ECE 8011 Software and Cyber Automation in Neuroscience

(1 credit; offered every semester)

Course Description: This seminar course will emphasize software and cyber automation tools in neuroscience to address the emerging needs of big data in neuroscience. Students will work in pairs to address such needs of various neuroscience Labs both within MU and with collaborators outside MU. The students pairs will be provided a list of automation projects to work on (one or maximum two) during the semester, under close supervision of the instructors. They will also be provided access to local cyberinfrastructure at MU, national cyberinfrastructure resources such as CyVerse ( and Neuroscience Gateway ( , as well as public clouds such as XSEDE and Amazon Web Services.

Prerequisites: Basic software programming, basic cell biology, or consent of instructor.

Instructors: Satish S. Nair, 229 Naka Hall (882-2964; and Prasad Calyam, 201 Naka Hall (882-9747;

Detailed listing of topics:

  • Basic lab exercises involving usage of neuroscience packages and cyberinfrastructure tools.
  • The project(s) will focus on the investigation and development of cyberinfrastructure tools in neuroscience to address emerging needs of big data in neuroscience; example projects include:
    • Work on collecting molecular data, brain imaging, synapses, fMRI and other related neuroscience datasets and putting them together under one web resource for neuroinformatics applications.
    • Compare cyberinfrastructure resource allocation technologies and policies in CyVerse and Neuroscience Gateway.
    • Integrate multiple cyberinfrastructure tools such NEURON ( and VCell Virtual Cell ( into one pipeline for complex neural simulations.
    • Build high performance computing and cloud based workflows and algorithm optimization as suitable for diverse analytics from distributed data sources.

Credits: 1

Grading: Class projects 100%

Letter grades: A > 90%; B 75-90%; C < 75%

Academic dishonesty: Academic honesty is fundamental to the activities and principles of a University. Any effort to gain an advantage not given to all students is dishonest whether or not the effort is successful. The academic community regards academic dishonesty as an extremely serious matter, with consequences that range from probation to expulsion. When in doubt about plagiarism, paraphrasing, quoting, or collaboration, consult the course instructor. If you are caught cheating on an exam or assignment, you will either receive a grade of zero for the exam/assignment, or an F for the course. Weekly assignments are individual assignments, so do not copy someone else's assignment. If you are caught committing academic dishonesty, your actions will be reported to the Provost's office, according to university policy.

Special needs: If you need accommodations because of a disability, if you have emergency medical information to share with me, or if you need special arrangements in case the building must be evacuated, please inform an instructor immediately. Please see an instructor privately after class, or during office hours. To request academic accommodations (e.g. a note-taker) students must register with Disability Services, AO38 Brady Commons, 882-4696. It is the campus office responsibility to review documentation provided by students requesting academic accommodations, and for accommodations planning in cooperation with students and instructors, as needed and consistent with course requirements. For other MU resources for students with disabilities, click on "Disability Resources" on the MU homepage.