In silico networks for the DREAM 2007 competition
We produced 3 networks for the 2007 DREAM data, challenge 4. The first two are gene networks, the third contains proteins and metabolites too. All networks were simulated with the software COPASI in deterministic mode. We provide the networks in COPASI and SBML formats. The data generated by these networks is available from the 2007 DREAM page (chose Challenge 4).
In silico networks for the DREAM 2007 competition:
InSilico_1
This is a gene network created with our AGN system and follows a Erdős-Rényi topology.
| COPASI file | SBML file | Diagram (SVG) |
| dream1n1.cps | dream1n1.xml | dream1n1.svg |
(click image for large view)
InSilico_2
This is a gene network created with our AGN system and follows a scale-free (Albert-Barabasi) topology.
| COPASI file | SBML file | Diagram (SVG) |
| dream1n2.cps | dream1n2.xml | dream1n2.svg |
(click image for large view)
InSilico_3
This is a small network that contains gene transcription, protein translation, signaling, and metabolism. It was designed manually by Pedro Mendes. This network is also known as "The Claytor Network" and has been presented publicly a few times. However, this version used for DREAM had all the names changed.
| COPASI file | SBML file | Diagram (SVG) |
| dream1n3.cps | dream1n3.xml | dream1n3.svg |
(click image for large view)
