BIOINF 3000 - Bioinformatics III
North Terrace Campus - Semester 2 - 2020
General Course Information
Course Code BIOINF 3000 Course Bioinformatics III Coordinating Unit School of Biological Sciences Term Semester 2 Level Undergraduate Location/s North Terrace Campus Units 3 Contact 12 x 1 hour lectures, 12 x 2 hour tutorials, 12 x 2 hour practicals Available for Study Abroad and Exchange N Assumed Knowledge GENETICS 2510 and BIOCHEM 2500 or BIOCHEM 2502 Course Description Recent technological advances have brought large-scale DNA sequencing within the reach of small companies and research laboratories, and opened the door for research and applied uses for sequencing. This course teaches analysis of these data sets, and interpretation of the significance of the patterns found therein. It also provides an understanding of the specific considerations of different sequencing technologies, as well as an understanding of the algorithms used to align, assemble, and annotate sequence data.While DNA sequencing is useful for sequencing genomes, it also has widespread applications in methods used to understand interactions, whether they be within a cell or organism (signaling, regulation, protein function) or between organisms (at the level of populations, symbioses, and communities). This course also provides an understanding of these systems.
Course Coordinator: Dr Dan Kortschak
The full timetable of all activities for this course can be accessed from Course Planner.
Course Learning Outcomes1. Perform simple alignment, assembly, and annotation algorithms for "toy" data sets.
2. Formulate and justify appropriate choices in technology, strategy, and analysis for a range of projects involving DNA, RNA, or protein sequence data.
3. Employ command line sequence analysis tools to analyze small real-world biological sequence data sets, and demonstrate familiarity with the syntax and options required to generate meaningful interpretations.
4. Discuss the contents of prokaryotic and eukaryotic genomes, the general function and origin of the main components, and considerations and difficulties in genome sequencing associated with these.
5. Demonstrate understanding of common methods and applications for analysis of gene expression.
University Graduate Attributes
This course will provide students with an opportunity to develop the Graduate Attribute(s) specified below:
University Graduate Attribute Course Learning Outcome(s) Deep discipline knowledge
- informed and infused by cutting edge research, scaffolded throughout their program of studies
- acquired from personal interaction with research active educators, from year 1
- accredited or validated against national or international standards (for relevant programs)
1, 2, 3, 5 Critical thinking and problem solving
- steeped in research methods and rigor
- based on empirical evidence and the scientific approach to knowledge development
- demonstrated through appropriate and relevant assessment
2, 3, 5 Teamwork and communication skills
- developed from, with, and via the SGDE
- honed through assessment and practice throughout the program of studies
- encouraged and valued in all aspects of learning
1, 4 Career and leadership readiness
- technology savvy
- professional and, where relevant, fully accredited
- forward thinking and well informed
- tested and validated by work based experiences
2, 3, 5 Self-awareness and emotional intelligence
- a capacity for self-reflection and a willingness to engage in self-appraisal
- open to objective and constructive feedback from supervisors and peers
- able to negotiate difficult social situations, defuse conflict and engage positively in purposeful debate
Learning & Teaching Activities
Learning & Teaching ModesPracticals are supported by lectures and tutorials that build students' understanding of the details of designing and performing bioinformatics analysis pipelines.
The information below is provided as a guide to assist students in engaging appropriately with the course requirements.A student enrolled in a 3 unit course, such as this, should expect to spend, on average 12 hours per week on the studies required. This includes both the formal contact time required to the course (e.g., lectures, tutorials and practicals), as well as non-contact time (e.g., reading and revision).
Learning Activities SummaryThe course covers theoretical and practical aspects of conducting bioinformatics research analyses using contemporary tools such as the R statistical environment using R Studio, literate programming using R markdown notebooks and presenting analyses.
The course will involve a scaffolded development of techniques used to perform bioinformatics and statistical analyses of small biological datasets with supporting lectures to establish an understanding of the background theory for the practical studies.
The University's policy on Assessment for Coursework Programs is based on the following four principles:
- Assessment must encourage and reinforce learning.
- Assessment must enable robust and fair judgements about student performance.
