around 1000 words
BIOL2254 - Assessment 3 Semester 2, 2021 Page 1 of 3 RMIT Classification: Trusted Bioinformatics Tutorial 3: Article Analysis and Press Release Overview: An important skill as a scientist is being able to effectively communicate complex topics to a general audience. In this assignment, you will read and analyse a journal article that covers a recent advance in a bioinformatics-related field (Part 1). Using the knowledge gained from this analysis and associated background reading, you will write a short scientific press release that explains the importance and broader context for your selected paper (Part 2). This should be aimed towards a general scientific audience. Part 1 (50 points): With your selected research paper, answer the following questions: • What is the fundamental research question or bioinformatics problem that this paper is trying to address? (100 words) (10 points) • What data has been used to answer the research question? In the case of a new tool/technique, what data is used to validate the tool/technique being presented? (100 words) (10 points) • Describe one main bioinformatics technique used in this paper. How does this technique work, and how does it help the researchers answer their question? (150 words) (10 points) • Describe the controls used in this study. Are these controls appropriate? Are there additional controls (or control experiments) you would use? (150 words) (10 points) • What alternative bioinformatics technique could be used to tackle the question/problem addressed in this paper? Describe how the suggested technique helps address the research question/problem (100 words) (10 points) Part 2 (50 points): Using your selected paper, write a short scientific press release that highlights the importance and broader context of your chosen paper to a general scientific audience. This should be 400 words in length (+/-10%, excluding reference list and in-text citations), and could cover: • The relevant background to the chosen paper: In what context has this work been done? What knowledge are they building on? What important concepts does the reader need to understand in order to understand the chosen paper? • Major results/conclusions/contributions for the chosen paper: What new knowledge has this paper added to the field? Have they introduced a new tool or analysis technique? Have they used existing bioinformatics techniques to answer a fundamental biological question? • Future directions for this research: What impact is this research likely to have on future work? Are there obvious follow-up studies that lead on from this research? Are there additional studies that need to be done to validate this research? This is a chance for you to express your scientific opinion. Note that you will need to be selective with what information you include within your press release, as you will not have enough space to cover every result in the article. While many press release do not include in-text citations, you will need to provide in-text citations and a reference list. To help guide you in this task, we have provided an example original research paper (Jumper et al., 2021) and associated scientific press release, as well as some hints for writing for a non-specialist https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0345-8 https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0345-8 https://www.biomedcentral.com/about/press-centre/science-press-releases/04-10-17 BIOL2254 - Assessment 3 Semester 2, 2021 Page 2 of 3 RMIT Classification: Trusted audience below. While many press releases contain direct quotes from the authors, this will generally not be possible for your selected articles. Topics/Articles: Choose one paper from any of the following topics (PDFs of these papers are available on Canvas): Single-cell RNA-Seq • Liu Y, Wang T, Zhou B, Zheng D. Robust integration of multiple single-cell RNA sequencing datasets using a single reference space. Nat Biotechnol. 2021;39: 877–884. • Cherry C, Maestas DR, Han J, Andorko JI, Cahan P, Fertig EJ, et al. Computational reconstruction of the signalling networks surrounding implanted biomaterials from single- cell transcriptomics. Nat Biomed Eng. 2021. doi:10.1038/s41551-021-00770-5 Genome Assembly: • Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F. HASLR: Fast Hybrid Assembly of Long Reads. iScience. 2020;23: 101389. Machine Learning • Elnaggar A, Heinzinger M, Dallago C, Rehawi G, Yu W, Jones L, et al. ProtTrans: Towards Cracking the Language of Lifes Code Through Self-Supervised Deep Learning and High Performance Computing. IEEE Trans Pattern Anal Mach Intell. 2021;PP. doi:10.1109/TPAMI.2021.3095381 Protein structure, function and modelling • Necci M, Piovesan D, CAID Predictors, DisProt Curators, Tosatto SCE. Critical assessment of protein intrinsic disorder prediction. Nat Methods. 