BOL: Related items

Update Genome Workbench 2.7.15 released

Surabhi Chaudhary — Wed, 26 Feb 2014 16:12:17 -0600

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.

Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix.

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. Genome Workbench was developed entirely in-house at NCBI and makes use of the NCBI C++ ToolKit. The C++ ToolKit provides a convenient and flexible cross-platform API for managing system internals, database connections, network sockets, and the NCBI data model. In addition, the C++ ToolKit provides the Object Manager, which abstracts handling of sequences and sequence-related objects.

New Features in Genome Workbench 2.7.15

Multiple Alignment View: implemented adaptive feature display when zooming in
Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.
Binary packages for Linux OpenSUSE 13.1 are now available

Bug Fixes and Improvements in Genome Workbench 2.7.15

Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities
Multiple Pane View: fixed crash on loading BLAST results
Graphical Sequence View: fixed crash on zooming in and out, related to SNP track
Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error
Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name
Text View / Flat File: fixed Mac OS rendering issues
Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands
File Import: optimization improvement to speed up load of files containing multiple project items
File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers
Mac OS: improved tooltips for toolbar buttons
Phylogenetic Tree Builder Tool: improved diagnostics of errors
Multiple Alignment View: optimizations to avoid main GUI freezes
Open Dialog: removed duplicate elements in table of genomes (load Genome)
PDF export: fixed issue with XREF table errors
Tree View: fixed issues with showing Force Layout progress on Mac OS
Tree View: PDF export fixed issues for showing labels of collapsed nodes
Tree View: added an option to stop layout
Tree View: broadcasting mechanism fixed not to accumulate selected nodes

Reference:

NCBI news

http://www.ncbi.nlm.nih.gov/tools/gbench/

A 3D Map of the Human Genome

Fri, 12 Dec 2014 22:27:55 -0600

Suhas Rao and Miriam Huntley (of the Aiden Lab) describe a 3D map of the human genome at kilobase resolution, revealing the principles of chromatin looping. Guest Origami Folding: Sarah Nyquist. Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell.

RCircos: an R package for Circos 2D track plots

Jit — Fri, 20 May 2016 11:01:13 -0500

RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

Genome Workbench 2.10.7

Gudiya Pal — Fri, 01 Jul 2016 12:09:59 -0500

Genome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

BLAST Tool: added support for local custom BLAST databases
Graphical Sequence View: added log scaling option for graph tracks
Generic Table View: new tutorial added

Bug Fixes and Improvements

Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
Tree View: layout updated to better accommodate nodes of different sizes
Table Import Dialog (MacOS): fixed issue with table visibility
Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
Graphical Sequence View: fixed protein coloration methods
Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
Search View: ORF Finder – fixed incorrect protein lengths
Fixed bug with not opening project file (.gbp) on a click
Fixed issues in GVF import
Fixed BLAST Search tool against NCBI databases not working
Fixed tblastn (protein BLAST) not working in standalone mode
Fixed GTF export failure

vcfR

Archana Malhotra — Fri, 19 Aug 2016 07:38:24 -0500

Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette ‘vcf data.’ These files are typically intended to be post-processed (i.e., filtered) as an attempt to remove false positives or otherwise problematic sites. The R package vcfR provides tools to facilitate this filtering as well as to visualize the effects of choices made during this process.

Address of the bookmark: https://cran.r-project.org/web/packages/vcfR/vignettes/visualization_1.html

Krona

Jit — Wed, 22 Mar 2017 04:47:35 -0500

Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with any modern web browser (see Browser support).

Address of the bookmark: https://github.com/marbl/Krona/wiki

sankeyNetwork with networkD3

Jit — Fri, 06 Apr 2018 12:07:55 -0500

You can also create Sankey diagrams with sankeyNetwork. Here is an example using downloaded JSON data:

https://en.wikipedia.org/wiki/Sankey_diagram

Address of the bookmark: https://christophergandrud.github.io/networkD3/#sankey

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

Rahul Nayak — Tue, 03 Jul 2018 05:05:55 -0500

NAViGaTOR – Network Analysis, Visualization, & Graphing TORonto is a software system for scaleable visualizing and analyzing networks. The current version, NAViGaTOR 3, increases modularity, improves scaleability, extends input/output options, brings new network views and analysis algorithms. http://142.150.188.236/navigatorwp/

Address of the bookmark: http://142.150.188.236/navigatorwp/

UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties

BioStar — Mon, 28 Jan 2019 18:38:44 -0600

UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.

