JChem for Office 21.15.603 – Chemical Structure Handling & Visualizing within Microsoft Office

JChem for Office 21.15.603

:: DESCRIPTION

JChem for Office integrates structure handling and visualizing capabilities within a Microsoft Office environment. The bundle includes JChem for Excel which is our long-standing Excel integration. With JChem for Office, chemistry is made live in your Office application and structures are fully supported within spreadsheets, documents, slides and e-mails. Implementation is robust with fast loading/scrolling of many thousands of structure rows and copy-paste throughout the Microsoft Office suite. More advanced functionality includes: structure based calculations, R-group decomposition and library enumeration.

::DEVELOPER

ChemAxon Ltd.

:: SCREENSHOTS

:: REQUIREMENTS

  • Microsoft Office®

:: DOWNLOAD

 JChem for Office

:: MORE INFORMATION

ClustVis – Visualizing Clustering of Multivariate data

ClustVis

:: DESCRIPTION

ClustVis allows users to upload their own data and easily create Principal Component Analysis (PCA) plots and heatmaps.

::DEVELOPER

Bioinformatics, Algorithmics and Data Mining Group (BIIT)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Metsalu, Tauno and Vilo, Jaak.
Clustvis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap.
Nucleic Acids Research, 43(W1):W566–W570, 2015. doi: 10.1093/nar/gkv468.

Xlink Analyzer v1.1.4 – Visualizing Cross-links on 3D Structures

Xlink Analyzer v1.1.4

:: DESCRIPTION

Xlink Analyzer is an interactive software for visualizing cross-links on structures and analyzing how the structures agree with the cross-links.

::DEVELOPER

Jan Kosinski kosinski@embl.de, Structural and Computational Biology Unit European Molecular Biology Laboratory (EMBL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Python
  • UCSF Chimera

:: DOWNLOAD

 Xlink Analyzer

:: MORE INFORMATION

Citation

J Struct Biol. 2015 Mar;189(3):177-83. doi: 10.1016/j.jsb.2015.01.014. Epub 2015 Feb 7.
Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures.
Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M.

KEGGtranslator 2.5 – Visualizing and Converting the KEGG PATHWAY database to various formats

KEGGtranslator 2.5

:: DESCRIPTION

KEGGtranslator is an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g., MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator converts KEGG files (KGML formatted XML-files) to SBML, BioPAX, SIF, SBGN, SBML-qual, GML, GraphML, JPG, GIF, LaTeX, etc.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

KEGGtranslator

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

   KEGGtranslator

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 15;27(16):2314-5. doi: 10.1093/bioinformatics/btr377. Epub 2011 Jun 23.
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.
Wrzodek C, Dräger A, Zell A.

MetaMapp – Mapping and Visualizing Metabolomic data

MetaMapp

:: DESCRIPTION

MetaMapp is a tool to construct metabolomics network graphs from the chemical similarity and mass spectral similarity matrices and the KEGG reaction pair database.

::DEVELOPER

The Fiehn laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 May 16;13:99.
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity.
Barupal DK, Haldiya PK, Wohlgemuth G, Kind T, Kothari SL, Pinkerton KE, Fiehn O.

Sushi 1.30.0 – Tools for Visualizing Genomics Data

Sushi 1.30.0

:: DESCRIPTION

Sushi.R is an R/Bioconductor package that allows flexible integration of genomic visualizations into highly-customizable, publication-ready, multi-panel figures from common genomic data formats including BED, bedGraph, and BEDPE.

::DEVELOPER

Douglas H Phanstiel <dphansti at stanford.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  Sushi

:: MORE INFORMATION

Citation

Sushi.R: Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures.
Phanstiel DH, Boyle AP, Araya CL, Snyder MP.
Bioinformatics. 2014 Jun 5. pii: btu379.

Protael 1.1.0 – JavaScript Library for Visualizing Biological Sequences and related data

Protael 1.1.0

:: DESCRIPTION

Protael is a vector graphics library for displaying various biological sequence related data on web pages.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JavaScript
:: DOWNLOAD

 Protael

:: MORE INFORMATION

Citation:

Protael: protein data visualization library for the web.
Sedova M, Jaroszewski L, Godzik A.
Bioinformatics. 2015 Oct 29. pii: btv605.

VisCHAINER – Visualizing Multiple Genome Comparisons

VisCHAINER

:: DESCRIPTION

VisCHAINER is the interactive visualization component of the software system CoCoNUT. The current version of VisCHAINER plots the chains output by the program CHAINER . Each chain corresponds to a region of similarity among two or multiple genomes. Because these chains are multi-dimensional VisCHAINER displays projections in 2D plots.

::DEVELOPER

Asem Othman , Mohamed Ibrahim Abouelhoda

:: SCREENSHOTS

VisCHAINER

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 VisCHAINER

:: MORE INFORMATION

Citation

Mohamed I. Abouelhoda, Stefan Kurtz, Enno Ohlebusch
CoCoNUT: an efficient system for the comparison and analysis of genomes
BMC Bioinformatics, 9:476, 2008.

RHH 0.1 – Visualizing Chromosome Mosaicism and Detecting Ethnic Outliers

RHH 0.1

:: DESCRIPTION

RHH (RHHcounter) is a software for visualizing chromosomal mosaicism in admixed individuals descended from two genetically distinct groups. The software also detects “outliers” whose ancestry is different or admixed compared to most other subjects in a dataset.

::DEVELOPER

William McLaren, Ralph McGinnis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Perl

:: DOWNLOAD

  RHH

:: MORE INFORMATION

Citation

Ralph E. McGinnis,
Visualizing Chromosome Mosaicism and Detecting Ethnic Outliers by the Method of “Rare” Heterozygotes and Homozygotes (RHH) ,
Human Molecular Genetics, 2010, Vol. 19, No. 13 2539–2553, doi:10.1093/hmg/ddq102