#acl All:read ##master-page:HomepageTemplate #format wiki = 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 |||| [[http://www.oxfordjournals.org/our_journals/nar/database/a/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/26740669|PubMed]] || || Pathguide |||| The Pathway Resource List |||| [[http://pathguide.org/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/16381921|PubMed]] || || The Registry |||| Collection of analytical tools and data services for bioinformatics |||| [[https://bio.tools/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/26538599|PubMed]] || || The Bioinformatics Links Directory |||| List of curated links to molecular resources, tools and databases |||| [[http://bioinformatics.ca/links_directory/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/21715385|PubMed]] || || OMICtools |||| Collection of classified omic tools |||| [[http://omictools.com/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/25024350 |PubMed]] || || MetaBase |||| A user-contributed database of biological databases |||| [[http://MetaDatabase.Org|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/22139927 |PubMed]] || === - Ontologies and semantics (R) === || '''Resource''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' || || The OBO Foundry |||| Collection of Biomedical Ontologies |||| [[http://www.obofoundry.org/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/17989687|PubMed]] || === - 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]] |||| -- || === - 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]] ||