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=== - Biological data visualization JS libraries (R) === || '''Tool''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' || || Cytoscape.js |||| JS library for network analysis and visualization |||| [[http://js.cytoscape.org/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/26415722|PubMed]] || || D3.js |||| JS library for producing dynamic and interactive data visualizations |||| [[http://d3js.org/|Link]] |||| -- || || jsPhyloSVG |||| JS library for rendering phylogenetic trees |||| [[http://www.jsphylosvg.com/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/20805892|PubMed]] || === - Search features examples (E) === || '''Website''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' || || iRefWeb |||| Web server for interactive analysis of PPI data |||| [[http://wodaklab.org/iRefWeb/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/20940177|PubMed]] || || GMOD |||| The Generic Model Organism Database |||| [[http://gmod.org/wiki/Main_Page|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/18570664|PubMed]] || || LOVD |||| Leiden Open-source Variation Database |||| [[http://www.lovd.nl/3.0/home|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/21520333|PubMed]] || === - Database monitoring and maintenance tools (R) === || '''Technology/Tool''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' || || Google Analytics |||| Web analytics service offered by Google |||| [[https://www.google.com/analytics|Link]] |||| -- || || Docker |||| Open platform for building and running distributed applications |||| [[https://www.docker.com/|Link]] |||| -- || || Dockerhub |||| Cloud hosted registry service with for Docker images |||| [[https://hub.docker.com/|Link]] |||| -- || || Github |||| Web-based Git repository |||| [[http://github.com|Link]] |||| -- || || Sensu |||| Infrastructure and application monitoring and telemetry solution |||| [[https://sensuapp.org/|Link]] |||| -- || || Snakemake |||| Scalable bioinformatics workflow engine |||| [[https://bitbucket.org/johanneskoester/snakemake|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/22908215|PubMed]] || || BioStars |||| Online question & answer resource for the bioinformatics community |||| [[https://www.biostars.org/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/22046109|PubMed]] || |
Ten Simple Rules for Developing Public Biological Databases
Supplementary Webpage for Tools and Technologies Recommendations
R: Recommendation, E: Example
- Resources for available databases (R)
Resource |
Description |
URl |
Reference |
|||
NAR 2016's Database Collection |
NAR collection of online Molecular Biology Database 2016 |
|||||
Pathguide |
The Pathway Resource List |
|||||
The Registry |
Collection of analytical tools and data services for bioinformatics |
|||||
The Bioinformatics Links Directory |
List of curated links to molecular resources, tools and databases |
|||||
OMICtools |
Collection of classified omic tools |
|||||
A user-contributed database of biological databases |
||||||
- Ontologies and semantics (R)
- File formats (E)
Format |
Description |
URl |
Reference |
|||
FASTA |
File format for representing biological sequences |
|||||
GFF3 |
File format for representing gene annotations |
-- |
||||
Pathway exchange language for Biological pathway data |
||||||
Extended Newick |
Standard for representation of phylogenetic networks |
|||||
- Biological libraries of programming languages (E)
Library |
Description |
URl |
Reference |
|||
Open source project for Java tools for bioinformatics |
||||||
Collection of Perl modules for bioinformatics applications |
||||||
Open source collection of Python tools for bioinformatics |
||||||
BioJS |
Full-featured biological workbench written in JS |
|||||
R Bioconductor |
Collection of R packages provides tools for the analysis biological data |
|||||
- Web and database technologies (R)
Technology/Tool |
Description |
URl |
Reference |
|||
HTML5 |
For webpage structure |
-- |
||||
CSS3 |
For webpage layout |
-- |
||||
For webpage interactivity |
-- |
|||||
JQuery |
JS library for client-side scripting |
-- |
||||
Shiny |
Web application framework for R |
-- |
||||
Django |
Web application framework for Python |
-- |
||||
Node.JS |
JS library for building scalable network applications |
-- |
||||
MySQL |
Relational database server |
-- |
||||
MongoDB |
NoSQL database server |
-- |
||||
Apache |
Web server |
-- |
||||
Apache Lucene |
Index for free text documents |
-- |
||||
Color Brewer |
Color palettes library |
-- |
||||
- Biological data visualization JS libraries (R)
Tool |
Description |
URl |
Reference |
|||
Cytoscape.js |
JS library for network analysis and visualization |
|||||
D3.js |
JS library for producing dynamic and interactive data visualizations |
-- |
||||
jsPhyloSVG |
JS library for rendering phylogenetic trees |
|||||
- Search features examples (E)
Website |
Description |
URl |
Reference |
|||
iRefWeb |
Web server for interactive analysis of PPI data |
|||||
GMOD |
The Generic Model Organism Database |
|||||
LOVD |
Leiden Open-source Variation Database |
|||||
- Database monitoring and maintenance tools (R)
Technology/Tool |
Description |
URl |
Reference |
|||
Google Analytics |
Web analytics service offered by Google |
-- |
||||
Docker |
Open platform for building and running distributed applications |
-- |
||||
Dockerhub |
Cloud hosted registry service with for Docker images |
-- |
||||
Github |
Web-based Git repository |
-- |
||||
Sensu |
Infrastructure and application monitoring and telemetry solution |
-- |
||||
Snakemake |
Scalable bioinformatics workflow engine |
|||||
Online question & answer resource for the bioinformatics community |
||||||