Examples | bionsi

Start Exploring BioNSi with One of Our Network Examples

If you don't feel like reading our user manual, simply open one of these networks in BioNSi and start exploring them. If you are new to BioNSi, we suggest starting with the toy example, accompanied by a step by step explanation.

To open a comma separated values file format (.csv), first download it to your computer, and then in Cytoscape's main menu choose: BioNSi → File Operations → import Network.

Networks can later be saved in a Cytpscape network file format (.cys). Such files can be opened in Cytoscape's main menu: File → Open.

.csv

Network

Yeast (S.cerevisiae) cell cycle [1]

Yeast (S.cerevisiae) cell cycle [2]

Yeast (S.cerevisiae) cell cycle [3]

Comments

Vertebrate circadian clock [2,4]

- ∆Clock mutant [2]

- hypothetical effect of light [2]

- TGFβ signaling [4]

Li, F., Long, T., Lu, Y., Ouyang, Q., Tang, C. (2004): The yeast cell-cycle network is robustly designed. Proceedings of the National Academy of Sciences of the United States of America.
Rubinstein, A., Bracha, N., Rudner, L., Zucker, N., Sloin, H. E., & Chor, B. (2016). BioNSi: A Discrete Biological Network Simulator Tool. Journal of Proteome Research.
Rubinstein, A., Hazan, O., Chor, B., Pinter, Y.R., Kassir, Y. (2013): The effctive application of a discrete transition model to explore cell-cycle regulation in yeast. BMC research notes.
Sloin, H., Gothilf, Y., and Rubinstein, A.: Bi-directional interactions between the circadian clock and TGF-beta signaling (submitted).
Rubinstein, A., Gurevich, V., Kasulin-Boneh, Z., Pnueli, L., Kassir, Y., and Pinter, Y.R. (2007): Faithful Modeling of Transient Expression and Its Application to Elucidating Negative Feedback Regulation, Proceedings of the National Academy of Sciences (PNAS).