Coronavirus (Covid-19) Information

Module MSE-4080:
Bioinformatics & Genomic Data

Module Facts

Run by School of Medical Sciences

15 Credits or 7.5 ECTS Credits

Semester 1 & 2

Organiser: Dr David Pryce

Overall aims and purpose

The main challenge for application of genomic data is in its analysis and interpretation. The aim of this module is to enable students to gain the knowledge and understanding required to critically interpret existing genomic research, and develop the skills to formulate their own research questions as well as to collect, analyse and interpret their own data using a basic range of statistical and bioinformatics techniques. Bioinformatics and statistical approaches introduced in this module will form a solid foundation for the topic specific computational and analytical techniques which will form part of subsequent modules.

Course content

  • Aligning genome data to reference sequence using up to date alignment programmes (e.g. BWA)
  • Assessment of data quality through application of quality control measures
  • How to determine the analytical sensitivity and specificity of genomic tests
  • Use of tools to call sequence variants e.g. annotation of variant-call files using established databases
  • Filtering strategies of variants, in context of clinical data, and using publically-available control data sets
  • Use of multiple database sources, in silico tools and literature for pathogenicity evaluation, and familiarity with the statistical programmes to support this
  • Principles of integration of laboratory and clinical information, and place of best- practice guidelines for indicating the clinical significance of results
  • Principles of downstream functional analysis e.g. knock-outs, and other cellular models

Assessment Criteria

good

Merit (B- to B+) (range 60-69%)

Primary criteria Good students demonstrate strong knowledge & understanding of most but not all of the subject area. Limited evidence of background study. The answers are focussed with good structure. Arguments are presented coherently, mostly free of factual/computational errors. Some limited original interpretation. Well know links between topics are described. Problems are addressed by existing methods/approaches. Good presentation with accurate communication

Secondary Criteria

B+ Good

  • Exceeds expectations for most primary criteria
  • Command of subject but with gaps in knowledge
  • Some ideas/arguments original

B Mid-level

  • Meets all primary criteria
  • Strong factual knowledge and understanding
  • Ideas/arguments are well presented by few are original

B- Meets requirements of class

  • Meets most but not all primary criteria
  • Strong factual knowledge with minor weaknesses in understanding
  • Most but not all ideas/arguments are well presented and few are original

threshold

Pass (C- to C+) (range 50-59%)

Primary criteria A pass level demonstrates knowledge and comprehension of key areas & principles, with understanding of the main elements of the subject area, although gaps and weaknesses in the argument are evident. No real evidence of background study and wider reading is evident. Answers are focussed on questions but also with some irrelevant material and weaknesses in structure & argument. Answers have several factual/computational errors. Lack of originality and interpretation. No links between topics are described. Limited problem solving skills. Some weaknesses in presentation accuracy & delivery.

Secondary Criteria

C+ Good within the class

  • Exceeds expectations for some primary criteria
  • Strong factual knowledge with some weaknesses in understanding
  • Ideas/arguments are limited but are well presented

C Mid-level

  • Matches all primary criteria
  • Moderate factual knowledge with some weaknesses in understanding
  • Ideas/arguments are limited presented with weaknesses in logic/presentation

C- Meets requirements of class

  • Matches most but not all primary criteria
  • Moderate factual knowledge with several weaknesses in understanding
  • Ideas/arguments are limited presented with weaknesses in logic/presentation

excellent

Distinction (A- to A) (range 70-100%)

Primary criteria Comprehensive knowledge & detailed understanding. Clear evidence of extensive background study & originality. Highly focussed, relevant and well structured answers. Arguments logically presented and defended with evidence and examples. Excellent presentation skills with very accurate communication.

