2011-2012 Bulletin – PDF - SEAS Bulletin - Columbia University

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BMEN E4737x Computer control of medical
instrumentation
3 pts. Lect: 2. Lab: 1. Not offered in 2011–2012.
Prerequisite: Basic knowledge of the C
programming language. Acquisition and
presentation of data for medical interpretation.
Operating principles of medical devices:
technology of medical sensors, algorithms
for signal analysis, computer interfacing and
programming, interface design. Laboratory
assignments cover basic measurement
technology, interfacing techniques, use of
Labview software instrument interrogation and
control, automated ECG analysis, ultrasonic
measurements, image processing applied to
x-ray images and CAT scans.
BMEN E4738y Transduction and acquisition
of biomedical data
3 pts. Lect: 2. Lab: 1. Not offered in 2011–2012.
Data transduction and acquisition systems used
in biomedicine. Assembly of bio-transducers
and the analog/digital circuitry for acquiring
electrocardiogram, electromyogram, and blood
pressure signals. Each small group will develop
and construct a working data acquisition board,
which will be interfaced with a signal generator
to elucidate the dynamics of timing constraints
during retrieval of bio-data. Lab Required.
BMEN E4750y Sound and hearing
3 pts. Lect: 3. Professor Olson.
Prerequisites: PHYS C1401 and MATH V1105-
MATH V1106. Introductory acoustics, basics of
waves and discrete mechanical systems. The
mechanics of hearing—how sound is transmitted
through the external and middle ear to the inner
ear, and the mechanical processing of sound
within the inner ear.
CBMF W4761y Computational genomics
3 pts. Lect: 3. Professor Leslie.
Prerequisites: Working knowledge of at least one
programming language, and some background
in probability and statistics. Computational
techniques for analyzing and understanding
genomic data, including DNA, RNA, protein
and gene expression data. Basic concepts in
molecular biology relevant to these analyses.
Emphasis on techniques from artificial
intelligence and machine learning. Stringmatching
algorithms, dynamic programming,
hidden Markov models, expectation -
maximization, neural networks, clustering
algorithms, support vector machines. Students
with life sciences backgrounds who satisfy the
prerequisites are encouraged to enroll.
BMCH E4810y Artificial organs
3 pts. Lect: 3. Professor Leonard.
Analysis and design of replacements for the
heart, kidneys, and lungs. Specification and
realization of structures for artificial organ
systems.
BMEN E4894x Biomedical imaging
3 pts. Lect: 3. Professor Hielscher.
This course covers image formation, methods
of analysis, and representation of digital
images. Measures of qualitative performance
in the context of clinical imaging. Algorithms
fundamental to the construction of medical
images via methods of computed tomography,
magnetic resonance, and ultrasound. Algorithms
and methods for the enhancement and
quantification of specific features of clinical
importance in each of these modalities.
BMEN E4898y Biophotonics
3 pts. Lect: 3. Professor Hielscher.
Prerequisites: BMEN E4894 Biomedical
imaging, PHYS C1403 Classical and quantum
waves, or instructor’s permission. This course
provides a broad-based introduction into the
field of Biophotonics. Fundamental concepts of
optical, thermal, and chemical aspects of the
light-tissue interactions will be presented. The
application of these concepts for medical therapy
and diagnostics will be discussed. The course
includes theoretical modeling of light-tissue
interactions as well as optical medical instrument
design and methods of clinical data interpretation.
BMEN E6001x Advanced scaffold design and
engineering complex tissues
3 pts. Lect: 2.5. Lab: 0.5. Professor H. Lu.
Prerequisites: BMEN E4501 or equivalent.
Corequisites: BMEN E4001 or E4002. Advanced
biomaterial selection and biomimetic scaffold
design for tissue engineering and regenerative
medicine. Formulation of bio-inspired design
criteria, scaffold characterization and testing,
and applications on forming complex tissues or
organogenesis. Laboratory component includes
basic scaffold fabrication, characterization and
in vitro evaluation of biocompatibility. Group
projects target the design of scaffolds for select
tissue engineering applications.
BMEN E6003x Computational modeling of
physiological systems
3 pts. Lect: 3. Professor Morrison.
Prerequisites: BMEN E4001 and E4002 or
equivalent, and APMA E4200 or equivalent.
Advanced computational modeling and
quantitative analysis of selected physiological
systems from molecules to organs. Selected
systems are analyzed in depth with an emphasis
on modeling methods and quantitative analysis.
Topics may include cell signaling, molecular
transport, excitable membranes, respiratory
physiology, nerve transmission, circulatory
control, auditory signal processing, muscle
physiology, data collection and analysis.
EEBM E6020y Methods of computational
neuroscience
4.5 pts. Lect: 3. Instructor to be announced.
Prerequisites: BMEB W4011. Formal methods in
computational neuroscience including methods
of signal processing, communications theory,
information theory, systems and control, system
identification and machine learning. Molecular
models of transduction pathways. Robust
adaptation and integral feedback. Stimulus
representation and groups. Stochastic and
dynamical systems models of spike generation.
Neural diversity and ensemble encoding. Time
encoding machines and neural codes. Stimulus
recovery with time decoding machines. MIMO
models of neural computation. Synaptic plasticity
and learning algorithms. Major project(s) in
MATLAB.
BMEE E6030y Neural modeling and
neuroengineering
3 pts. Lect: 3. Professor Sajda.
Prerequisites: APMA E3101, ELEN E3801, and
BMEB W4011, or equivalent, or instructor’s
permission. Engineering perspective on the study
of multiple levels of brain organization, from
single neurons to cortical modules and systems.
Mathematical models of spiking neurons, neural
dynamics, neural coding, and biologically-based
computational learning. Architectures and learning
principles underlying both artificial and biological
neural networks. Computational models of cortical
processing, with an emphasis on the visual system.
Applications of principles in neuroengineering;
neural prostheses, neuromorphic systems
and biomimetics. Course includes a computer
simulation laboratory. Lab required.
EEBM E6090-6099x or y Topics in
computational neuroscience and
neuroengineering
3 pts. Lect: 2. Not offered in 2011–2012.
Prerequisite: Instructor’s permission. Selected
advanced topics in computational neuroscience
and neuroengineering. Content varies from year
to year, and different topics rotate through the
course numbers 6090-6099.
BMEN E6301y Modeling of biological tissues
with finite elements
3 pts. Lect: 3. Not offered in 2011–2012.
Prerequisite: MECE E6422, or ENME E6315,
or equivalent. Structure-function relations and
linear/nonlinear constitutive models of biological
tissues: anisotropic elasticity, viscoelasticity,
porous media theories, mechano-electrochemical
models, infinitesimal and large deformations.
Emphasis on the application and implementation
of constitutive models for biological tissues
into existing finite element software packages.
Model generation from biomedical images by
extraction of tissue geometry, inhomogeneity and
anisotropy. Element-by-element finite element
solver for large-scale image based models
of trabecular bone. Implementation of tissue
remodeling simulations in finite element models.
MEBM E6310x-E6311y Mixture theories for
biological tissues, I and II
3 pts. Lect: 3. Not offered in 2011–2012.
Prerequisites: MECE E6422 and APMA E4200,
or equivalent Development of governing
equations for mixtures with solid matrix,
interstitial fluid, and ion constituents. Formulation
of constitutive models for biological tissues.
Linear and nonlinear models of fibrillar and
viscoelastic porous matrices. Solutions to special
problems, such as confined and unconfined
compression, permeation, indentation and
contact, and swelling experiments.
engineering 2011–2012