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.

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**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 

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**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.*

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**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 <https://portal.brain-map.org/explore/models/mv1-all-layers>`_ 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 


