Bioinformatics (BIOI)

BIOI 1000  INTRODUCTION TO BIOINFORMATICS (3 credits)

Bioinformatics is a scientific discipline that integrates mathematical and computational techniques with biological knowledge to develop and use computational tools to extract, organize and interpret information from genetic sequence data. The field is growing rapidly with the advancement in molecular technology to sequence the genomes of many different organisms. This course will provide an introduction to the field and will examine some of the problems of interest to bioinformaticians and how these relate to biology, computer science, mathematics and engineering. Topics covered in the course will include an overview of the biology, mathematics and computer science needed to understand these problems and an examination of some of the tools used by bioinformaticians to address them.

Distribution: Natural/Physical Science General Education course

BIOI 2000  FOUNDATIONS OF BIOINFORMATICS (3 credits)

Bioinformatics is a new scientific discipline that integrates mathematical and computational techniques with biological knowledge to develop and use computational tools to extract, organize and interpret information from genetic sequence data. The field is growing quickly due to rapid advances in sequencing and other biological techniques that allow the genomes of different organisms to be easily sequenced. This course provides an overview of the field and covers the chemical, biological, mathematical and computational foundations of bioinformatics upon which later courses will depend. In addition, it introduces problems of interest to bioinformaticians and the methods and tools used to address them.

Prerequisite(s)/Corequisite(s): BIOI 1000 or BIOL 1450

BIOI 3000  APPLIED BIOINFORMATICS (3 credits)

This course will provide students with the practical skills needed for the analysis of -omics data. Topics covered will include biological databases, molecular biology tools (e.g., primer design, contig assembly), gene prediction and mining, database searches, genome comparison, sequence alignments, phylogenetic inference, gene expression data analyses, functional annotation of protein sequences, protein structure and modeling. Specialized software (e.g., Vector NTI) and widely used web-based computation tools (e.g.., Entrez, BLAST, ClustalX, Phylip, PyMOL, and SwissPDBviewer) will be illustrated. Multiple approaches for solving particular problems will be presented.

Prerequisite(s)/Corequisite(s): BIOI 1000, BIOL 1450, and CIST 1400; or permission.

BIOI 3500  ADVANCED BIOINFORMATICS PROGRAMMING (3 credits)

Because of the volume and complexity of biological data, advanced programming skills are required for researchers in order to get the most out of their data analyses. This course will provide the expanded programming skills necessary to develop software that can exploit the complex information landscape of bioinformatics. Specific topics covered will include molecular biology basics, Unix/Linux shell programming, Perl and BioPerl, databases and using the Perl DBI, and data visualization.

Prerequisite(s)/Corequisite(s): BIOI 1000 and CSCI 1620. CSCI 3320 and an introductory course in biology (e.g., Biology 1450) are strongly recommended but not required.

BIOI 4500  INDEPENDENT STUDY (1-3 credits)

This course allows students to research a topic of their interest that is not available in a formal course. The topic to be studied must be agreed upon by the student and the instructor.

Prerequisite(s)/Corequisite(s): Junior or Senior within the Bioinformatics undergraduate program. Not open to non-degree graduate students.

BIOI 4510  BIOINFORMATICS INTERNSHIP (1-3 credits)

The purpose of this course is to provide the students with an opportunity for practical application and further development of knowledge and skills acquired in the Bioinformatics undergraduate program. The internship gives students professional work experience and exposure to the challenges and opportunities faced by IT professionals in the workplace.

Prerequisite(s)/Corequisite(s): Junior/Senior standing and permission of Director of the School of Interdisciplinary Informatics. Not open to non-degree graduate students.

BIOI 4860  BIOINFORMATICS ALGORITHMS (3 credits)

The main objective of this course is to provide an organized forum for students to learn recent developments in Bioinformatics, particularly, from the algorithmic standpoint. The course will present basic algorithmic concepts in Bioinformatics and show how they are connected to molecular biology and biotechnology. Standard topics in the field such as restriction mapping, motif finding, sequence comparison, and database search will be covered. The course will also address problems related to Bioinformatics like next generation sequencing, DNA arrays, genome rearrangements and biological networks. (Cross-listed with BMI 8866).

