVELOPER

PGB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

PGB

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W192-7. doi: 10.1093/nar/gku361. Epub 2014 May 5.
The personal genome browser: visualizing functions of genetic variants.
Juan L, Teng M, Zang T, Hao Y, Wang Z, Yan C, Liu Y, Li J, Zhang T, Wang Y2.

GOTreePlus 20080131 – Interactive Gene Ontology Browser

GOTreePlus 20080131

:: DESCRIPTION

GOTreePlus is an interactive gene ontology visualization tool that can superimpose annotation information over gene ontology structures. GOTreePlus can facilitate the identification of important GO terms while visualizing them in the gene ontology structure. The interactive pie chart summary for a selected gene ontology term provides users with a succinct overview of their experimental results.

::DEVELOPER

SNU HCI LAB

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET Framework 2.0

:: DOWNLOAD

 GOTreePlus

:: MORE INFORMATION

Citation

Bongshin Lee, Kristy Brown, Yetrib Hathout, and Jinwook Seo,
“GOTreePlus: An Interactive Gene Ontology Browser,”
Bioinformatics (2008) 24 (7): 1026-1028.

PyBamView 1.0.8 – Browser-based application for Visualizing Complex Bam Alignments

PyBamView 1.0.8

:: DESCRIPTION

PyBamView is a python-based application that allows you to view BAM sequence alignments through your web browser.

::DEVELOPER

Gymrek Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  PyBamView

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Aug 21. pii: btu565. [Epub ahead of print]
PyBamView: a browser based application for viewing short read alignments.
Gymrek M.

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