ALLEN INSTITUTE

# How to Cite

The following are general citation guidelines for referencing our tools. Please consult the particular journal’s formatting requirements for the appropriate formatting.

How to cite BMTK:

[1] Dai, K., Gratiy, S. L., Billeh, Y. N., Xu, R., Cai, B., Cain, N., Rimehaug, A. E., Stasik, A. J., Einevoll, G. T., Mihalas, S., Koch, C., & Arkhipov, A. (2020). Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits. PLoS Computational Biology, 16(11), e1008386. https://doi.org/10.1371/journal.pcbi.1008386

[2] Brain Modeling ToolKit v1.0.6 [Computer software]. (2020). Available: https://alleninstitute.github.io/bmtk/, Accessed on: Aug. 26, 2022.

Replace with the appropriate version number and accessed date.

The BioNet module of BMTK was described in an earlier paper. If using BioNet, please cite BMTK as described above and feel free to add the following citation:

[3] Gratiy, S. L., Billeh, Y. N., Dai, K., Mitelut, C., Feng, D., Gouwens, N. W., Cain, N., Koch, C., Anastassiou, C. A., & Arkhipov, A. (2018). BioNet: A Python interface to NEURON for modeling large-scale networks. PLOS ONE, 13(8), e0201630. https://doi.org/10.1371/journal.pone.0201630

How to cite SONATA:

[1] Dai, K., Hernando, J., Billeh, Y. N., Gratiy, S. L., Planas, J., Davison, A. P., Dura-Bernal, S., Gleeson, P., Devresse, A., Dichter, B. K., Gevaert, M., King, J. G., Geit, W. A. H. V., Povolotsky, A. V., Muller, E., Courcol, J.-D., & Arkhipov, A. (2020). The SONATA data format for efficient description of large-scale network models. PLOS Computational Biology, 16(2), e1007696. https://doi.org/10.1371/journal.pcbi.1007696

[2] SONATA Data Format. (2020). Available: https://github.com/AllenInstitute/sonata, Accessed on: Aug. 26, 2022.

Replace with the appropriate version number and accessed date.

How to cite the V1 models:

Development of BMTK and SONATA was driven to a large degree by our efforts to model cortical circuits. Models of the mouse primary visual cortex (area V1) are publicly available here and should be cited as follows:

[1] Billeh, Y. N., Cai, B., Gratiy, S. L., Dai, K., Iyer, R., Gouwens, N. W., Abbasi-Asl, R., Jia, X., Siegle, J. H., Olsen, S. R., Koch, C., Mihalas, S., & Arkhipov, A. (2020). Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex. Neuron, 106(3), 388-403.e18. https://doi.org/10.1016/j.neuron.2020.01.040