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, 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.


New Major in Applied Mathematics Available Fall 2018

Starting in the fall of 2018, Brandeis students will have a new option for their major: a Bachelor of Science in applied mathematics. This new major is part of a broader expansion of the mathematics department into applied areas, with a strong emphasis on interdisciplinary research and training of undergraduate and graduate students.

Course description and other information about this new major can be found in the Brandeis Provisional Bulletin.

Thomas FaiThis transformation of the mathematics department, and the creation of the applied mathematics major, aim at addressing long term changes at Brandeis and in the world. The last ten years at Brandeis have seen a dramatic rise in interest in applied mathematics courses, motivated by the increasing use of mathematical ideas throughout society. The world has become more quantitative with the advent of the ability of computers to collect and process enormous amounts of data. This has led to a true revolution in such diverse areas as medical and pharmaceutical industries (algorithmic analysis of the genome), weather and climate prediction (numerical approximation of intractable systems), insurance and risk management, investment, marketing strategies (statistical analysis), and beyond.

Jonathan TouboulThis shift toward quantitative reasoning is hardly new, but it now feels more acute than ever. There are excellent job opportunities for well-trained applied mathematicians in the private sector, as well as in academia. This has, in turn, affected education strategies at all levels. The evolution of Brandeis’ student body is in line with this current shift. The aim of the new program is to offer Brandeis students the possibility to acquire the general toolkit used by applied mathematicians to solve problems in various scientific and engineering fields, and to allow them to harness the “unreasonable effectiveness of mathematics” evoked by Eugene Wigner.

John WilmesThe applied major introduces a series of new core courses entitled, Applied Mathematics, Mathematics for the Natural Sciences, Scientific Computing and Simulations, and Mathematical Modeling. These will be coupled with advanced topics courses to be developed by the new faculty joining the department. Students will supplement courses in the mathematics department with classes throughout the university with strong mathematical content. In this way, students will have a strong foundation and a thorough exposure to the way that mathematics can be used in diverse fields.

Central to this effort is the hiring of three new faculty members, Jonathan Touboul, Thomas Fai, and John Wilmes, who will expand the mathematical horizons of undergraduate and graduate students, and establish new research connections across the sciences at Brandeis. The initial focus of the new major will be on the applications of mathematics to natural sciences. In the future, additional tracks could be added to the major, with applications to computer science and operation research, and to social science and economics.

Maria de Boef Miara Promoted to Assistant Professor

Maria MiaraMaria de Boef Miara was recently promoted to Assistant Professor of Biology. Since joining Brandeis five years ago as an adjunct instructor, she has particularly enjoyed teaching the Human Physiology course and is excited to be developing an accompanying lab course for Fall 2018. This course will give students the opportunity to learn about human physiology experientially, using the most up-to-date technology. It will also allow students interested in health careers an opportunity to complete an important prerequisite.

By studying how their physiology changes under a variety of conditions, students will get a hands-on feel for the subject. For instance, they will observe how cardiovascular and respiratory systems change when they exercise. They will witness how muscle activation differs between different body positions, such as the difference between winning and losing an arm wrestling match. They will determine whether they are able to respond more quickly to visual or auditory stimuli. And, by the end of the semester, they will be able to design and conduct their own experiments to study a physiological phenomena of their choosing.

Maria is excited for the opportunity to work more closely with her students in these smaller lab sections. She feels very fortunate to be able to work with the motivated, curious, and collaborative undergraduates found at Brandeis and she looks forward to giving them the space and support to explore their interests in human physiology.

Congratulations to Maria!


Waltham Teachers Meet with Brandeis Scientists

Brandeis scientists & Waltham teachers

On Tuesday, November 7th, 32 science teachers from Waltham Public Middle and High Schools visited the Brandeis science labs as part of the Third Annual Brandeis Scientists in the Classroom Workshop. The workshop is designed to be an opportunity to connect middle and high school science teachers with Brandeis scientists. The teachers were grouped and matched with 14 Brandeis graduate students, postdocs and faculty who shared their Brandeis science research directly with the teachers to help them understand what we do, so they can better integrate science into their classroom lessons.

This event was an extension of an ongoing partnership between Brandeis and Waltham High School and was sponsored by the Brandeis MRSEC. The Waltham school district has a high percentage of students from backgrounds underrepresented in the sciences. Brandeis offers several on-going programs with Waltham teachers and students in an effort to broaden their participation in STEM.

Brandeis’ Pioneering Science Posse Program

Photo: Mike Lovett

Samia Tamazi ’20

BrandeisNow has posted an article about the history and accomplishments of the Brandeis’ Science Posse program. Read the following excerpt or the entire article:

In June, Macareno and his posse, all Class of 2020, get off Amtrak’s Acela Express train and take a shuttle bus to Brandeis for science boot camp. On the first day, they gather in a classroom in the Abelson physics building […]

(Melissa) Kosinski-Collins, who earned a PhD at MIT, tells them college science is profoundly different from high-school science. With equal parts candor and caring, she sets high expectations, describing the intense workload. The students know that they will be held to lofty standards and that she will support them.

Later in the day, they gather around a long lab table in the Shapiro Science Center, in an area Kosinski-Collins calls Hufflepuff — a nod to one of the houses at Harry Potter’s Hogwarts School. An array of equipment is scattered before them — pipettes, balances, bottles of acetic acid (vinegar) and sodium bicarbonate (baking soda). There are also aluminum foil, Kimwipes, Scotch tape and Ziploc bags.

The students’ assignment is to build an air bag. When acetic acid combines with sodium bicarbonate, they produce carbon dioxide. The students must figure out how much of each chemical to add to fully inflate a quart-size Ziploc bag. But they also have to protect an egg placed inside the bag. This is where the foil, tape and extra bags come in. Along with the cushion of air, these items can be used to keep the egg from cracking when they drop the bag from the Science Center steps, about 15 feet above the ground.

There’s an important catch. Several months earlier, at a meeting in New York, the students got the same assignment. They also completed lab reports describing the quantities of chemicals they used and how they arranged the materials inside the bag to protect the egg. These lab reports are now handed out to different students. They have 10 minutes to repeat the earlier experiment using the reports as a guide […]

Read more at BrandeisNow

DIY your own Programmable Illumination Microscope

The Fraden Group describes how to build your own Programmable Illumination Microscope in the American Journal of Physics

Have you ever marveled at the equipment used in a research lab? Have you ever wondered how a specialized piece of equipment was made? Have you ever wondered how much it would cost to build your own research microscope? Have you ever considered trying to make your own research microscope? The details on how the Fraden Group builds their Programmable Illumination Microscope for under $4000 was recently published in the American Journal of Physics.


The Programmable Illumination Microscope or PIM is a highly specialized microscope where the illumination for the sample being imaged comes from a modified commercial projector, nearly identical to the ones mounted in every classroom. For the PIM the lens that projects the image onto the screen is removed and replaced with optics (often the same lens in reverse) that shrinks the image down so that it can be focused through the microscope objective onto the sample. The light coming from the projector, which is the illumination source for the microscope, can be modified in realtime based on the image being captured by the camera. Thus the illumination is not only programmable but can also be algorithmic and provide active feedback.

This new publication in the American Journal of Physics, which is published by the American Association of Physics Teachers, is intended to help small teaching and research labs across the country develop their own PIMs to be built and used by undergraduate students. The paper includes schematics and parts lists for the hardware as well as instructions and demonstration code for the software. Any other questions can be directed to the authors Nate Tompkins and Seth Fraden.

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