BMS5021 S1 2025 - Topic 2 Assessment
Bioinformatics Data Formats & Algorithms Oral Presentation
Task Instructions
1. The Brief
The head of a biomedical research lab has heard you have experience in bioinformatic analysis and has tasked you and your colleagues with performing a pilot RNAseq analysis to help them understand the transcriptomic changes that occur at a cellular level in response to radiation.
You will do this by characterising the changes in gene expression induced by gamma radiation treatment in their C. elegans model, and identifying up-and down-regulated genes as well as the biological processes these genes are associated with.
This research lab also has a particular interest in a gene (the name of this gene will be supplied on Moodle) which they have asked you to investigate specifically. In addition to your other findings, they would like to know whether the expression of this gene is regulated by the cellular response to radiation.
The lab has asked you to present at an upcoming lab meeting to give an overview of your analytical pipeline and findings. As they would like to learn more about bioinformatics, they have asked that you explain your process and give some suggestions for alternative tools that could also be used at each stage.
You will need to present your analysis in a manner appropriate for a scientific audience, explaining your work while keeping focus on the ultimate goal of helping these researchers answer their biological question. Concise explanations and good visual communication will be key to doing this successfully!
2. Learning Outcomes // Skill Development
This task addresses the following unit learning outcomes:
● ULO2 Explain the health data life cycle and the relevance of computation in modern life sciences research.
● ULO3 Explain how nucleotide and protein sequence and structure data are represented and processed in computational biology.
● ULO4 Evaluate the merits and limitations of the major bioinformatics algorithms to solve specific computational biomedical problems.
● ULO5 Use bioinformatic tools and algorithms to analyse nucleotide or protein sequences.
Completing this task will further your skills in using tools & technology, problem identification & solving, teamwork and communication.
3. Assessment Components
You will present your analysis as a group to the broader ‘lab group’ (peers and unit staff) in your Week 8 lecture and workshop session. Your group will need to submit a .pdf file of your slides before the session commences.
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Component
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Weighting
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Submission details
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Due date
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Oral presentation and response to questions
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30%
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● Slides submitted via Moodle
dropbox (.pdf form)
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28/04/2025 8.00 am
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4. Assessment Requirements and Expectations
Your group’s presentation should be no more than 10 minutes in length. 5 minutes will be allowed for questions afterwards. Speaking time is to be divided equally between group members. You should prepare a slide deck with key points to help convey your ideas and should include relevant figures.
Note: At 9 minutes 30 seconds you will receive a warning that your time will soon elapse. After 10 mins, you will be interrupted, and the remainder of your presentation will not be assessed.
Your presentation needs to include the following content:
• Introduction
o Goals of the presentation (remember the context – you are at a lab meeting reporting your findings to researchers)
o Overview of RNAseq data analysis using bioinformatics algorithms
Include a brief background on the technique of RNA sequencing
• Briefly explain the biological question that underpins the experiment and analysis carried out in the workshop sessions
o Intention of the experiment i.e. understanding how C. elegans responds to gamma radiation at the cellular level
o Dataset used for the analysis (what was done to produce this data?)
o Aim of the analysis you have performed
• Brief summary of the workflow/pipeline/steps, describing the algorithm/tool used at each stage, and suggesting one alternative (if applicable) for each that could also be used. Include discussion of:
o The importance of the parameters that were used, and how these affect the results of the analysis (Hint: Not parameters like memory allowance, but rather those that change the behaviour of the algorithm)
o The importance of post-processing of sequence data (Why are these steps carried out?) Note: you will need to do some searching to find alternatives for each tool 一 there are plenty so this will not be difficult
• Explain the overall transcriptomic response to radiation from the DE gene list you obtained
o Specify the parameters used to obtain the DE gene list and gene ontology results
Note: These do not need to be the default parameters in the DE R script provided in the workshop 一 try changing these parameters and see how this affects your results
o Show which genes are up- and down-regulated (think about how this can be communicated visually)
o Explain your gene ontology results and what this tells us about which kinds of genes were differentially expressed in response to the radiation treatment
• Explain how the expression of your team’s specific assigned gene changed (or perhaps didn’t change!) in response to the radiation treatment
o Was it up- or down-regulated? Was the change statistically significant?
o Think about how best to visually show the expression of a single gene between different samples/groups
o We have not given you a ready-to-use solution for this. You will need to use your critical thinking and data science skills!
• Give an overall conclusion(s) that summarises the outcomes of your analysis
o Final summary of your findings from the analysis carried out in the workshop session and in your own time
Remember the purpose of a conclusion is to give the audience a simple“take-home
message”一 keep it simple and focus on what you think are the most important messages from your findings
• References
o Please use APA 7th style.
o Following convention for scientific presentations, references must be included on the same slide the citation is made. Do not put references on a separate slide at the end of the presentation – this is not helpful for an audience who may want to follow up on specific references.
Your presentation will also be assessed for organisation, clarity, use of language and your responses to questions. See the assessment rubric available on the BMS5021 Moodle site (Assessment section) for a detailed breakdown.
5. Recommendations for Effective Assessment
● Use appropriate language and work to logically sequence your ideas - assume the lab group
(your audience) are literate in the areas of Biology and Bioinformatics understanding, though are not experts in this particular area.
● Use good quality figures to help convey your ideas and refer to these during your presentation.
● Schedule time to practise your presentation as a group.
● For additional assistance on how to plan and prepare your presentation, check out LearnHQ. You can also book a 1:1 consultation for language and learning advice.
6. Preparation
You are asked to choose a group of 3-4 via Moodle. You can choose to work in these groups during Topic 2 workshop sessions. It is strongly recommended that you maintain contact with your group in your own time to continue making progress on the task. If you are experiencing difficulties working with your group, please first endeavour to resolve it amongst yourselves, though do not hesitate to contact staff if issues continue.
Your attendance and engagement in workshops of Topic 2 will be critical for effective completion of this task. It is recommended you stay on track by completing each week as mentioned in the workshop manual.
Furthermore, staying up to date with weekly readings and lectures is strongly recommended.
7. Assessment and Feedback
You will receive a group mark and a written comment for your presentation content, and an individual mark for your presentation/communication skills.
A detailed marking rubric for this assessment can be found on the BMS5021 Moodle site (Assessment section).
8. Any Questions?
If you have questions about this task, please:
● Add them to the Assessment discussion forum on Moodle
● Ask in weekly workshop sessions
● Ask the teaching team (remember that all communications via email or other mediums must adhere to the university’s professionalism standards)