| Course Code | BINF3010/9010 | ||||||
| Course Title | Applied Bioinformatics | ||||||
| Convenor | Bruno Gaeta | ||||||
| Admin | Bruno Gaeta | ||||||
| Classes |
This course is worth 6 units of credit. Lectures are held online. Lectures will either be pre-recorded with a discussion session, or held live (with recording) at the following times:
Laboratories (shown in Bold on the course schedule) will be set up as self-directed exercises. The timetabled lab session on Thursdays 11am-1pm will be for consultation and discussion. Labs will open one week before the timetabled lab slot, and the lab quizzes will be due one week after the lab slot. The midterm exam details will be advised closer to the date. Important note: most labs will require the use of computers running a UNIX-based operating system. It is recommended that students who are not familiar with this environment attempt the optional Intro lab scheduled in week 1. This lab will include a live discussion of how to access the necessary resources remotely. Timetable for all classes |
||||||
| Consultations | By appointment | ||||||
| Units of Credit | 6 | ||||||
| Course Website |
https://moodle.telt.unsw.edu.au/course/view.php?id=51304
Note that webcms3 is used only for the course outline and is not otherwise monitored |
||||||
| Handbook Entry | http://www.handbook.unsw.edu.au/undergraduate/courses/current/BINF3010.html |
Bioinformatics (the use of computing methods for the management and analysis of molecular biology data) has become an integral component of biomolecular sciences, especially genomics and proteomics. This course focuses on the practical use of bioinformatics methods and resources for the analysis of DNA and protein sequences and structures, as well as results from microarray and proteomics, with emphasis on their evolutionary underpinnings and statistical foundations.
General course aims
BINF3010 is a core course in the BE (Bioinformatics) program, and an elective in Science programs.
BINF9010 is a core course in the MIT (bioinformatics) program, and an elective in a number of other graduate programs including Biomedical Engineering and Biostatistics.
BINF3010/9010 does not cover bioinformatics algorithms in depth (these are covered in BINF6111 and BINF6112). The course focuses on the intelligent application of common bioinformatics methods to assist in biological discovery and is primarily targeted at students with a biology background. For students with a computing background the course provides an introduction to bioinformatics and its biological context.
This course is about using bioinformatics methods for biological research. It is not about developing new bioinformatics methods. As such it assumes a working knowledge of molecular biology. Biology provides the context of the content and all the examples used in its presentation, and students with no knowledge of biology are likely to fail the course (this is especially important for postgraduate BINF9010 students as no biology prerequisite is available for these students). In terms of computing, the course only assumes ability to use computers, although a working knowledge of the UNIX command line and of the basics of the R statistical computing environment is an advantage. Some resources will be provided for students new to UNIX and R.
At the end of this course, students should be able to:
This course contributes to the development of the following graduate capabilities:
The skills involved in scholarly enquiry – students need to research, compare and evaluate different bioinformatics methods as part of the practical work and final examination
An in-depth engagement with the relevant disciplinary knowledge in its interdisciplinary context – bioinformatics is presented in the context of its applications to biology, and of the computer science methods it draws on
The capacity for analytical and critical thinking and for creative problem-solving – laboratory work and assignments require students to solve a range of problems by choosing appropriate bioinformatics methods and applying them
The ability to engage in independent and reflective learning – the midsession and final examinations require students to reflect and provide a critical synthesis of the course contents
The skills required for collaborative and multidisciplinary work – the laboratory exercises are to be carried out in teams of mixed student background
The skills of effective communication – written communication is assessed principally through laboratory reports and the final examination. Effective communication between students of different backgrounds is also necessary for carrying out the laboratory assignments.
Bioinformatics now pervades biological research, and new methods and technologies are constantly developed. This course is aimed at teaching bioinformatics from a user ’s perspective (as opposed to that of a developer ), to emphasise the use of bioinformatics to assist in biological discovery. Since bioinformatics constantly evolves the goal is not to teach the use of specific tools and methods but to focus on principles , limitations and assumptions of common approaches to provide the means for students to research and evaluate new methods and apply them intelligently to produce meaningful results.
Online delivery
In 2020 the course is being delivered online. This is the first time this is happening and although we are using methods that have been successful in other courses, this is new and is likely to present a challenge. The methods we are proposing (subject to change) are as follow:
The Student Code of Conduct ( Information , Policy ) sets out what the University expects from students as members of the UNSW community. As well as the learning, teaching and research environment, the University aims to provide an environment that enables students to achieve their full potential and to provide an experience consistent with the University's values and guiding principles. A condition of enrolment is that students inform themselves of the University's rules and policies affecting them, and conduct themselves accordingly.
In particular, students have the responsibility to observe standards of equity and respect in dealing with every member of the University community. This applies to all activities on UNSW premises and all external activities related to study and research. This includes behaviour in person as well as behaviour on social media, for example Facebook groups set up for the purpose of discussing UNSW courses or course work. Behaviour that is considered in breach of the Student Code Policy as discriminatory, sexually inappropriate, bullying, harassing, invading another's privacy or causing any person to fear for their personal safety is serious misconduct and can lead to severe penalties, including suspension or exclusion from UNSW.
If you have any concerns, you may raise them with your lecturer, or approach the School Ethics Officer , Grievance Officer , or one of the student representatives.
Plagiarism is defined as using the words or ideas of others and presenting them as your own. UNSW and CSE treat plagiarism as academic misconduct, which means that it carries penalties as severe as being excluded from further study at UNSW. There are several on-line sources to help you understand what plagiarism is and how it is dealt with at UNSW:
Make sure that you read and understand these. Ignorance is not accepted as an excuse for plagiarism. In particular, you are also responsible that your assignment files are not accessible by anyone but you by setting the correct permissions in your CSE directory and code repository, if using. Note also that plagiarism includes paying or asking another person to do a piece of work for you and then submitting it as your own work.
