New Computational Neuroscience Textbook

Paul Miller bookComputational Neuroscience is an exciting branch of science, which is helping us understand how simple biophysical processes within cells such as neurons lead to complex and sometimes surprising neural responses, and how these neurons, when connected in circuits can give rise to the wide range of activity patterns underlying human thinking and behavior. To bridge the scales from molecules to mental activity, computer simulations of mathematical models are essential, as it is all too easy for us otherwise to produce descriptions of these complex interacting systems that are internally inconsistent. Simulations allow us to ask “given these ingredients, what is possible?”

Simulation showing how weaker input that is localized can produce spiking when stronger dispersed input does not.

The best way to study computational neuroscience is to write the computer codes that model a particular biological phenomenon, then see what the simulation does when you vary a parameter in the model. Therefore, the course I teach at Brandeis (NBIO 136B) is based around a large number of computer tutorials, in which students, some of whom have no computer-coding background, begin with codes of 5-10 lines that simulate charging of a capacitor, and end up completing codes that simulate the neural underpinnings of learning, pattern recognition, memory, and decision-making. It turns out that very few computational principles are needed to build such codes, making these simulation methods far more easily understood and completed than any mathematical analysis of the systems. However, in the absence of a suitable introductory textbook—most computational neuroscience textbooks are designed by Ph.D. physicists and mathematicians for Ph.D. physicists and mathematicians—it proved difficult for me to use the flipped classroom approach (see below). Therefore, my goal was to create a text that students could read and understand on their own.

Different behaviors of a three-unit circuit as connection-strengths are changed. (Multistable constant activity states, multiple oscillating states, chaotic activity, heteroclinic state sequence). Each color represents firing rate of a unit as a function of time.

In keeping with the goal of the course—to help students gain coding expertise and understand biological systems through manipulations of computer codes—I produced over 100 computer codes (in Matlab) for the book, the vast majority of which are freely available online. (All codes used to produce figures and some tutorial solutions are accessible, but I retained over half of the tutorial solutions in case instructors wish to assign tutorials without students being able to seek a solution elsewhere.)

Learn more at MIT Press.

From the Preface of the book:

I designed this book to help beginning students access the exciting and blossoming field of computational neuroscience and lead them to the point where they can understand, simulate, and analyze the quite complex behaviors of individual neurons and brain circuits. I was motivated to write the book when progressing to the “flipped” or “inverted” classroom approach to teaching, in which much of the time in the classroom is spent assisting students with the computer tutorials while the majority of information-delivery is via students reading the material outside of class. To facilitate this process, I assume less mathematical background of the reader than is required for many similar texts (I confine calculus-based proofs to appendices) and intersperse the text with computer tutorials that can be used in (or outside of) class. Many of the topics are discussed in more depth in the book “Theoretical Neuroscience” by Peter Dayan and Larry Abbott, the book I used to learn theoretical neuroscience and which I recommend for students with a strong mathematical background.

The majority of figures, as well as the tutorials, have associated computer codes available online, at github.com/primon23/Intro-Comp-Neuro, and at my website. I hope these codes may be a useful resource for anyone teaching or wishing to further their understanding of neural systems.

 

SciFest VIII wrap-up

SciFest 2018SciFest 2018SciFest 2018SciFest 2018SciFest 18SciFest 18

The Brandeis University Division of Science held its annual undergraduate research poster session SciFest VIII on August 2, 2018, as more than one hundred student researchers presented summer’s (or last year’s) worth of independent research. We had a great audience of grad students and postdocs (many of whom were mentors), faculty, proud parents, friends, and senior administrators.

SciFest VIII by numbers

  • 105 posters
  • 105 student presenters out of approx. 175 summer student researchers
    • 84 Brandeis students
    • 2 international students (from India)
    • 19 visiting domestic students
  • 41 Brandeis faculty advisors from 7 departments
    • Biochemistry (7)
    • Biology (17)
    • Chemistry (5)
    • Computer Science (1)
    • Mathematics (1)
    • Physics (7)
    • Psychology (4)
  • 12 different Brandeis undergraduate majors represented

Grant funding for undergraduates doing Computational Neuroscience

The Division of Science is pleased once again to announce the availability of Traineeships for Undergraduates in Computational Neuroscience through a grant from the National Institute on Drug Abuse. Traineeships will commence in summer 2018 and run through the academic year 2018-19.

Please apply to the program by March 1, 2018 at 6 pm to be considered.

