Diff for "TenRulesResources" - Bader Lab @ The University of Toronto

Differences between revisions 2 and 12 (spanning 10 versions)

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	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 Recommendations

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

- File formats Examples

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 Examples

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 Recommendations

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	--
Prototyping Tools	Comparison between collection of prototyping Tools	Link	--

- Biological data visualization JS libraries Recommendations

Tool	Description	URl	Reference
Cytoscape.js	JS library for network analysis and visualization	Link	PubMed
D3.js	JS library for producing dynamic and interactive data visualizations	Link	--
jsPhyloSVG	JS library for rendering phylogenetic trees	Link	PubMed

- Search features examples Examples

Website	Description	URl	Reference
iRefWeb	Web server for interactive analysis of PPI data	Link	PubMed
GMOD	The Generic Model Organism Database	Link	PubMed
LOVD	Leiden Open-source Variation Database	Link	PubMed

- Database monitoring and maintenance tools Recommendations

Technology/Tool	Description	URl	Reference
Google Analytics	Web analytics service offered by Google	Link	--
Docker	Open platform for building and running distributed applications	Link	--
Dockerhub	Cloud hosted registry service with for Docker images	Link	--
Github	Web-based Git repository	Link	--
Sensu	Infrastructure and application monitoring and telemetry solution	Link	--
Snakemake	Scalable bioinformatics workflow engine	Link	PubMed
BioStars	Online question & answer resource for the bioinformatics community	Link	PubMed

* Recommendations last updated: February 2016

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-= Ten Simple Rules for Developing Public Biological Databases =
== Supplementary Webpage for Tools and Technologies Recommendations ==
R: Recommendation, E: Example
+== Ten Simple Rules for Developing Public Biological Databases ==
=== Supplementary Webpage for Tools and Technologies Recommendations ===
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-=== - Resources for available databases (R) ===
+==== - Resources for available databases Recommendations ====
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-=== - Ontologies and semantics (R) ===
+=== - Ontologies and semantics Recommendations ===
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+=== - File formats Examples ===
|| '''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 Examples ===
|| '''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 Recommendations ===
|| '''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]] ||||  -- ||
|| Prototyping Tools |||| Comparison between collection of prototyping Tools |||| [[http://www.cooper.com/prototyping-tools|Link]] ||||  -- ||


=== - Biological data visualization JS libraries Recommendations ===
|| '''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 Examples ===
|| '''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 Recommendations ===
|| '''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]] ||

* Recommendations last updated: February 2016