Secondary Criteria A Outstanding

  • Exceeds expectations for most primary criteria
  • Complete command of subject and other relevant areas
  • Ideas/arguments are highly original

A+ Excellent

  • Exceeds expectations for some primary criteria
  • Complete command of subject
  • Ideas/arguments are highly original

A Good - Meets all primary criteria - Command of subject but with minor gaps in knowledge areas - Ideas/arguments are mostly original

A- Meets requirements of Class

  • Meets most but not all primary criteria
  • Complete command of subject but with some gaps in knowledge
  • Ideas/arguments are mostly original

Learning outcomes

  1. Demonstrate in-depth subject expertise and understanding of the place of Professional Best Practice Guidelines in reporting of genomic variation.

  2. Demonstrate in-depth subject expertise and understanding of bioinformatic pipelines and computational methodologies in generation and analysis of 'omic data'

  3. Demonstrate in-depth subject expertise and understanding of interrogate data sources, e.g. genomic sequences, protein sequences, variation, pathways, (EVS, dbSNP, ClinVar, etc.)

Assessment Methods

Type Name Description Weight
Reflective report 50
Coursework. 50

Teaching and Learning Strategy

Hours
Lecture
  • Lecture sessions will be held through first week of delivery period.
  • Lectures will be delivered in 4 x 3hr sessions, on days 1, 2, 3 and 4 of the teaching week
12
Tutorial
  • Tutorials may vary in length, be conducted via individual or groups sessions and may utilise online conference facilities.
  • Timing are expected to be held within week 2 and 3 of the module (self study period).
  • Tutorial topics may be from any area of the module, including assessments, and/or from self-researched outside reading.
  • Students will supply topics for discussion and review.
3
Private study
  • Self-directed study to develop in-depth knowledge and understanding, data processing/analysis and assessment preparation
126
Seminar
  • Seminars sessions will present posters, or formal oral presentations or flash talks
  • Sessions will be delivered via 2 x 1.5hr sessions, on day 5 of the teaching week
3
Practical classes and workshops
  • Laboratory (wet lab), computer sessions or workshops.
  • Sessions will be delivered through first week of delivery period in 2 x 3hr sessions, on days 2 and 4 of the teaching week
6

Transferable skills

  • Literacy - Proficiency in reading and writing through a variety of media
  • Numeracy - Proficiency in using numbers at appropriate levels of accuracy
  • Computer Literacy - Proficiency in using a varied range of computer software
  • Self-Management - Able to work unsupervised in an efficient, punctual and structured manner. To examine the outcomes of tasks and events, and judge levels of quality and importance
  • Exploring - Able to investigate, research and consider alternatives
  • Information retrieval - Able to access different and multiple sources of information
  • Inter-personal - Able to question, actively listen, examine given answers and interact sensitevely with others
  • Critical analysis & Problem Solving - Able to deconstruct and analyse problems or complex situations. To find solutions to problems through analyses and exploration of all possibilities using appropriate methods, rescources and creativity.
  • Safety-Consciousness - Having an awareness of your immediate environment, and confidence in adhering to health and safety regulations
  • Presentation - Able to clearly present information and explanations to an audience. Through the written or oral mode of communication accurately and concisely.
  • Teamwork - Able to constructively cooperate with others on a common task, and/or be part of a day-to-day working team
  • Mentoring - Able to support, help, guide, inspire and/or coach others
  • Caring - Showing concern for others; caring for children, people with disabilities and/or the elderly
  • Management - Able to utilise, coordinate and control resources (human, physical and/or financial)
  • Argument - Able to put forward, debate and justify an opinion or a course of action, with an individual or in a wider group setting
  • Self-awareness & Reflectivity - Having an awareness of your own strengths, weaknesses, aims and objectives. Able to regularly review, evaluate and reflect upon the performance of yourself and others
  • Leadership - Able to lead and manage, develop action plans and objectives, offer guidance and direction to others, and cope with the related pressures such authority can result in

Resources

Resource implications for students

None foreseen

Reading list

PGT (level 7). A literature reading list will predominately be peer reviewed papers. The list will be dynamic and populated when module is active. Journals that are currently not available for direct access, will require digitising.