2021;18: 472–481. Submission and Grading This assignment is worth 11.4% of the final marks for the course. Both Part 1 and Part 2 are to be submitted as either a Microsoft Word or PDF document and will be reviewed for plagiarism using Turnitin. Late submission will be penalised at 10% of the total available marks for this assignment per day. BIOL2254 - Assessment 3 Semester 2, 2021 Page 3 of 3 RMIT Classification: Trusted Tips for writing for a non-specialist audience Writing about complex scientific research can be challenging and presenting research for a general scientific audience is no exception. Here are a few tips to keep in mind that may make the process a bit easier (although these are just suggestions - and you may not have space to adequately cover all of these in your press release!). • Remember that your audience does not have the knowledge that you do (imagine your audience is from the Physics or Geology department!). It is your job to cover the important background concepts that will help them understand the research you are writing about. There may be 2-3 key concepts that need to be explained before the reader can understand the importance of your chosen research article. • Avoid excessive use of acronyms or complex domain-specific terms. If possible, limit yourself to 3-4 complex terms/acronyms, and make sure you explain each of these when they are introduced. • You don’t need to cover all the results presented in the primary research article. Choose what you think are the 1 or 2 most important results or advances and discuss these. • A well-chosen diagram or figure can help to reinforce key ideas or concepts for the reader. This might be a diagram or figure modified from the original article (with appropriate attribution) or it may be a figure you have created yourself. • Start with the big picture, and slowly narrow down till you get to the problem that your research article is tackling. This can be an effective way of structuring your introduction and initial discussion of the research article. • End with a big-picture view of the research area – where is it going and what might it lead to? • Try to identify the knowledge gap that your research article is trying to fill. Make sure you clearly explain to the reader what this knowledge gap is, and how the research article helps to fill this gap. • There may be potential flaws in your chosen research article. It can be helpful to discuss alternative approaches, or potential issues with the research. If there are conflicting studies, you may want to briefly discuss these (making sure to reference appropriately). • You will likely need to read beyond the original research article to understand the context for the research. There may be recent review articles that could help you get an overview of the broader subject area (try a PubMed or Google Scholar search). BIOL2254 Tutorial 3 Assessment Rubric Semester 2, 2021 Page 1 of 4 RMIT Classification: Trusted Part 1 Rubric: High Distinction Distinction Credit Pass Not satisfactory Total Marks All questions There is an advanced and thorough understanding of the bioinformatics approaches used in the chosen research article, including an understanding of data sources/controls/similar techniques. There is a strong understanding of the bioinformatics approaches used in the chosen research article, including an understanding of data sources/controls/similar techniques. There may be minor omissions or errors. There is a reasonable understanding of the bioinformatics approaches used in the chosen research article. There may be omissions or errors. There is limited understanding of the bioinformatics approaches used in the chosen research article. There are major omissions or errors. There is an inadequate understanding of the bioinformatics approaches used in the chosen research article. 50 points Total: /50 BIOL2254 Tutorial 3 Assessment Rubric Semester 2, 2021 Page 2 of 4 RMIT Classification: Trusted Part 2 Rubric: High Distinction Distinction Credit Pass Not satisfactory Total Marks Introduction Introduction clearly introduces the topic and broader context, demonstrating an advanced understanding of the broader research field. Key bioinformatics terms are defined clearly and simply. Introduction includes an appropriate level of detail to enable a general scientific audience to understand the research being discussed. Introduction clearly introduces the topic and broader context, demonstrating a good understanding of the broader research field. Key bioinformatics terms are defined. Introduction includes an appropriate level of detail to enable a general scientific audience to understand the research being discussed. There may be minor errors in understanding. Introduction introduces the topic and broader context, demonstrating a reasonable understanding of the broader research field. Key bioinformatics terms may be defined but are difficult to understand from the description. There may be errors in understanding. Introduction adequately describes the topic, demonstrating an acceptable understanding of the broader research field. Key bioinformatics terms are either defined poorly or otherwise missing. There are major errors in understanding. Introduction does not adequately describe the topic. Key bioinformatics terms are not defined. There are major errors in understanding. 10 points Body Discussion of chosen research article is clear and articulate, demonstrating an advanced understanding of the chosen research