- Assessment practices must be fair and equitable to students and give them the opportunity to demonstrate what they have learned.
- Assessment must maintain academic standards.
Assessment task Type of assessment Percentage of total assessment Hurdle Outcomes being assessed Approximate timing of assessment Practical tasks Formative and Summative 60 No 1-5 Weeks 2-12 Exam Summative 40 No 1-5 Exam period
Assessment DetailPractical tasks (total of 60%)
Each practical will include an assessment task which will be dependent on the aspects of the work being performed in the practical, to be submitted at the beginning of the subsequent practical. Each report will be approximately 1000-1500 words.
In order to allow appropriately scoped practicals that are within the capabilities of the students and that will allow adequate coverage of the material being taught, approximately 6 assessment tasks will comprise this component of the course.
Assessments for practical tasks will be returned to students within two weeks of completion of the task to allow students to incorporate assessor feedback into their learning and practice.
Exam (total of 40%)
The final theory exam will examine all components of the course. It will consist of short answer and long answer questions. Duration of exam is 3 hours.
SubmissionIf an extension is not applied for, or not granted then a penalty for late submission will apply. A penalty of 10% of the value of the assignment for each calendar day that the assignment is late (i.e. weekends count as 2 days), up to a maximum of 50% of the available marks will be applied. This means that an assignment that is 5 days late or more without an approved extension can only receive a maximum of 50% of the marks available for that assignment.
Grades for your performance in this course will be awarded in accordance with the following scheme:
M10 (Coursework Mark Scheme) Grade Mark Description FNS Fail No Submission F 1-49 Fail P 50-64 Pass C 65-74 Credit D 75-84 Distinction HD 85-100 High Distinction CN Continuing NFE No Formal Examination RP Result Pending
Further details of the grades/results can be obtained from Examinations.
Grade Descriptors are available which provide a general guide to the standard of work that is expected at each grade level. More information at Assessment for Coursework Programs.
Final results for this course will be made available through Access Adelaide.
The University places a high priority on approaches to learning and teaching that enhance the student experience. Feedback is sought from students in a variety of ways including on-going engagement with staff, the use of online discussion boards and the use of Student Experience of Learning and Teaching (SELT) surveys as well as GOS surveys and Program reviews.
SELTs are an important source of information to inform individual teaching practice, decisions about teaching duties, and course and program curriculum design. They enable the University to assess how effectively its learning environments and teaching practices facilitate student engagement and learning outcomes. Under the current SELT Policy (http://www.adelaide.edu.au/policies/101/) course SELTs are mandated and must be conducted at the conclusion of each term/semester/trimester for every course offering. Feedback on issues raised through course SELT surveys is made available to enrolled students through various resources (e.g. MyUni). In addition aggregated course SELT data is available.
- Academic Support with Maths
- Academic Support with writing and speaking skills
- Student Life Counselling Support - Personal counselling for issues affecting study
- International Student Support
- AUU Student Care - Advocacy, confidential counselling, welfare support and advice
- Students with a Disability - Alternative academic arrangements
- Reasonable Adjustments to Teaching & Assessment for Students with a Disability Policy
Policies & Guidelines
This section contains links to relevant assessment-related policies and guidelines - all university policies.
- Academic Credit Arrangement Policy
- Academic Honesty Policy
- Academic Progress by Coursework Students Policy
- Assessment for Coursework Programs
- Copyright Compliance Policy
- Coursework Academic Programs Policy
- Elder Conservatorium of Music Noise Management Plan
- Intellectual Property Policy
- IT Acceptable Use and Security Policy
- Modified Arrangements for Coursework Assessment
- Student Experience of Learning and Teaching Policy
- Student Grievance Resolution Process
Students are reminded that in order to maintain the academic integrity of all programs and courses, the university has a zero-tolerance approach to students offering money or significant value goods or services to any staff member who is involved in their teaching or assessment. Students offering lecturers or tutors or professional staff anything more than a small token of appreciation is totally unacceptable, in any circumstances. Staff members are obliged to report all such incidents to their supervisor/manager, who will refer them for action under the university's student’s disciplinary procedures.
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