Ten Simple Rules for Developing Public Biological Databases
Supplementary Webpage for Tools and Technologies Recommendations
- Resources for available databases Recommendations
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 Recommendations
- File formats Examples
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 Examples
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 Recommendations
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 |
-- |
||||
Prototyping Tools |
Comparison between collection of prototyping Tools |
-- |
||||
- Biological data visualization JS libraries Recommendations
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 Examples
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 Recommendations
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 |
||||||
* Recommendations last updated: February 2016