= Satellite meeting for G-language development =

== Topics ==

Development of REST/SOAP web services for G-language Genome Analysis Environment

== Participants ==

 * Kazuharu Arakawa
 * Nobuhiro Kido
 * Kazuki Oshita

== REST ==

=== genome flatfile access ===

 * Base URL (list of available genomes):[[BR]]
   * http://www.g-language.org/gb/
 * Syntax:[[BR]]
   * {{{http://www.g-language.org/gb/[genome]/[gene]/[feature]}}}
 * Genomes (nucleotide composition)[[BR]]
   * {{{http://www.g-language.org/gb/[genome]}}}
      * examples:[[BR]]
         * http://www.g-language.org/gb/ecoli (G-language preset genome)[[BR]]
         * http://www.g-language.org/gb/NC_000908 (NCBI RefSeq accession)[[BR]]
         * http://www.g-language.org/gb/B619CD (G-language REST temporary reference id)
 * Genes[[BR]]
   * {{{http://www.g-language.org/gb/[genome]/[gene]}}}
     * examples:[[BR]]
         * http://www.g-language.org/gb/ecoli/recA (common gene name)[[BR]]
         * http://www.g-language.org/gb/ecoli/b2699 (canonical gene name / locus tag)[[BR]]
         * http://www.g-language.org/gb/ecoli/FEATURE5804 (G-language feature id)[[BR]]
         * http://www.g-language.org/gb/ecoli/CDS2646 (G-language CDS id)
 * features[[BR]]
   * {{{http://www.g-language.org/gb/[genome]/[gene]/[feature]}}}
     * examples:[[BR]]
         * http://www.g-language.org/gb/mgen/metX/gene (gene name)[[BR]]
         * http://www.g-language.org/gb/mgen/metX/translation (amino acid sequence)[[BR]]
         * http://www.g-language.org/gb/mgen/*/translation (amino acid sequence of all genes)

=== file upload ===

 * Base URL:[[BR]]
   http://www.g-language.org/gbi/
 * Syntax
   * POST a file to fileform=file
   * File types are automatically interpreted by the system. Supported formats are: ABI, ACE, ALF, BSML, CTF, EMBL, Entrez Gene, Exp, FastA, FastQ, GCG, GenBank, Phd, PIR, PLN, raw, SCF, SWISS.
 * Return
   * Returns a unique reference ID for the uploaded file. You can use this ID for the rest of the analysis so that the large file is not transferred over the network.

=== genome analysis methods ===

 * Base URL (list of available analysis methods):[[BR]]
   * http://www.g-language.org/gba/
 * Syntax:[[BR]]
   * {{{http://www.g-language.org/gb/[genome]/[method]/[required input (if any)]/[option1=value]/[option2=value]...}}}
 * Genome data access[[BR]]
      * examples:[[BR]]
         * http://www.g-language.org/gba/ecoli/before_startcodon/recA (5' upstream sequence of recA gene)[[BR]]
         * http://www.g-language.org/gba/ecoli/get_geneseq/recA (nucleotide sequence of recA gene)[[BR]]
         * http://www.g-language.org/gba/ecoli/cds (get a list of all feature ids)
 * Analysis methods[[BR]]
     * examples:[[BR]]
         * http://www.g-language.org/gb/ecoli/gcskew (GC skew analysis - produces a graph)[[BR]]
         * http://www.g-language.org/gb/ecoli/gcskew/cumulative=1 (cumulative GC skew)[[BR]]
         * http://www.g-language.org/gb/ecoli/gcskew/at=1/cumulative=1/output=f/ (cumulative AT skew - output as csv data)[[BR]]
         * http://www.g-language.org/gb/ecoli/gcsi (GC Skew Index analysis - single double value)
 
== SOAP ==