BIOINF 7120 - Research Methods in Bioinformatics

North Terrace Campus - Semester 1 - 2018

Research Methods in Bioinformatics provides the basis for students wishing to undertake research in the field. Bioinformatics exists at the nexus between biological research, statistics and software engineering. Research Methods in Bioinformatics introduces students to the practical aspects of conducting research in the field bioinformatics, dealing with large datasets, ensuring that research is both auditable and reproducible and communication approaches and results with stakeholders.

  • General Course Information
    Course Details
    Course Code BIOINF 7120
    Course Research Methods in Bioinformatics
    Coordinating Unit School of Biological Sciences
    Term Semester 1
    Level Postgraduate Coursework
    Location/s North Terrace Campus
    Units 3
    Contact 12 x 1 hour Lectures; 12 x 2 hour Tutorials; 3 x 4 hour Workshops
    Available for Study Abroad and Exchange Y
    Corequisites Introduction to Programming or equivalent, Maths 1A/B or equivalent
    Restrictions Available to Graduate Certificate in Bioinformatics, Graduate Diploma in Bioinformatics and Master of Bioinformatics (Translational).
    Course Description Research Methods in Bioinformatics provides the basis for students wishing to undertake research in the field.
    Bioinformatics exists at the nexus between biological research, statistics and software engineering. Research Methods in Bioinformatics introduces students to the practical aspects of conducting research in the field bioinformatics, dealing with large datasets, ensuring that research is both auditable and reproducible and communication approaches and results with stakeholders.
    Course Staff

    Course Coordinator: Professor David Adelson

    Course Timetable

    The full timetable of all activities for this course can be accessed from Course Planner.

  • Learning Outcomes
    Course Learning Outcomes

    On successful completion of this course students should be able to:

    1. Analyse a biological question in order to develop a small programme of research.

    2. Explain the ethical implications of conducting a given bioinformatics research programme.

    3. Use contemporary version control systems to maintain a software or text repository.

    4. Explain the importance of reproducible research and its ethical basis.

    5. Devise approaches to ensure reproducibility of a research programme.

    6. Explain the limitations of a variety of sequencing technologies.

    7. Use a variety of database systems for simple datamining.

    8. Employ effective communication techniques within a teamwork environment.

    9. Identify areas of confusion that may arise when bioinformaticians communicate with biologists and develop approaches to deal with this.

     

    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)
    1-10
    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
    1,2,4,6,9
    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
    6,8,9
    Career and leadership readiness
    • technology savvy
    • professional and, where relevant, fully accredited
    • forward thinking and well informed
    • tested and validated by work based experiences
    3,6
    Intercultural and ethical competency
    • adept at operating in other cultures
    • comfortable with different nationalities and social contexts
    • Able to determine and contribute to desirable social outcomes
    • demonstrated by study abroad or with an understanding of indigenous knowledges
    2,4,9
    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
    8
  • Learning & Teaching Activities
    Learning & Teaching Modes

    Lectures are supported by face-to-face tutorials that build on student’s understanding of the details of running a research programme from the developmental through to the operational stages. The preparation and presentation of workshops based on practical aspects of running a research programme will help develop students’ capacity to work in small groups, analyse and develop solutions and communicate these to others.

    Workload

    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 and practicals), as well as non-contact time (e.g., reading and revision).
    Learning Activities Summary

    The course covers concepts in three themes: Conducting Research, Dealing with Data, Software and Communication.

     

    Conducting Research:

    • Project proposal/planning/management

    • Team work skills

    • Entrepreneurship

    • Research ethics

       

      Dealing with Data:

    • Sequencing technologies – limitations and error profiles

    • Datamining and databases

       

      Software:

    • Version control

    • Reproducible research approaches

       

      Communication:

    • Communicating with biologists

    • Report writing

    • Publishing

       

      The lecture stream for this will be:

      2x Project proposal, planning and management (ECIC?)

      1x Team work skills and entrepreneurship (ECIC?)

      1x Research ethics (ECIC?)

      2x Communication (ECIC?)

      1x Version control

      2x Reproducible research

      2x Sequencing technologies

      1x Datamining and databases

       

      Lectures will have associated tutorials.

       

      Workshops will be held three times in which students will present their research. The topics for the three workshops will be: Communicating with biologists and other stake holders; Reproducible research and version control; and Dealing with data.

  • Assessment

    The University's policy on Assessment for Coursework Programs is based on the following four principles:

    1. Assessment must encourage and reinforce learning.
    2. Assessment must enable robust and fair judgements about student performance.
    3. Assessment practices must be fair and equitable to students and give them the opportunity to demonstrate what they have learned.
    4. Assessment must maintain academic standards.

    Assessment Summary
    Assessment Task Task Type Percentage of total assessment Hurdle Yes/No Learning Outcome Approximate timing of assessment
    Tutorial tasks Formative & Summative

    20%

    No 1,2,4,5,6,7,9 Weekly
    Workshop presentations/reports Formative &Summative 40% No 3,4,5,7,8,9 4,8,12
    Exam Summative 40% No 1,2,4,5,6,7,9 Exam Period
    Assessment Detail

    Tutorial tasks (total of 20%)

    Each tutorial will include an assessment task which may be one of 1) a short answer quiz at the start of the tutorial or 2) a short written piece on the topic of the tutorial directed by provided questions, to be submitted at the beginning of the subsequent tutorial.

     

    Workshop presentations/reports (3x: total of 40%)

    Groups of students will be given a choice of topics in biology relating to bioinformatics to select from. In groups, the students will research approaches to analysing the biological system using bioinformatics techniques. The research will include analysis of the problems associated with the approaches. Individually, students will write a 1500 word report on their research. Students will present a 20 min group oral presentation as well as hand in a copy of their presentation and the associated report. Students will also complete a peer assessment for their group members, which will be taken into account in allocating the final mark. The report and the workshop presentation components would contribute equally to the assessment weighting. The contribution of the peer assessment task would make up 10% of the report component and be comprised a brief (less than one page) assessment of the contributions of each of the members of the group, including the assessing student.

     

    The assessment breakdown for each workshop will be 60% for the report and 40% for the group presentation.

     

    Theory exam (40%)

    The final theory exam will examine all components of the course. It will consist of short answer and long answer questions.

     

     

    Submission

    If 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.

    Course Grading

    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.

  • Student Feedback

    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.

  • Student Support
  • Policies & Guidelines
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