ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing

• Published in: PLoS computational biology 2017-03, Vol.13 (3), p.e1005467-e1005467
• Main Authors: Aleksin, Sergey G, Zheng, Kaiyu, Rusakov, Dmitri A, Savtchenko, Leonid P
• Format: Article
• Language: English
• Subjects: Algorithms; Alternating current; Amplification; Animal models; Antibodies; Architecture; Artificial neural networks; Assemblies; Astrocytes; Biology and Life Sciences; Brain; Brain research; Calcium; Calcium (intracellular); Calcium signalling; Cell Communication - physiology; Cell culture; Cell interactions; Circuits; Computational Biology; Computational neuroscience; Computer and Information Sciences; Computer architecture; Computer memory; Computer networks; Computer programs; Computer Simulation; Conductance; Cooperativity; Cortex; Data acquisition; Data collection; Data processing; Dendritic spines; Documentation; Dopamine receptors; Electric bridges; Electric fields; Engineering and Technology; Functions (mathematics); Grants; Hippocampus; Humans; Lymphocytes B; Medicine and Health Sciences; Models, Neurological; Modulation; Nerve Net - physiology; Nervous system; Neural circuitry; Neural networks; Neural Networks, Computer; Neuroglia - physiology; Neurology; Neuronal-glial interactions; Neurons; Neurons - physiology; Neurosciences; Physical Sciences; Physiological aspects; Programming languages; Remote control; Robots; Simulation; Simulators; Software; Supercomputers; Three dimensional models; University colleges; User-Computer Interface; Zinc; α-Amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1005467

Creating and running realistic models of neural networks has hitherto been a task for computing professionals rather than experimental neuroscientists. This is mainly because such networks usually engage substantial computational resources, the handling of which requires specific programing skills. Here we put forward a newly developed simulation environment ARACHNE: it enables an investigator to build and explore cellular networks of arbitrary biophysical and architectural complexity using the logic of NEURON and a simple interface on a local computer or a mobile device. The interface can control, through the internet, an optimized computational kernel installed on a remote computer cluster. ARACHNE can combine neuronal (wired) and astroglial (extracellular volume-transmission driven) network types and adopt realistic cell models from the NEURON library. The program and documentation (current version) are available at GitHub repository https://github.com/LeonidSavtchenko/Arachne under the MIT License (MIT).