56:198:500 Introduction to Programming for Computational Scientists 
This course introduces the basics of modern computer programming to beginning graduate students without a background in computer science. Topics covered are: control statements; arrays and lists; classes, objects and methods; inheritance; polymorphism; exception handling; file streams and serialization; recursion; searching and sorting. Students are required to use an up-to-date integrated development environment (IDE) to complete a number of programming assignments.
Prerequisites: None
Term: Fall

56:198:501 Data Structures and Algorithmic Problem Solving in Python 
Introduction to algorithms, data structures, and algorithmic paradigms: binary search trees, hashing, sorting, searching, shortest paths, and dynamic programming.
Prerequisites: 56:198:500 or equivalent
Term: Spring

56:198:521 Compiler Construction
Introduction to compiler design and implementation, including lexical analysis, formal syntax specifications, parsing techniques, syntax-directed translation, semantic analysis, execution environment, storage management, code generation, and optimization techniques.
Prerequisites: 56:198:501 or equivalent

50:198:523 Software Engineering (3 credits) 
Principles and techniques for the design and construction of reliable, maintainable, and useful software systems. Software life cycle, requirements specifications, and verification and validation issues. Implementation strategies (e.g., top-down, bottom-up, teams), support for reuse, and performance improvement. A treatment of human factors and user interfaces included.
Prerequisites: 56:198:501 or equivalent 
Term: Fall

56:198:531 Computer Systems Architecture
Processor design; memory hierarchy; cache coherence and consistency; input/output subsystems; multiprocessor and massively parallel architectures.
Prerequisites: Permission of instructor

56:198:541 Parallel, Distributed, Grid, and Cloud Computing(3 credits)  
This course introduces the concepts, models, implementations, and applications of parallel and distributed systems.  Topics include parallel and distributed architectures, grid and cloud computing frameworks; programming models and algorithmic techniques; performance analysis and evaluation; and applications of parallel and distributed computing.  The course provides students experience in programming using different parallel/distributed programming paradigms and the opportunity to examine a course topic in depth through a significant term project.
Prerequisites: 56:198:501 or equivalent
Term: Spring

56:198:543 Operating Systems(3 credits)  
A comprehensive, hands-on coverage of operating system principles, design, and implementation. Topics include: kernel development; process concurrency issues such as starvation, mutual exclusion, deadlock avoidance, and concurrency models and mechanisms; producer-consumer problems; synchronization; scheduling policies and algorithms for preemptive and nonpreemptive scheduling; real-time scheduling; memory management and analysis of paging and segmentation policies; security and protection; file systems; fault tolerance; performance evaluation.
Prerequisites: Permission of instructor

56:198:546 Computer Networks(3 credits)
Introduction to computer communication networks, including physical and architectural components, communication protocols, switching, network routing, congestion control, and flow control. End-to-end transport services, network security, and privacy. Networking software and applications. Network installation, testing, and maintenance.
Prerequisite: 56:198:501 or equivalent.
Term:Spring

56:198:548 Mobile and Wireless Computing
Digital communication, radio transmission basics, the mobile environment, communication channels, access technologies (FDMA, CDMA, TDMA), channel assignment algorithms, user location and tracking, handoff, packet radio networks, ad-hoc networks, satellite networks, security and authentication issues, mobile IP, power control.
Prerequisite: 56:198:546 or equivalent.

56:198:551 Database Systems(3 credits) 
Relational database theory and practice, including database design. Database concepts, relational algebra, data integrity, query languages, and views. Introduction to object-oriented databases. Application project with a practical database management system.
Prerequisites: 56:198:501 or equivalent 
Term: Fall

56:198:552 Advanced Database Systems
Query processing, including indexing and hashing; query optimization; transaction management, including concurrency control and recovery; database architecture, including server and network systems. Project based on designing and implementing enterprise systems.
Prerequisite: 56:198:551 or equivalent

56:198:556 Computer Graphics(3 credits) 
Graphics systems and imaging principles, graphics programming using packages like OpenGL, input devices and interactive techniques, animation techniques, geometric transformations and modeling in two and three dimensions, viewing in 2D and 3D, lighting and shading, fundamental graphics algorithms (such as clipping, hidden surface removal, etc.)
Prerequisites: 56:198:501 or equivalent 
Term: Fall

56:198:557 Advanced Computer Graphics
Advanced topics in computer graphics with a focus on rendering (hidden surface and visibility algorithms, material properties and reflection models, techniques for global illumination calculations, including ray tracing and radiosity algorithms) and modeling (methods for describing geometric primitives such as implicit surfaces and parametric patches, solid modeling, and constructive solid geometry).
Prerequisite: 56:198:556 or equivalent.

