Curriculum

Overview of Curricular Requirements

Core Credit Requirements
Focus Area Courses
Scientific Ethics
Scientific Communication
Proposal Writing
Analysis of Data
Training Group Introductory Courses
Additional Requirements
Seminar Course
Recommended First-Year Classes

Curricular Requirements

The PULSe curriculum has been designed to provide students with the basic information they will need to succeed in the PULSe TGs during their Ph.D. work. In addition, the curriculum provides a broad and interdisciplinary program of study with the maximum possible flexibility so that students may tailor their programs to their individual needs and explore several training areas before deciding on one for their thesis program. The core requirements are a combination of general courses, TG-specific survey courses and laboratory rotations.

Credit Hours

The core requirements comprise 16-19 credits:

  • 7 credits of general course work, divided into four focus areas (described below);
  • 4-7 credits of TG Introductory courses (2 courses of 2 - 4 credits each); TGs may require additional, specialty coursework, beyond the core requirements.
  • 1 credit of a participatory seminar course;
  • 4 rotation credits of GRAD 60100, performing lab rotations in the first year. Not to be listed on the Plan of Study;

69900 research credits (number of 69900 hours taken are determined on an individual basis by the PULSe Office each semester; note that a total of 90 credit hours are required for the Ph.D.);

The student's research progress will be monitored for its ability to meet demands for publication in a peer-reviewed journal. This is one component of the Advisory Committee evaluation performed each year.

Focus Area Courses

There are four required focus areas. One course must be taken to satisfy each area. The core is designed to provide breadth to otherwise very specialized training; therefore, the same course may not be counted as satisfying multiple areas.

Scientific Ethics: One of the following courses must be taken at any time during PULSe graduate training.

  • GRAD 61200 - Responsible Conduct in Research (1 credit) Lecture once per week for 50 minutes per meeting for 8 weeks. Offered: Fall, Spring.Overview of values, professional standards, and regulations that define responsible conduct in research. Students learn the values and standards of responsible research through readings and lecture/discussion and practice application of these values and standards to research situations through class discussion of case studies from life sciences research.
  • HORT 60100 - Plan & Research Plant Science Research (1 credit) Lecture once per week for 50 minutes per meeting for 16 weeks. Typically Offered Fall. The purpose of this course is to acquaint students with the culture of scientific research and the processes of scientific discovery and review. The course will: 1) acquaint students with techniques used in presenting short scientific talks, as e.g., at national meetings, 2) expose students to procedures used in preparing scientific papers, proposals, etc., 3) introduce students to the outcomes expected to be achieved by graduate education and the processes by which students are mentored and evaluated, 4) help students begin formulating their research project proposal, 5) acquaint students with guidelines for biosafety and responsible conduct of research and provide a forum for discussion of ethical issues confronting researchers.

Scientific Communication: 

  • GRAD 60100 - PULSe Scientific Communications (1 credit/taken twice). Designed to develop the skills needed for effective scientific presentations. Students register for this course in the Fall and Spring semesters of Year 1 of study.

Proposal Writing: One of the following courses must be completed before the end of Year 2 of PULSe graduate training; however, the proposal writing class should not be taken during the first year.

  • HORT 60300 - Grants and Grantsmanship (1 credit). Lecture once per week for 50 minutes per meeting for 16 weeks. Offered Spring. Focuses on funding opportunities in agricultural research and techniques of writing successful scientific grant proposals. Students will write a proposal on a research topic of their choice during the course, and they will gain experience in the peer review process by preparing written reviews of proposals and participating in a panel meeting in which proposals are discussed and ranked.
  • MCMP 62500 - Grant Writing (1 credit). Offered Fall. Instructions for the preparation and submission of an NIH-style RO1 grant proposal will be covered. Each student will write and submit a complete proposal. The proposals will be student reviewed in a mock study section at the end of the course.

Analysis of Data: This requirement is designed to train students from a variety of backgrounds in methods of acquiring and/or analyzing data in any of the various disciplines within PULSe. As such, there is a menu of courses from which students (and TGs) can choose depending on individual student or TG needs. These courses and their descriptions are listed below. Students must satisfy this requirement by the end of Year 2.