For further details about the original technique see the UpSet website. You can also check out the UpSetR shiny app. Here is the source code for the shiny wrapper.

A Python package called py-upset to create UpSet plots has been created by GitHub user ImSoErgodic.

Address of the bookmark: https://github.com/hms-dbmi/UpSetR/

Comprehensive list of visualization tools for biological pathways

Neel — Tue, 30 Jan 2018 06:01:31 -0600

The study of biological pathways is a key to understand the different processes inside a cell: proteins exert their function not in isolation but in a tightly controlled network of interactions and reactions. Activation of a pathway typically leads to a change of state in the cell. Pathways come in different flavors, depending on their functions in the cell – the three main types are metabolic pathways, gene regulatory pathways, and signaling pathways. These biological pathways and networks are not only an appropriate approach to visualize molecular reactions. They have also become one leading method in -omics data analysis and visualization.

Following are the comprehensive list of visualization tools for biological pathways:

BiNA

Drawings of metabolic networks supporting hiding of cofactors and drawing of chemical structures

http://bina.unipax.info/

BioTapestry

Interactive tool for building, visualizing and sharing gene regulatory network models over the web

http://www.biotapestry.org/

Caleydo

Visual analysis framework targeted at biomolecular data. Visualization of interdependencies between multiple datasets

http://www.caleydo.org/

CellDesigner

A modeling tool for biochemical networks

http://www.celldesigner.org/

Edinburgh Pathway Editor

Edit and draw pathway diagrams

http://epe.sourceforge.net/SourceForge/EPE.html

GenMAPP

Visualization of gene expression and other genomic data on maps representing biological pathways and groupings of genes

http://www.genmapp.org/

Ingenuity IPA

Data integration platform and manually annotated pathways

http://tinyurl.com/IngenuityPath

JDesigner

Graphical modeling environment for biochemical reaction networks

http://jdesigner.sourceforge.net/Site/JDesigner.html

KaPPA View

Plant pathways

http://kpv.kazusa.or.jp/

KEGG Atlas

Interactive Kyoto Encyclopedia of Genes and Genomes pathways

http://www.genome.jp/kegg/

Omix

Visualizing multi-omics data in metabolic networks

https://www.omix-visualization.com

PathVisio

Biological pathway analysis software that allows drawing, editing and analysis of biological pathways

http://www.pathvisio.org/

VitaPad

Application to visualize biological pathways and map experimental data to them

http://tinyurl.com/vitapad/

Web tools for pathways

ArrayXPath

Mapping and visualizing microarray gene-expression data and integrated biological pathway resources using SVG

http://tinyurl.com/ArrayXPath/

GEPAT

Integrated analysis of transcriptome data in genomic, proteomic and metabolic contexts

http://gepat.sourceforge.net/

iPath

Web-based tool for the visualization, analysis and customization of pathway maps

http://pathways.embl.de/

Kegg-Based Viewer

KEGG-based pathway visualization tool for complex high-throughput data

http://www.g-language.org/data/marray/

MapMan

User-driven tool that displays large datasets onto diagrams of metabolic pathways or other processes

http://mapman.gabipd.org/web/guest/mapman

MetPA

Analysis and visualization of metabolomic data within the biological context of metabolic pathways

http://metpa.metabolomics.ca

Omics Viewer

Data mapping on BioCyc pathways (collection of 5500 pathway/genome databases)

http://www.biocyc.org/

Pathway Explorer

Interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them

http://genome.tugraz.at/pathwayexplorer/pathwayexplorer_description.shtml

Pathway projector

Zoomable pathway browser using KEGG atlas and Google Maps API

http://www.g-language.org/PathwayProjector/

PATIKA

Integrated environment composed of a central database and a visual editor, built around an extensive ontology and an integration framework

http://www.cs.bilkent.edu.tr/~patikaweb/

Reactome SkyPainter

Visualization of over-represented pathways and reactions from gene lists

http://www.reactome.org/skypainter-2

WikiPathways

Wiki-based, open, public platform dedicated to the curation of biological pathways by and for the scientific community

http://www.wikipathways.org/