56:198:561 Optimization Methods (3 credits) 
This course introduces various methods based on linear programming to solve discrete optimization problems. The topics covered in the course will include introduction to linear programming (LP), network flows, and application of LP-based techniques to solve various optimization problems. 
Prerequisites: None 
Term: Fall

56:198:562 Big Data Algorithms (3 credits) 
Study of algorithmic techniques and modeling frameworks that facilitate the analysis of massively large amounts of data. Introduction to information retrieval, streaming algorithms and analysis of web searches and crawls.
Prerequisites: 56:198:501 or equivalent 
Term: Fall

56:198:564 Data Mining
Introduction to major concepts, techniques, and algorithms in data mining, machine learning, and analytics: classification, decision trees, decision rules, regression, nearest neighbor, evaluation, data preparation, clustering, associations, visualization, summarization and deviation detection, applications in targeted marketing, and genomics.
Prerequisite: 56:198:501 or equivalent

56:198:567 Applied Probability (3 credits)
An introduction to probability theory and the modeling and analysis of probabilistic systems with emphasis on applications in computer science, engineering, and data science. Probabilistic models, conditional probability. Discrete and continuous random variables. Expectation and conditional expectation. Limit Theorems. Bernoulli and Poisson processes. Markov chains. Bayesian estimation and hypothesis testing. Elements of statistical inference.
Prerequisites: 50:640:122

56:198:571 Algorithms
Review of general tools and techniques in the design and analysis of algorithms and their proof of correctness. Selected topics from: graph algorithms, algebraic and geometric algorithms, randomized algorithms, and online algorithms.
Prerequisite: 56:198:501 or equivalent.

56:198:573 Computational Geometry (3 credits) 
Algorithms and data structures for geometric problems that arise in various applications such as computer graphics, CAD/CAM, robotics, and geographical information systems (GIS). Topics include: point location, range searching, intersection, decomposition of polygons, convex hulls, Voronoi diagrams, and line arrangements.
Prerequisites: 56:198:501 or equivalent 
Term: Spring

56:198:575 Crytography and Computer Security(3 credits)
Secret-key cryptography, public-key cryptography, key agreement, secret sharing, digital signatures, message and user authentication, one-way functions, key management; attacks; practical applications to computer and communications security.
Prerequisites: 56:198:501 or equivalent.
Term:Fall

56:198:576 Theory of Computation (3 credits)
Formal languages, automata and computability; regular languages and finite-state automata; context-free grammars and languages; pushdown automata; the Church-Turing theses; Turing machines; decidability and undecidability. 
Prerequisites: Permission of instructor. 
Term: Spring

56:198:577 Computational Complexity Theory
Fundamental mathematical concepts: models of computation, uncomputability, notions of space and time complexity. Complexity classes and reductions.
Prerequisite: 56:198:576 or equivalent.

56:198:578 Combinatorial Optimization
Introduction to linear optimization and the theory of linear programming. Topics include the simplex method; duality; network flow problems; graph matching; integer programming; NP-completeness; and introduction to both LP-based and combinatorial techniques for designing approximation algorithms.
Prerequisite: 56:198:501 or equivalent.

56:198:581 Numerical Methods (3 credits) 
Computational techniques for solving scientific problems:  Precision, IEEE floating point representation, interpolation, root finding, numerical integration, numerical differentiation, approximation of functions, functions minimization, numerical linear algebra, numerical solutions of ordinary differential equations.
Prerequisites: 56:198:501 or equivalent 
Term: Fall

56:198:582 Computational Modeling of Biological Systems
Biology is entering a new era where detailed description and observation are giving way to systems-level understanding and computer modeling. This course introduces students to computer modeling of living cells, focusing particularly on metabolic, regulatory, and signaling networks. Specific topics include constraint-based modeling, properties of stoichiometric matrices, flux-balance analysis, and motifs in transcriptional networks. Knowledge of molecular biology is useful but not required.
Prerequisite: 56:198:500 or equivalent.

56:198:584 Mathematical Methods in Systems Biology
Provides an introduction to computational and systems biology, focusing on advanced mathematical tools. In particular, ordinary and partial differential equations, control theory, and discrete mathematics (networks) will be used to address a wide set of biological and biomedical applications. The latter will range from classical prey-predator populations examples to cancer immuno and drug therapies, from evolutionary math to gene networks.
Prerequisite: 56:198:500 or equivalent.

56:198:693 Master’s Project (3 credits)
Open only to students pursuing the project option. Design, implementation, and demonstration of a significant software project. Project proposals must be approved by instructor. The project completion requires a report and a presentation.
Prerequisite: Permission of instructor.

56:198:697 Computer Science Internship (3 credits)
The practical application of computer science knowledge and skills through an approved internship in a sponsoring organization. Arrangements for the internship must be agreed upon by the sponsoring organization and approved by the department before the beginning of the semester. Students should consult the department for detailed instructions before registering for this course.
Prerequisite: Approval by department 

56:198:701,702 Research in Computer Science (3 + 3 credits)
Open only to students pursuing the thesis option. This will involve two semesters’ worth of substantial and independent research on a topic approved and supervised by a faculty member (the thesis adviser) who will work closely with the student. This research will be exposited in the student’s M.S. thesis.
Prerequisite: Permission of thesis adviser and graduate director.