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 |
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NAR 2016's Database Collection |
NAR collection of online Molecular Biology Database 2016 |
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Pathguide |
The Pathway Resource List |
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The Registry |
Collection of analytical tools and data services for bioinformatics |
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The Bioinformatics Links Directory |
List of curated links to molecular resources, tools and databases |
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OMICtools |
Collection of classified omic tools |
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A user-contributed database of biological databases |
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- Ontologies and semantics (R)
- File formats (E)
Format |
Description |
URl |
Reference |
|||
FASTA |
File format for representing biological sequences |
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GFF3 |
File format for representing gene annotations |
-- |
||||
Pathway exchange language for Biological pathway data |
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Extended Newick |
Standard for representation of phylogenetic networks |
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- Biological libraries of programming languages (E)
Library |
Description |
URl |
Reference |
|||
Open source project for Java tools for bioinformatics |
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Collection of Perl modules for bioinformatics applications |
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Open source collection of Python tools for bioinformatics |
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BioJS |
Full-featured biological workbench written in JS |
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R Bioconductor |
Collection of R packages provides tools for the analysis biological data |
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- 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 |
-- |
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