Computational Tools

  1. ASTRO is a computational platform for constructing and exploring realistic multi-compartmental astrocyte models that can be biophysically interrogated in NEURON computational environment, on the scale from nanometers to the entire cell moprhology. ASTRO generates stochastically cell nanoscopic protrusions based on their real-world parameters and enables dynamic interactions between the modelled astorcyte and the surrounding 3D tissue environment.

    Documentation: PDF file.

  2. ARACHNE is designed to model multi-cell spiking networks of neurons and astrocytes. In ARACHNE environment, the network organisation, optimisation, and execution benefit from pre-set, optimised parallel algorithms for remote computations and a friendly user interface operated from your own computer. A neuroscientist without IT background should be able to incorporate the representative variety of biophysical mechanisms pertinent to nerve and astroglial cells, within a single network model.

    Documentation: PDF file.

  3. BRAINCELL is a platform that combines theoretical aspects of computational neuroscience with real-world aspects of cell and tissue physiology of the brain, including the capacity to replicate some common experimental designs. The immersive modelling environment enables neuroscientists and neurologists to investigate brain cellular mechanisms and assess the physiological effects of experimental or therapeutic interventionse. Its key features include stochastic generation of nano-morphology and function, stop-save-go control of simulation runs, dynamic extracellular and inter-cellular interactions, adaptive import of cell morphologies.

    Documentation: PDF file, or in Word format BRAINCELL_User_Guide.docx (alternatively, check experimental PDF->HTML conversion).

  4. CLOUD COMPUTATION PLUGIN: we are currently working with Neuroscience Gateway - a portal for computational Neuroscience to enable computations on their HPC supercomputer. When the integration is complete, registered Neuroalgebra users will be able to benefit from the HPC power and run our tools on a supercomputer cluster in the cloud.

    Installation: To perform computations in the cloud please download our latest and greatest CLOUD COMPUTATION PACKAGE. You will find instructions on how to unpack and set it up after [Registration at our FORUM].

    OPEN SOURCE COMMITMENT: Our software packages are open for you to download, install, and explore under the MIT license.