Computational Neuroscience undergraduate trainees were first authors on 2 papers in 2017; figure above from Christie et al., J. Neurophysiol., 2017

Traineeships in Computational Neuroscience are intended to provide intensive undergraduate training in computational neuroscience for students interested in eventually pursuing graduate research. The traineeships will provide approximately $5000 in stipend to support research in the summer, and $3000 each for fall and spring semesters during the academic year. Current Brandeis sophomores and juniors (classes of ’19, ’20) may apply. To be eligible to compete for this program, you must

  • have a GPA > 3.0 in Div. of Science courses
  • have a commitment from a professor to advise you on a research project related to computational neuroscience
  • have a course work plan to complete requirements for a major in the Division of Science
  • complete some additional requirements
  • intend to apply to grad school in a related field.

Interested students should apply online (Brandeis login required). Questions that are not answered in the online FAQ may be addressed to Steven Karel <divsci at brandeis.edu> or to Prof. Paul Miller.

Full year funding for undergraduates working in computational neuroscience

The Division of Science is pleased to announce the availability of Traineeships for Undergraduates in Computational Neuroscience through a recently-renewed grant from the National Institute on Drug Abuse. Traineeships will commence in summer 2017 and run through the academic year 2017-18.

Please apply to the program by February 27, 2017 at 6 pm to be considered.

Traineeships in Computational Neuroscience are intended to provide intensive undergraduate training in computational neuroscience for students interested in eventually pursuing graduate research. The traineeships will provide approximately $5000 in stipend to support research in the summer, and $3000 each for fall and spring semesters during the academic year. Current Brandeis sophomores and juniors (classes of ’18, ’19) may apply. To be eligible to compete for this program, you must

  • have a GPA > 3.0 in Div. of Science courses
  • have a commitment from a professor to advise you on a research project related to computational neuroscience
  • have a course work plan to complete requirements for a major in the Division of Science
  • intend to apply to grad school in a related field.

Interested students should apply online (Brandeis login required). Questions that are not answered in the online FAQ may be addressed to Steven Karel <divsci at brandeis.edu> or to Prof. Paul Miller.

Research Funding for Undergrads: Computational Neuroscience Traineeships for 2016-17

The Division of Science is pleased to announce the availability of Traineeships for Undergraduates in Computational Neuroscience through a grant from the National Institute on Drug Abuse. Traineeships will commence in summer 2016 and run through the academic year 2016-17.

Please apply to the program by February 24, 2016 at 6 pm to be considered.

Traineeships in Computational Neuroscience are intended to provide intensive undergraduate training in computational neuroscience for students interested in eventually pursuing graduate research. The traineeships will provide a $5000 stipend to support research in the summer, and $3000 each for fall and spring semesters during the academic year. Current Brandeis sophomores and juniors are eligible to apply. In addition, to be eligible to compete for this program, you must

  • have a GPA > 3.0 in Div. of Science courses
  • have a commitment from a professor to advise you on a research project related to computational neuroscience
  • have a course work plan to complete requirements for a major in the Division of Science
  • intend to apply to grad school in a related field.compneuroimage

The curricular requirements are listed on the program website.  The application form is online (Brandeis login required). Also, see Frequently Asked Questions.

There will be a question-and-answer session about summer research funding applications on Thursday, Jan 14 at 5 pm in Gerstenzang 123

Research Support for Undergrads: Computational Neuroscience Traineeships for 2015-16

The Division of Science wishes to announce the availability of Traineeships for Undergraduates in Computational Neuroscience through a grant from the National Institute on Drug Abuse. Traineeships will commence in summer 2015 and run through the academic year 2015-16.

Please apply to the program by February 24, 2015 at 6 pm to be considered (NOTE DATE CHANGE). If applying after Feb 24, be sure to contact divsci at brandeis dot edu to inquire about the availability of training slots.

Traineeships in Computational Neuroscience are intended to provide intensive undergraduate training in computational neuroscience for students interested in eventually pursuing graduate research. The traineeships will provide a $5000 stipend to support research in the summer, and $3000 each for fall and spring semesters during the academic year. Trainees are appointed for at least a year and up to two years, depending on satisfactory progress.  Current Brandeis sophomores and juniors are eligible to apply. In addition, to be eligible to compete for this program, you must

  • have a GPA > 3.0 in Div. of Science courses
  • have a commitment from a professor to advise you on a research project related to computational neuroscience
  • have a course work plan to complete requirements for a major in the Division of Science
  • intend to apply to grad school in a related field.

The curricular requirements are listed on the program website.  The application form is online (Brandeis login required). Also, see Frequently Asked Questions.

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