Prerequisite(s)/Corequisite(s): CSCI 3320 and BIOL 1450; Or permission of instructor.

BIOI 4870  DATABASE SEARCH AND PATTERN DISCOVERY IN BIOINFORMATICS (3 credits)

The course provides students basic knowledge on database aspects related to bioinformatics. The course presents fundamental materials on database management systems, including data modeling, relational database design and queries, XML, as well as basics of information retrieval. Various approaches related to biodatabase search, machine learning and pattern discovery will be covered.

Prerequisite(s)/Corequisite(s): CSCI 3320

BIOI 4890  COMPUTERIZED GENETIC SEQUENCE ANALYSIS (3 credits)

The goal of this course is to introduce students to major topics in computerized analysis of genetic sequences. In particular the class will allow students to become familiar with the computational tools and software that aid in the modern molecular biology experiments and analysis of experimental results. Following the completion of this course, it is expected that the students will have a basic understanding of the theoretical foundations of the sequence analysis tools and develop competence in evaluating the output from these tools in a biological context. This course will emphasize hands-on experience with the programs for nucleotide and amino acid sequence analysis and molecular phylogeny.

Prerequisite(s)/Corequisite(s): Junior or senior-level standing in the Bioinformatics program or permission from the instructor. Not open to nondegree students.

BIOI 4950  SPECIAL TOPICS IN BIOINFORMATICS (3 credits)

This course is intended to provide a mechanism for offering instruction in subject areas that are not covered in other regularly scheduled courses. In general, courses offered under the BIOI 4950 designation will focus on evolving subject areas in bioinformatics.

Prerequisite(s)/Corequisite(s): Prerequisites of a specific offering of BIOI 4950 will be determined by the supervising faculty member and identified in the course proposal. It is anticipated that permission of the faculty member teaching the course will be required for registration.

BIOI 4960  SEMINAR IN BIOINFORMATICS (1 credit)

This is a variable-content course that engages students in current research in bioinformatics and develops skills in the oral and written presentation of scientific research..

Prerequisite(s)/Corequisite(s): Senior level status in the Bioinformatics program.

BIOI 4970  SENIOR PROJECT IN BIOINFORMATICS I (1 credit)

This course is the first part of a two-part series that allows students to work on a guided research project on a specific topic in bioinformatics. The goal of this course is for the student to decide on a research topic and to write a detailed proposal based on this topic that outlines the goals and objectives of the proposed research. The topic and proposal will be approved by the supervising faculty member.

Prerequisite(s)/Corequisite(s): Senior level status in the Bioinformatics program. Not open to nondegree students.

BIOI 4980  SENIOR PROJECT IN BIOINFORMATICS II (2 credits)

This course is the second part of a two-part series that allows the student to work on a guided research project on a specific topic in bioinformatics. The goal of this course is for the student to perform the research proposed in Part I of the course and to present the results of his or her work. Presentations will be made in the form of a report, written as a scientific research paper, and an oral defense.

Prerequisite(s)/Corequisite(s): Senior-level standing in the Bioinformatics program and successful completion of BIOI 4970. Not open to nondegree students.

BIOI 4990  INDEPENDENT STUDY IN BIOINFORMATICS (1-3 credits)

This is a variable-credit course designed for the junior or senior bioinformatics major who would benefit from independent reading assignments and research-type problems. Independent study enables coverage of topics not taught in scheduled course offerings.

Prerequisite(s)/Corequisite(s): Junior/senior standing, permission of supervising faculty member & approval of Bioinformatics UG Prog Comm Chair. A formal description of the problem area to be investigated, the resources to be used, & the results to be produced must be prepared.