UNSW has an ongoing commitment to fostering a culture of learning informed by academic integrity. All UNSW staff and students have a responsibility to adhere to this principle of academic integrity. Plagiarism undermines academic integrity and is not tolerated at UNSW. Plagiarism at UNSW is defined as using the words or ideas of others and passing them off as your own.
If you haven't done so yet, please take the time to read the full text of
The pages below describe the policies and procedures in more detail:
You should also read the following page which describes your rights and responsibilities in the CSE context:
Computer laboratory work
– 30%
Computer laboratories will emphasise the use of common bioinformatics applications. Most labs will be assessed using an online moodle quiz. Laboratory quizzes will not be accepted after their set submission deadline.
The labs evaluate your ability to use bioinformatics software and interpret results in the light of the theoretical background discussed in the lectures. The labs have been structured so that they can be completed on your own on your own computer as much as possible. The lab sessions are meant to be for consultation and discussion of any difficulties you have encountered doing the lab. It is recommended that you attempt to complete the lab by yourself before the corresponding lab session so you can bring your questions for the online lab session.
Midterm examination – 20% An examination held during the term covering the first part of the lecture and lab material.
Final examination
– 40%
A 2-hour examination covering the second part of the lecture material (and some material covered in the labs) taking place in the exam period.
Biology quizzes – 2% Short quizzes to remind you of biology fundamentals relevant to the bioinformatics methods being studied. Quizzes will be administered online through the course website.
Computer laboratory work – 28% Computer laboratories will emphasise the use of common bioinformatics applications. Most labs will be assessed using an online moodle quiz. Laboratory quizzes will not be accepted after their set submission deadline. The labs evaluate your ability to use bioinformatics software and interpret results in the light of the theoretical background discussed in the lectures. The labs have been structured so that they can be completed on your own on your own computer as much as possible. The lab sessions are meant to be for consultation and discussion of any difficulties you have encountered doing the lab. It is recommended that you attempt to complete the lab by yourself before the corresponding lab session so you can bring your questions for the online lab session.
Important notes :
Midterm examination – 20% An examination held during the term covering the first part of the lecture and lab material.
Final examination – 40% A 2 hour examination covering the second part of the lecture material (and some material covered in the labs) taking place in the exam period.
Course lecturers:
Each section of the course is taught by a lecturer who actively works in the specific area.
| Week | Starting | Lec Mon 10-12 | Lec 2 Wed 10-12 | Lab Thu 11-1 |
| 1 | Jun 1 | Sequence Analysis Gaeta | Sequence Analysis Gaeta | Intro lab (optional) Gaeta |
| 2 | Jun 8 | Public holiday | Sequence Analysis Gaeta | Alignment and databases Gaeta |
| 3 | Jun 15 | Sequence Analysis Gaeta | Genome Informatics Lan | MSA and phylogeny Gaeta |
| 4 | Jun 22 | RNA-Seq Corley | Statistics Humburg | Genome Assembly Gaeta |
| 5 | Jun 29 | Statistics Humburg | Proteomics Raftery | Midterm (TBC) |
| 6 | Jul 6 | Flexibility week | ||
| 7 | Jul 13 | Structural Bioinformatics Curmi | Structural Bioinformatics Curmi | Visualisation and analysis using R Gaeta |
| 8 | Jul 20 | Structural Bioinformatics Curmi | Structural Bioinformatics Curmi | RNA-Seq Corley |
| 9 | Jul 27 | Structural Bioinformatics Curmi | PTMs and Proteogenomics Wilkins | Proteomics Wilkins |
| 10 | Aug 3 | ncRNA analysis Vafaee | Protein Interactions and Networks Wilkins | Structure Comparison Gaeta |
There is no textbook for this course. Individual lecturers will provide lists of reference books and articles.
Readings and discussion boards will be made available on the course website, which can be accessed through Moodle.
A number of bioinformatics textbooks are available through the UNSW Library for reference reading. One starting point for assistance is: info.library.unsw.edu.au/web/services/services.html
Feedback on this course and on individual lecturers will be gathered through a survey at the end of session, as part of the MyExperience process. Feedback from this survey is the basis for improving the course in subsequent years. Given the course is running online this year in quite a different format, the feedback will be extremely useful in evaluating our online implementation. Feedback from last year was that there was too much content in the course. As a result some of the content was revised and pruned to keep only the most relevant aspects. Also as a result of student feedback that some students had difficulties using command line programs, some of the labs were modified to allow using web resources (when available) as an alternative to command line programs.
If your work in this course is affected by unforeseen adverse circumstances, you should apply for Special Consideration through MyUNSW, including documentation on how you have been affected. If your request is reasonable and your work has clearly been impacted, then
Note the use of the word "may". None of the above is guaranteed. It depends on you making a convincing case that the circumstances have clearly impacted your ability to work.
If you are registered with Disability Services, please forward your documentation to Bruno Gaeta within the first two weeks of semester.
Occupational Health and Safety: students are reminded of the university’s OHS policies and recommendations, which are accessible at
www.riskman.unsw.edu.au/ohs/ohs.shtml
Information specific to OHS in the school of CSE, and especially of ergonomics issues related to use of computers can be accessed at
http://www.cse.unsw.edu.au/~ohs/
Equity and diversity: note that students who have a disability that requires some adjustment in their learning and teaching environment are encouraged to discuss their study needs with the course convener prior to, or at the commencement of the course, or with the Equity Officer (Disability) in the Equity and Diversity Unit (9385 4734). Information for students with disabilities is available at:
Resource created Tuesday 19 May 2020, 10:07:53 AM, last modified Thursday 21 May 2020, 08:10:06 PM.