  • BIOL 59500 - Methods and Measurements in Physical Biochemistry (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Fall. Introduction to physical methods in biochemistry and physical measurements of biological systems, such as UV/Visspectroscopy, circular dichroism, IR and Raman spectroscopy, fluorescence, neutron diffraction, light scattering, scattering from ordered materials, x-ray crystallography, NMR and ESR spectroscopy, electron microscopy, mass spectroscopy. Application of these techniques to studies of structure and dynamic behavior of biological macromolecules, composition and orientation of structural elements and cofactors, ligand binding and conformational change in biological interactions and detailed probes of local changes in structure, solvent accessibility and specific bonds formed in biological reactions. Interpretation of the resulting data and analysis of strengths and limitations of each technique. Examples from research articles are discussed that illustrate how these methods are used in modern biochemistry. Prerequisite: Introductory Calculus and Physics or permission of the instructor.
  • STAT 50300 - Statistical Methods for Biology (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Fall, Spring. Introductory statistical methods, with emphasis on applications in biology. Topics include descriptive statistics, binomial and normal distributions, confidence interval estimation, hypothesis testing, analysis of variance, introduction tononparametric testing, linear regression and correlation, goodness-of-fit tests, and contingency tables. Credit allowed in either 50300 or 51100 but not both. Prerequisite: Calculus.
  • STAT 51100 - Statistical Methods (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Fall, Spring. Descriptive statistics; elementary probability; sampling distributions; inference, testing hypotheses, and estimation; normal, binomial, Poisson, hypergeometric distributions; one-way analysis of variance; contingency tables; regression. Credit allowed in either 503 or 511 but not both. Prequisite: MA 16200 or authorized equivalent courses or consent of instructor.
  • STAT 51200 - Applied Regression Analysis (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Fall, Spring. Inference in simple and multiple linear regression, residual analysis, transformations, polynomial regression, model building with real data, nonlinear regression. One-way and two-way analysis of variance, multiple comparisons, fixed and random factors, analysis of covariance. Use of existing statistical computer programs. Prequisite: STAT 50300, STAT 51100, STAT 51700, or consent of instructor.
  • CS 59000 Computing for Life Sciences (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks.  Offered: Fall.  Basic bioinformatics algorithms and Python programming.  Course topics include biological databases, algorithms for biological sequence (DNA, protein), sequence alignment and database search, sequence motif search (DNA, protein), sequence alignment and database search, sequence motif search, protein tertiary (3D0 structure comparison, protein-proteing interaction and comparative genomics.  This course is targeted at non-CS majors who are working or interested in the bioinformatics field.  No programming experience is required.
  • CS 66200 - Pattern Recognition and Decision-Making Processes (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Spring. Introduction to the basic concepts and various approaches of pattern recognition and decision-making processes. Topics include various classifier designs,evaluation of classifiability, learning machines, feature extraction, and modeling. Prerequisite: ECE 30200 or authorized equivalent courses or consent of instructor.
  • CS 53000 -Introduction to Scientific Visualization (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Spring. Teaches the fundamentals of scientific visualization and prepares students to apply these techniques in fields such as astronomy, biology, chemistry, engineering, and physics. Emphasis is on the presentation of scalar, vector, and tensor fields; data sampling and resampling; and reconstruction using multivariate finite elements (surfaces, volumes, and surfaces on surfaces). Prerequisite: CS 25100 or authorized equivalent courses or consent of instructor.

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Training Group Introductory Courses

(4-7 credits) The Training Group Introductory courses generally involve two classes of two to four (2-4) credits each. PULSe students must enroll in at least two of these courses in addition to the core courses. One introductory course must be within a student's Training Group, and the second introductory class must be taken outside of a student's Training Group. These courses are to be completed by the end of Year 2. Some Training Groups require more than one introductory course within the group.

Biomolecular Structure and Biophysics - For students in this Training Group, BIOL 59500 must be taken:
  • BIOL 59500 - Methods and Measurement in Biophysical Chemistry (3 credits) Offered Fall
  • BCHM 60501 Macromolecules (3 credits) Offered in Fall
Biotechnology - For students in this Training Group, six credit hours from the courses below mujst be taken. Course availability is dependent on enrollments. For this reason, appropriate courses may be substituted. Contact the PULSe office and/or the Biotechnology Training Group Curriculum Committee representative for course advice and approval.
  • ABE 56000/BME 52100 Biosensors: Applications and Fundamentals (3 credits) Typically Offered Every Other Fall
  • ABE 62700 Colloidal Phenomena in Bioprocessing (3 credits) Typically Offered Every Other Fall
  • Additional Biotechnology Requirements listed below
Chemical Biology
  • MCMP 57000 Basic Principles of Chemical Action on Biological Systems (3 credits) Typically Offered Fall
Chromatin and Regulation of Gene Expression - For students in this Training Group, both of the following must be taken:
  • BCHM 61000 Regulation of Eukaryotic Gene Expression (3 credits) Typically Offered Spring
  • BCHM 61100 Chromatin Biology & Chromosome Dynamics (2 credits) Typically Offered Fall
Computational and Systems Biology
  • CS 59000 Computing in Life Science (3 credits)
  • CS 50100 Computing for Science and Engineering (3 credits)
  • Additional Computational and Systems Biology Requirements listed below
Integrative Neuroscience
  • BIOL 53800 Molecular, Cellular & Developmental Neurobiology (3 credits) Typically Offered Spring
  • BIOL 56200 Neural Systems (3 credits) Typically Offered Spring
  • BIOL 60200 Cellular Neurobiology (3 credits) Typically Offered Fall
Membrane Biology - For students in this Training Group, both of the following courses must be taken:
  • BIOL 64700 Membrane Protein Structural Biology (2 credits) Typically Offered Spring
  • CHM 63200 Membranes: Structure and Function (3 credits) Typically Offered Fall
Microbiology, Immunology and Infectious Diseases
  • AGRY 64900 Molecular Microbial Ecology (3 credits) Typically Offered Fall
  • BIOL 53300 Medical Microbiology (3 credits) Typically Offered Fall
  • BIOL 54900 Microbial Ecology (2 credits) Typically Offered Every Other Spring
Molecular Signaling and Cancer Biology - For students in this Training Group, both of the following courses must be taken:
  • BIOL 51600 Molecular Biology of Cancer (3 credits) Typically Offered Spring
  • BCHM 61501 Pathways (3 credits) Typically Offered Spring
Plant Biology
  • BTNY 59000 Plant Development Genetics

