Software architecture

The CycADS architecture

CycADS workflow

CycADS is centered on an ad hoc SQL database, complemented by a set of Java programs to import and export relevant information. Data from GenBank and from different gene annotation tools (such as KAAS, PRIAM, PhylomeDB, Blast2GO, MetaPhOrs) are collected into the database and later extracted, to generate a complete input file to build and/or update a BioCyc database using the Pathway Tools Software (SRI International).

CycADS allows the integration in a BioCyc database of specific links to custom information resources (in AcypiCyc: AphidBASE, KEGG orthology and PhylomeDB) together with the already existing databases cross references included using Pathway tools (e.g. GenBank, BRENDA, Gene Ontology, ...).

We used CycADS to generate three collections of metabolism databases:

  • AcypiCyc, dedicated to the pea aphid metabolism
  • ArthropodaCyc, more generally dedicated to the arthropod metabolism
  • ArtSymbioCyc, dedicated to the symbiosis between insect and its symbionts (beta version)

See also

Modification date : 18 July 2023 | Publication date : 06 May 2010 | Redactor : Stefano Colella, Patrice Baa-Puyoulet