Open source libraries and frameworks for biological data visualisation: a guide for developers (Q27687756)

publication date

April 2015

1 reference

1 April 2015

2 references

10 November 2020

25 November 2020

3 references

10 November 2020

25 November 2020

15

1 reference

page(s)

1356-74

1 reference

issue

8

1 reference

Creative Commons Attribution 3.0 Unported

copyright license

2 references

Europe PubMed Central

10 November 2020

Europe PubMed Central

describes a project that uses

25 November 2020

copyright status

copyrighted

0 references

Jupyter notebook file

1 reference

1 reference

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409855/

Cytoscape

object named as

cytoscape

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

Cytoscape

0 references

ggplot2

object named as

ggplot

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

AHaH computing-from metastable switches to attractors to machine learning

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

SCOP2 prototype: a new approach to protein structure mining

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Visualizing multidimensional cancer genomics data

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Biopython: freely available Python tools for computational molecular biology and bioinformatics

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

OpenMS - an open-source software framework for mass spectrometry

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

An automated method for finding molecular complexes in large protein interaction networks

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

The human genome browser at UCSC

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Network biology: understanding the cell's functional organization

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

PIQMIe: a web server for semi-quantitative proteomics data management and analysis

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Making proteomics data accessible and reusable: current state of proteomics databases and repositories

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

PRIDE Inspector: a tool to visualize and validate MS proteomics data

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Cytoscape 2.8: new features for data integration and network visualization

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

A travel guide to Cytoscape plugins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

PivotPaths: Strolling through Faceted Information Spaces

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

DyCoNet: a Gephi plugin for community detection in dynamic complex networks.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

A web-based protein interaction network visualizer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

NeXO Web: the NeXO ontology database and visualization platform.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Saccharomyces genome database provides new regulation data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

WholeCellViz: data visualization for whole-cell models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Data visualization in environmental proteomics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

BioJS: an open source JavaScript framework for biological data visualization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

A knowledge-based decision support system in bioinformatics: an application to protein complex extraction.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

CircaDB: a database of mammalian circadian gene expression profiles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

The UCSC Genome Browser database: extensions and updates 2013.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Volcano plots in analyzing differential expressions with mRNA microarrays.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

More than meets the eye. Modern experimental techniques require increasingly sophisticated approaches to data visualization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Relax with CouchDB--into the non-relational DBMS era of bioinformatics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Isoelectric point optimization using peptide descriptors and support vector machines.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

D³: Data-Driven Documents

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Hierarchical clustering of shotgun proteomics data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Visualization of omics data for systems biology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Visualizing biological data-now and in the future

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Rover: a tool to visualize and validate quantitative proteomics data from different sources

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

29 September 2017

The UCSC Genome Browser

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Breast cancer diagnosis from proteomic mass spectrometry data: a comparative evaluation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

A survey of visualization tools for biological network analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Visualizing changes of hierarchical data using treemaps

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Protégé: a tool for managing and using terminology in radiology applications

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

3D complex: a structural classification of protein complexes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

BiologicalNetworks: visualization and analysis tool for systems biology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

The Ensembl Web site: mechanics of a genome browser

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

A literature network of human genes for high-throughput analysis of gene expression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

PIES, a protein interaction extraction system.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

On best practices in the development of bioinformatics software

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

EpiExplorer: live exploration and global analysis of large epigenomic datasets

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

CING: an integrated residue-based structure validation program suite

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Protovis: a graphical toolkit for visualization

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.

2 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

Matplotlib: A 2D Graphics Environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

Observing and interpreting correlations in metabolomic networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

Quantitative proteomics reveals subset-specific viral recognition in dendritic cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

The murine testicular transcriptome: characterizing gene expression in the testis during the progression of spermatogenesis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

A literature network of human genes for high-throughput analysis of gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

NodeTrix: a hybrid visualization of social networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

Hive plots--rational approach to visualizing networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

ggplot2: Elegant Graphics for Data Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

A tour through the visualization zoo

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

Peptide fractionation by acid pH SDS-free electrophoresis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

On Open Problems in Biological Network Visualization

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPMIC.201400377

Rolling the dice: multidimensional visual exploration using scatterplot matrix navigation

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4409855

The FlowVizMenu and parallel scatterplot matrix: hybrid multidimensional visualizations for network exploration

27 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/25475079

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies

1 reference

https://pubmed.ncbi.nlm.nih.gov/25475079

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

PathGuide - model-based generation of guideline-compliant pathways for the use in different hospital information systems

1 reference

https://pubmed.ncbi.nlm.nih.gov/25475079

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The eyes have it: a task by data type taxonomy for information visualizations

1 reference

19 May 2022

https://opencitations.net/index/coci/api/v1/references/10.1002/PMIC.201400377

Gephi: An Open Source Software for Exploring and Manipulating Networks

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1002/PMIC.201400377

Erratum: FragmentationAnalyzer: An open-source tool to analyze MS/MS fragmentation data

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1002/PMIC.201400377

Identifiers

DOI

10.1002/PMIC.201400377

1 reference

5113540

5113540

1 reference

1 reference

1 reference