Differences between revisions 2 and 4 (spanning 2 versions)

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	Link	PubMed
Pathguide	The Pathway Resource List	Link	PubMed
The Registry	Collection of analytical tools and data services for bioinformatics	Link	PubMed
The Bioinformatics Links Directory	List of curated links to molecular resources, tools and databases	Link	PubMed
OMICtools	Collection of classified omic tools	Link	PubMed
MetaBase	A user-contributed database of biological databases	Link	PubMed

- Ontologies and semantics (R)

Resource	Description		URl		Reference
The OBO Foundry	Collection of Biomedical Ontologies		Link		PubMed

- File formats (E)

Format	Description	URl	Reference
FASTA	File format for representing biological sequences	Link	PubMed
GFF3	File format for representing gene annotations	Link	--
BioPax	Pathway exchange language for Biological pathway data	Link	PubMed
Extended Newick	Standard for representation of phylogenetic networks	Link	PubMed

- Biological libraries of programming languages (E)

Library	Description	URl	Reference
BioJava	Open source project for Java tools for bioinformatics	Link	PubMed
BioPerl	Collection of Perl modules for bioinformatics applications	Link	PubMed
BioPython	Open source collection of Python tools for bioinformatics	Link	PubMed
BioJS	Full-featured biological workbench written in JS	Link	PubMed
R Bioconductor	Collection of R packages provides tools for the analysis biological data	Link	PubMed

- Web and database technologies (R)

Technology/Tool	Description	URl	Reference
HTML5	For webpage structure	Link	--
CSS3	For webpage layout	Link	--
JavaScript	For webpage interactivity	Link	--
JQuery	JS library for client-side scripting	Link	--
Shiny	Web application framework for R	Link	--
Django	Web application framework for Python	Link	--
Node.JS	JS library for building scalable network applications	Link	--
MySQL	Relational database server	Link	--
MongoDB	NoSQL database server	Link	--
Apache	Web server	Link	--
Apache Lucene	Index for free text documents	Link	--
Color Brewer	Color palettes library	Link	--

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+=== - File formats (E) ===
|| '''Format''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' ||
|| FASTA |||| File format for representing biological sequences |||| [[http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/3162770|PubMed]] ||
|| GFF3 |||| File format for representing gene annotations  |||| [[http://www.sequenceontology.org/gff3.shtml|Link]] ||||  -- ||
|| BioPax |||| Pathway exchange language for Biological pathway data |||| [[http://www.biopax.org/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/20829833|PubMed]] ||
|| Extended Newick |||| Standard for representation of phylogenetic networks |||| [[http://dmi.uib.es/~gcardona/BioInfo/enewick.html|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/19077301|PubMed]] ||

=== - Biological libraries of programming languages (E) ===
|| '''Library''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' ||
|| BioJava |||| Open source project for Java tools for bioinformatics  |||| [[http://www.biojava.org|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/22877863|PubMed]] ||
|| BioPerl |||| Collection of Perl modules for  bioinformatics applications  |||| [[http://www.bioperl.org/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/12368254|PubMed]] ||
|| BioPython |||| Open source collection of Python tools for bioinformatics  |||| [[http://www.biopython.org|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/19304878|PubMed]] ||
|| BioJS |||| Full-featured biological workbench written in JS  |||| [[http://www.ebi.ac.uk/tools/biojs/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/25075290|PubMed]] ||
|| R Bioconductor |||| Collection of R packages provides tools for the analysis biological data  |||| [[http://www.bioconductor.org/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/15461798|PubMed]] ||


=== - Web and database technologies (R) ===
|| '''Technology/Tool''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' ||
|| HTML5 |||| For webpage structure  |||| [[http://www.w3schools.com/html/default.asp|Link]] ||||  -- ||
|| CSS3 |||| For webpage layout  |||| [[http://www.w3schools.com/css/default.asp|Link]] ||||  -- ||
|| JavaScript |||| For webpage interactivity  |||| [[http://www.w3schools.com/js/default.asp|Link]] ||||  -- ||
|| JQuery |||| JS library for client-side scripting   |||| [[http://www.w3schools.com/jquery/default.asp|Link]] ||||  -- ||
|| Shiny |||| Web application framework for R  |||| [[http://shiny.rstudio.com/|Link]] ||||  -- ||
|| Django |||| Web application framework for Python  |||| [[https://www.djangoproject.com/|Link]] ||||  -- ||
|| Node.JS |||| JS library for building scalable network applications  |||| [[https://nodejs.org/en/|Link]] ||||  -- ||
|| MySQL |||| Relational database server  |||| [[https://www.mysql.com/|Link]] ||||  -- ||
|| MongoDB |||| NoSQL database server  |||| [[https://www.mongodb.org/|Link]] ||||  -- ||
|| Apache |||| Web server  |||| [[https://httpd.apache.org/|Link]] ||||  -- ||
|| Apache Lucene |||| Index for free text documents  |||| [[https://lucene.apache.org/core/|Link]] ||||  -- ||
|| Color Brewer |||| Color palettes library  |||| [[http://colorbrewer2.org|Link]] ||||  -- ||