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About the problem

Published on

Abstract

GENI-ACT allows collaborative genome annotation. Researchers or students can collectively suggest changes to an existing genome with supporting evidence. Changes can be ported back to genbank by exporting to a sequin file format.

GENI-ACT also has ported the education components from IMG-ACT. Teachers can assign students work to be completed in a lab notebook that is integrated with the classroom.

GENI-ACT is the next generation of software to annotate bacterial genomes and republish sequin files to NCBI Genbank.

The site automatically pulls text-based genbank files from NCBI FTP and converts them into an indexed binary form that can be easily searched and queried. These files are stored at http://bgbk.geni-act.org/. The site also uses a three-tier architecture with a load-balancer, server nodes and dedicated database server.
 

Publications
  1. Ditty JL, Kvaal CA, Goodner B, Freyermuth SK, Bailey C, et al. (2010) Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. PLoS Biol 8(8): e1000448. doi:10.1371/journal.pbio.1000448
  2. Arshinoff BI, Suen G, Just EM, Merchant SM, Kibbe WA, Chisholm RL, Welch RD. Xanthusbase: adapting wikipedia principles to a model organism database. Nucleic Acids Res. 2007;35:D422-D426.
  3. Pratt-Szeliga PC, Skewes AD, Yan J , Welch LG, Welch RD. Xanthusbase after five years expands to become Openmods. Nucleic acids research 40 (D1), D1288-D1294

 

Submitter

Bob Sheehy

Radford University

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