17.09.2020

SUNY Downstate and MetaCell launch a graphical tool to model, simulate and analyze brain neuronal circuits

Figure 1 - Graphical User Interface (GUI) of NetPyNE, a tool for multiscale modeling of brain circuits, developed by SUNY Downstate and MetaCell.

Background

Unlocking the mysteries of the brain has become one of the major challenges for humanity in the 21st century. Understanding the brain's neural code is likely to have a profound and transformative impact in both medicine and technology. Brain research is helping scientists develop novel artificial intelligence (AI) algorithms, such as the revolutionary deep learning algorithms derived from studying neurons in the visual cortex. Computational modeling of brain circuits is helping to develop treatments for epilepsy, schizophrenia and other neurological conditions.

However, decoding the brain requires an understanding of complex interactions across a wide range of scales: from molecules to cells to circuits to behavior. Despite the vastly expanding amount of neuroscience data being gathered, the development of approaches to interpret and gain meaningful insight from this data is lagging. Therefore, powerful new brain simulation tools that work at the molecular level such as SUNY Downstate's tool, NetPyNE, are quickly gaining popularity amongst neuroscientists.

About NetPyNE

NetPyNE (Networks using Python and NEURON) is a project funded by the National Institute for Biomedical Imaging and Bioengineering at the NIH (U24 grant), the National Science Foundation (E-CAS grant), and the New York State Department of Health (SCIRB grant). NetPyNE provides a user-friendly, declarative language and a graphical interface to define the properties of molecules, neurons, and circuits. It also provides an easy way to validate the models against experimental data. The software is unique in that it allows students and scientists without programming expertise to build sophisticated brain models. NetPyNE also facilitates running parallel simulations on supercomputers and offers a variety of ways to visualize and analyze the resulting output, e.g. connectivity matrices, voltage traces, spike raster plots, local field potentials and information transfer measures. Users can export their models in standardized formats (NeuroML and SONATA), making them compatible with other modeling software. For more information, see the peer-reviewed publication in the eLife journal.

Adoption of NetPyNE

NetPyNE is rapidly gaining adoption by neuroscientists and is being increasingly deployed in the classroom to teach neurobiology and neural modeling. Over 40 labs have benefited from NetPyNE and have developed nearly 80 models of multiple brain regions and phenomena including:

  • Brown University, Human Neocortical Neurosolver, linking biophysical circuit properties to EEG/MEG markers of neurological illnesses,
  • Duke University, studying the effects of transcranial magnetic stimulation (TMS) in the motor cortex,
  • University of Sao Paulo, building a large-scale sensory thalamocortical model to explore dynamics and synchrony,
  • Italian National Research Council, building large-scale hippocampal circuits, linking neural dynamics to memory function,
  • Cincinnati Hospital, studying the mechanisms of epilepsy in cortical networks,
  • Yale University, simulating the multiscale effects of ischemic strokes on neuronal circuits.

Introducing the New NetPyNE GUI

The latest version of NetPyNE GUI (0.6.0), developed in partnership with MetaCell, features numerous improvements that enable researchers to do everything they would normally do programmatically straight from a state-of-the-art and easy-to-use graphical interface. Through the web-based GUI, users can intuitively define their network models, visualize cells and networks in 3D, run simulations, and visualize and analyze data. The GUI includes an innovative, interactive Python console synchronized with the underlying Python-based model, making it incredibly easy to go back and forth from the coding to the GUI domain.

The NetPyNE GUI is now being integrated with two widely-used online neuroscience platforms: the Open Source Brain and the Human Brain Project E-BRAINS. This will allow interaction with online repositories to pull data and models into NetPyNE projects from resources such as GitHub, ModelDB, etc. These web platforms will significantly increase the exposure of NetPyNE and allow many more researchers and students to make use of it.

Figure 2 - Detailed models of cortical neurons simulated and visualized in the NetPyNE GUI.

The Team

Salvador Durá-Bernal, Assistant Professor at State University of New York Downstate Health Sciences University commented: "We're excited to see the rapidly growing community of NetPyNE users. One of our ultimate goals is to make this tool user-friendly enough such that the 'non-computational community' can use it to, for example, predict outcomes of specific neuromodulatory techniques, or model circuit deficits underlying specific neuropsychiatric disorders like schizophrenia. The new GUI, developed with our partner MetaCell, is really impressive and is driving the continued success and adoption of the tool."

Matteo Cantarelli, CTO and Co-Founder of MetaCell said: "MetaCell shares SUNY and the NetPyNE team's vision of trying to decipher the brain's neural coding mechanisms with far-reaching applications, including developing treatments for brain disorders. Researchers who take advantage of the new NetPyNE GUI will be able to run thousands of parallel simulations to explore how a range of parameters impact neuronal circuits."

Resources

NetPyNE Tutorial (CNS 2020) | www.netpyne.org | www.netpyne.org/gui | www.github.com/Neurosim-lab/NetPyNE-UI/wiki

About SUNY

DownstateSUNY Downstate Health Sciences University (Downstate) is a public medical school and hospital in New York City. It is part of the State University of New York (SUNY), the largest comprehensive system of universities, colleges, and community colleges in the United States, with over $1 Billion in research funding in FY2019. SUNY Downstate is the only academic medical center for health education, research, and patient care serving Brooklyn’s 2.5 million residents, and it is also the only healthcare facility in Brooklyn that holds the Nobel Prize in Medicine or Physiology. Downstate’s research spans the entire “bench to bedside” spectrum as an integrated entity, bringing together basic scientists, clinical researchers, and practitioners with common interests. Research programs range from explorations focused on the development of new treatments and therapeutics to faculty and student-led research driving groundbreaking innovations in health and medicine.

About MetaCell

MetaCell is a life science-focused software company composed of PhD-level scientists and software engineers, with deep domain expertise in computational neuroscience, molecular biology, data science, and enterprise-grade online software development. MetaCell works at the interface of cutting edge bioinformatics and the broader research community, helping build collaborative online platforms that facilitate communication and lead to better insights. MetaCell’s partners include Biogen, Pfizer, University College London (UCL), Arizona State University (ASU), State University of New York (SUNY), University of Edinburgh, The International Neuroinformatics Coordinating Facility (INCF), The European Bioinformatics Institute (EMBL-EBI), The Centre for Addiction and Mental Health (CAMH), and many more.

Contact details

SUNY Downstate: www.downstate.edu | salvador.dura-bernal@downstate.edu | @sunydownstate | +1 (917) 446 2747

MetaCell: www.metacell.us | info@metacell.us | @metacell | +1 (347) 878 3679 | +44 (0)7450 948685