Sentence examples for models were downloaded from inspiring English sources

E. grandis scaffolds were downloaded from EucalyptusDB [ 18]. A. thaliana gene models were downloaded from the TAIR website [ 62] and O. sativa gene models were downloaded from the MSU website [ 63].

For each target, the experimental structures and predicted models were downloaded from the CASP8 website.

The models were downloaded from the BiGG database (http://bigg.ucsd.edu) and parsed by the COBRA toolbox (Becker et al. 2007).

All the selected genomic gene models were downloaded from the US Department of Energy Joint Genome Institute website at http://genome.jgi.doe.gov/ (Additional file 2: Table S8).

The starting models were downloaded from the National Center for Biotechnology Information PubChem database [compound identification numbers 193305 (GSA) and 11966181 (P5C)].

The latest gene annotation models were downloaded from the PlasmoDB [ 12], CryptDB [ 15] and ToxoDB datasets[ 18] (pv_rel5.4, py_rel5.4, pb_rel5.4, pb_rel5.4, cp_rel3.7 and tg_rel4.3).

The set of Amphimedon gene models was downloaded from the ftp site provided in the genome paper [ 96].

The model was obtained from the CellML repository (http://www.cellml.org/models/tentusscher_panfilov_2006_version04) on the 11th of April 2009 (Note: after the model was downloaded the CellML website has been restructured and the model can now be found at http://models.cellml.org/exposure/de5058f16f829f91a1e4e5990a10ed71).org/exposure/de5058f16f829f91a1e4e5990a10ed71

Pfam-A HMM model was downloaded from the Pfam database [ 47].

A curated CellML implementation [ 7- 9] of the model was downloaded from http://models.cellml.org.org

The L. lactis model was downloaded from the Supplementary Materials in Oliveira et al. [ 24].