School of CSE - Details Needed for New Course Proposal Course Title: Bioinformatics Methods Proposer: Bruno Gaeta Rationale Why is the new course being proposed? This course replaces BINF2001 in the revised bioinformatics program, and consolidates the elements of BINF2001 and BINF3001 that are targeted at biologists who want to use bioinformatics. While this course would be core in the revised bioinformatics program, the change of emphasis and prerequisites would make it suitable as an elective (or even a core course in some majors) for life science students What are the academic objectives? The emphasis of the course is on using bioinformatics (rather than developing new bioinformatics applications) to solve problems in biology. Students will learn about the range of tools and resources available in sequence, microarray, proteomics and structure analysis, the data types they operate on, the computational approaches underlying them, their relative advantages and applications, and how to interpret the outputs of these tools intelligently. Students will also learn how to select suitable tools to address biological questions, and to evaluate new tools. They will receive hands-on training in the use of commonly used methods and learn the basics of scripting to automate bioinformatics analysis. Which programs/stage does it serve? Bioinformatics programs (3647, 3755, 3756, 3757, Bioinformatics/Commerce) in 3rd year or equivalent, as well as BSc (molecular biology, biochemistry, genetics, microbiology) as a 3rd year elective. Why can the same objectives not be achieved with existing courses? The current bioinformatics courses (BINF2001/3001) are suited exclusively for bioinformatics students as they assumed knowledge both in biology and computing. This makes them unavailable for students in other programs which still would find part of the courses relevant to their studies. How does the proposed course relate to other courses? BINF3010 and BINF3020 replace BINF2001 and BINF3001 and re-arrange content between these two courses so they become suitable for life science and computing students respectively, in addition to bioinformatics students. This course could also be offered as a postgraduate version suitable for Masters in Biotechnology, as a replacement for BINF9010 which is currently targeted at a mixed audience and suffers as a result. What overlap is there? If there is any overlap, why is this justified/not a problem? Stakeholders and Consultation Who are the potential stakeholders, who was consulted about the proposal (inside the School as well as outside), what was the result of that consultation? External stakeholders are mainly the school of BABS, who has been consulted Enrolment Impacts Likely enrolment (with justification), and impact on enrolments of other courses. The new courses should have an increased enrolment compared to current BINF courses as they would be open to students outside the bioinformatics program and would have less prerequisites. A course similar to BINF3010 is offered at the university of Sydney for life sciences majors and has enrolments around 90 students/year. Justification of Prerequisites (or lack thereof) The course assumes knowledge of molecular biology as the methods discussed analyse data obtained through molecular biological methods, and are used to answer molecular biology questions. Any Courses this is Replacing, and Why? BINF3010/3020 replace BINF2001/3001 Delivery and Assessment Anything noteworthy about delivery mode, assessment (with justification). Handbook Entry Textbooks/References Syllabus Indicative syllabus / overview of contents (at a level of detail well beyond that of the handbook entry) Sequence analysis: Sequence databases Sequence comparison: uses and tools Sequence database similarity searching: uses and tools Multiple sequence alignment tools Molecular phylogeny Population genetics Protein family databases Genome informatics Structure bioinformatics: Protein structure fundamentals Structure databases Structure prediction Proteomics: MS spectra analysis and interpretation Glycomics Protein-protein interaction databases Microarrays: Processing and statistical analysis of microarray data Using and scripting in R Statistical genetics Effect on School Resources: 1. Who is proposed to teach the proposed new course, and what impact would this have on their planned/current allocation? Coordinated by Bruno Gaeta or Mike Bain, with guest lecturers from BABS 2. What sort of tutorial component is proposed, if any? Weekly hands-on computer lab component. 3. What is the likely impact on lab utilisation (this relates to assignment and project work as well as scheduled labs? This course would run weekly computer labs where students use bioinformatics tools. The setup of the computer labs would not change relative to their current use in BINF2001. However if the proposal results in increased enrolments, there may be increased need for lab space for the scheduled labs. 4. Any other resource needs? E.g. special print/disk quota, access to servers, access to special machines, special labs.