Neuroscience Development Environment Software and Disseminated Tools
The Neuroscience Gateway (NSG) provides neuroscience software developers access to a cloud platform at the San Diego Supercomputer Center (SDSC). The cloud environment is suitable for developing, enhancing, testing and benchmarking of neuroscience software used for modeling and data processing. The developed software can be disseminated through NSG and made available on resources for wider community use. NSG development environment will support development of neuroscience software that are implemented in shared memory (such as threaded codes parallel across the cores of a multi-core node) or distributed memory (such as using the Message Passing Interface library) parallel mode. The SDSC cloud platform contains a comprehensive software stack of OS (such as Ubuntu, CentOS), compilers (such as Intel, gcc), middleware (such as MPI library), analysis software and packages (such as Matlab, R, Python), computational and data processing neuroscience software (such as NEURON, Brian, EEGLAB, FreeSurfer), ML/DL tools (such as Tensorflow) and collaborative tools (such as VNC server, Jupyter Notebook, Docker and Singularity containers). Additional software can be added to the cloud software stack based on neuroscience software developers’ needs. Access to NSF funded High Performance Computing and High Throughput Computing resources such as the Open Science Grid are also available as a part of this software development effort by neuroscientists.
Request an account on the NSG cloud environment by filling in the form
Neuroscience Software Repository and Dissemination
NSG provides a software repository where mature and robust software reside. A web frontend provides detailed description of the software for the user community and ability for users to download the software. Developers who use NSG developer platform can disseminate their software by publicly sharing their software and guidelines for usage. The software can be installed on various large scale computing resources and made available to wider neuroscience community through NSG. The software can be made available in a containerized form or as an image usable on the cloud that can be downloaded by interested researchers to be used in other computing resources not offered through NSG.
The web frontend for the disseminated software is available here
User doc for setting up and using the cloud environment is available
User doc for Jupyter Notebook on the cloud environment is available
User doc for setting up MPI on the cloud environment is available
User doc for VNC on the cloud environment is available at