NSG FAQ

Q: What is NSG?
A: NSG is a Science Gateway which allows neuroscientists and other researchers and students, involved in neuroscience research, to run pre-installed neuronal simulation software and data processing tools primarily on high performance computing (supercomputers) and cloud resources located at various academic supercomputer centers such as the San Diego Supercomputer Center, Texas Advacned Computing Center, Indiana University Pervasive Technology Institute, Pittsburgh Supercomputer Center etc. During each year time is available on some or all of these resources for the NSG users. The resources at SDSC, TACC, IU and PSC are allocated via the allocation processes managed by the Extreme Science and Engineering Discovery Environment (XSEDE) program. Based on the evolving needs of the neuroscience research community NSG identifies new resources for the user community.

Q: What is the difference between NSGportal and NSG-R?
NSGportal is a simple online portal that the user can login to run their simulation code/tool and retrieve results. The same functionality if accessed programmatically using RESTful services is called NSG-R. Please note that the underlying infrastructure is different for both access points. If you run/save output through the web portal, you will not be able to access the same data using NSG-R and vice versa.

Q: Do I have different passwords for NSG portal and NSG-R?
When you register for a 'NSG User' account from the 'Register' pull-down menu, the password you choose will be the same password that you can use both for NSGportal (i.e. the web interface) and NSG-R. But later if you chose to change either your NSGPortal or NSG-R password (and you are allowed to do that either from NSGportal's or NSG-R's 'Forgot Password?' link), you will have different passwords for NSGportal and NSG-R.

Q: What is the cost to use NSG?
A: Free!(for all academic and non-profit institution users). Industry and for-profit organizations please contact us for usage restrictions by sending email to [email protected].

Q: Who may use NSG?
A: Anyone who is involved in neuroscience research and education! NSG users can be researchers from academic and non-profit institutions, students, educators, and industry researchers.

Q: How do I get an account for NSG?
A: Please go to the NSG registration to fill out the form. Once approved you will have an account to access both NSGportal and NSG-R services. We recommend users to choose the best access mechanism according to their comfort level and needs; if required email [email protected] for guidance. NSG users will also be enlised in the NSG email list via which we announce NSG downtimes, workshop news, availability of new tools etc.

Q: What tools and software applications are available through the NSG?
A: The list of tools and applications are listed here. This list changes over time i.e. new tools are added and unused/unsupported tools are removed. Users can also run model code written in Python. Commonly used python modules are made available. Analysis tools such as R, Matlab, Octave are also available through our backend HPC resources. We are always interested to know what other neuronal simulation or analysis tools users might be interested in. Please [email protected]

Q: Can I use human subject data?
A:Yes, you can but the data needs to be de-identified. Only de-identified data can be transferred and run on NSG. Your institution's IRB requirements should also be satisfied.

Q: I need you to install a software, what is the procedure?
A: Please contact us at [email protected] for any new software or features request.

Q: Is there an illustrated document showing how to: request an account, submit a job, find models to run, retrieve output data, etc.?
A: Our user guide has step-by-step instructions on basic usage -- user guide You can also find our NSG-R usage instructions here

Q: How should I upload my input file?
A: NSG supports only zipped file format. Please compress your directory and upload the input file. The zip file should have only one directory (containing the model code) in the top level. In unix or mac, once you have a directory with your model, use tar and gzip to create a compressed tar file:
cd <model directory>
cd ..
zip -r input <model directory>

Q: What is the largest number of nodes and cores I can request?
A: It depends on the resource you choose to run on. Some supercomputers allow to run jobs on many hundreds of cores and some others allow to run on many thousands of cores. When you chose to run a tool on a particular supercomputer or clour resource you will be able to see the limits.

Q: What is the longest time I may request?
A: This depends on the wall clock limit set by the supercomputer at a particular institution. For example typically the wall clock limit on SDSC's supercomputers is 48 hours.

Q: How do I request help?
A: Email [email protected] If the question is about a NSG job MAKE SURE to provide the job handle which is a long number starting with NGBW-JOB..... .

Q: I am an user from the United States and have my own allocation on NSF's XSEDE computing resources. Can I still use NSG provided tools via NSG and charge to my own allocation?
A: Yes; multiple NSG users take advantage of this feature of NSG. Please email [email protected] to discuss this and use this feature.

Q: How do I cite usage of NSG in my publications?
A: See How to cite

Q: I need to do parameter sweep study on my model. How can I do it on NSG?
A: Bundled job submission is available for Brian. Please create a file called jobs-list and write your executable command line options, one per line Eg.
jobs-list:
python one.py 1 2
python one.py 4 5
python one.py 5 7
(if you have question, please email [email protected])

Q: Is bundled job submission only available for Brian?
A: Yes currently it is only available for Brian. We are looking into providing bundled job submission for other neuronal simulation tools also. If you have request for this, please email [email protected]

Q: I am teaching a neurooscience course (or workshop). Can my students use NSG for the class (or workshop)?
A: Yes and this is very much intended. Please email [email protected] well ahead of the start date of the class.