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Additional Requirements

Biotechnology Training Group - Additional Requirements (9-12 credits of math/statistics):
  • ABE 65100 Environmental Informatics (3 credits)
  • CHE 63000 Applied Mathematics for Chemical Engineers (3 credits)
  • CS 50100 Computing for Science and Engineering (3 credits)
  • CS 51500 Numerical Linear Algebra (3 credits)
  • CS 52500 Parallel Computing (3 credits)
  • CS 53000 Introduction to Scientific Visualization (3 credits)
  • CS 59000 Computing for Life Sciences (3 credits)
  • ECE 60200 Lumped System Theory (3 credits)
  • FNR 64700 Quantitative Methods for Ecologists (3 credits)
  • IE 58000 Systems Simulation (3 credits)
  • MA 51100 Linear Algebra with Applications (3credits)
  • MA 51400 Numerical Analysis (3 credits)
  • MA 52300 Introduction to Partial Differential Equations (3 credits)
  • MA 52700 Advanced Mathematics for Engineers and Physicists (3 credits)
  • ME 58100 Numerical Methods in Mechanical Engineering (3 credits)
  • STAT 50300 Statistical Methods for Biology (3 credits)
  • STAT 51100 Statistical Methods (3 credits)
  • STAT 51200 Applied Regression Analysis (3 credits)
  • STAT 51300 Statistical Quality Control (3 credits)
  • STAT 51400 Design of Experiments (3 credits)
  • STAT 51600 Basic Probability and Applications (3 credits)
  • STAT 51700 Statistical Inference (3 credits)
  • For introductory course outside of a student’s Training Group, select one of the following:
    • ABE 56000/BME 52100 Biosensors: Applications and Fundamentals (3 credits) Typically Offered Every Other Fall
    • 1 credit of ABE/BME seminar: ABE 69700 Doctoral Professional Development (1 credit) or other pending Training Group approval
Computational and Systems Biology - Additional Requirements (9-12 credits of math/statistics/ computational courses):
  • AGRY 55300 Introduction to SAS for Statistical Analysis (3 credits)
  • BCHM 69500 Intro to R and Bioconductor (3credits)
  • BIOL 56310 Protein Bioinformatics (3 credits)
  • BIOL 59500 Introduction to Bioinformatics (3 credits)
  • BIOL 59500 Practical Biocomputing
  • BME 69500 Multi-scale Modeling in Biological Systems (new in Spring 2019)
  • BME 69900/ABE 69100 Quantitative Systems Biology
  • CHM 57900 Molecular Modeling and Simulations
  • CS 53000 Introduction to Scientific Visualization (3credits)
  • CS 54100 Database System (3credits)
  • CS 57300 Data Mining (3credits)
  • CS 57900 Bioinformatics Algorithms (3credits)
  • ECE 56200 Introduction to Data Management (3 credits)
  • FS 59100 Microbial Genomics and Metabolism
  • STAT 50300 Statistical Methods for Biology (3 credits)
  • STAT 51200 Applied Regression Analysis (3 credits)
  • STAT 51300 Statistical Quality Control (3 credits)
  • STAT 51400 Design of Experiments (3 credits)
  • STAT 51600 Basic Probability and Applications (3 credits)
  • STAT 51700 Statistical Inference (3 credits)
  • STAT 52500/52600 Intermediate/Advanced Statistical Methodology (3 credits)
  • STAT 52900 Applied Decision Theory and Bayesian Statistics (3 credits)
  • STAT 54500 Introduction to Computational Statistics (3 credits)
  • STAT 54600 Computational Statistics (3credits)

Seminar

(1 credit) PULSe students are required to take one additional participatory seminar course offered by a department or a training group.  In this course, the students are required to attend weekly seminars and to give a presentation during one of the class periods.

For students in the Integrative Neuroscience Training Group, the seminar presented must be on a neuroscience-related topic and not a presentation of one’s own research or something closely related to it. Therefore, the seminar topic will need to be approved by the curriculum chair of the PULSe Integrative Neuroscience Training Group to fulfill this Training Group requirement.  It is recommended this requirement be completed by the end of the third year.

First-Year PULSe Students

Recommended classes for First-Year PULSe Students.

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