The Assessment - 2018
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Welcome to the assessment...
Overview
We have discussed the assessment in the pre-training seminar (S01), and below are the key points from that discussion:
  1. you will be provided with data from a series of experiments carried out in the lab
  2. using these data will perform a series of bioinformatics tests
  3. based on the results of the bioinformatics tests you will form a hypothesis as to the mechanism of action of the disease/condition
  4. you will suggest some experiments to test the hypothesis
  5. you will present your research, findings, and hypothesis in the form of a 1500 word mini–scientific paper
  6. your final report should contain: an abstract, the method section, a results section, a discussion section, and a reference section
  7. you should also include appropriate tables, and figures, in the report
  8. the use of R is not compulsory, it is optional
Guidance on the specific parts of the paper:
  1. Title: Give your final write up a good title
  2. Abstract: The abstract should be similar to the type you would find on a standard scientific paper. That is, it should contain a summary of the work and findings of the report
  3. Introduction: The introduction section should 'set the scene'. It should explain the relevant background, and why the work is being done
  4. Methods: The method section should be concise, and should describe any tools used to complete the work. Detailed function of the tools is not expected, please try to provide a relevant reference, please give any settings that were used
  5. Results: The results should contain, as the name suggest, the results. Don't forget to use figures and tables to show your findings. Don't forget to include any relevant lists of data used (for example, if you use a particular list of gene or protein identifiers in a particular piece of analysis please include that list in a table, or if the list is long, in the appendices– this is so I can repeat the analysis if needed). There should be no, or very limited, discussion of your findings in the results section.
  6. Discussion: The discussion section should discuss the results, and draw any conclusions. Please do not forget to include 'suggested further work'.
  7. References: Please list your references numerically using the Vancouver style.
Please note: I am not giving you specific guidance on how much should be in each section, you need to make a judgement call on that. I am also not awarding specific marks to a given section. The final piece of work will be marked as a 'whole'.
Specific points regarding the final piece of written work:
  1. use Vancouver style for referencing (see document on Blackboard)
  2. the report is to be no more than 1500 words
  3. the following are not included in the word count – the title, the reference section, contents of tables or figures, any table or figure legends, headers and footers on the page, your name, appendices
  4. do not use footnotes
  5. the report does not have to be formatted to look like a scientific paper
  6. font: any font can be used, no font smaller than 10 point (ideally aim for 11 or 12 point depending upon font). If writing out sequences, and showing alignments, use a monospaced font (for more information on the use of monospaced fonts please see this PDF)
  7. spacing: please use double spacing of the lines in your report (This does not mean you have to put a double carriage return at the end of each line – use the built in double line spacing in your word processor.)
  8. you must hand-in a hardcopy for the School Office
  9. you must submit a copy via Blackboard for plagiarism scanning
The scenario
You are working in a lab studying diabetes. As part of an ongoing study surgical liver biopsies have been taken from the following (human) patients:
  1. lean healthy individuals (n = 10)
  2. obese non-diabetic individuals (n = 9)
  3. obese diabetic individuals with the condition well controlled (n = 11)
  4. obese diabetic individuals with the condition poorly controlled (n = 8)
The patients were controlled for gender and age.
Two-dimensional gel electrophoresis was performed on the samples, and the results were disappointing as producing reliable and consistent data was difficult, and also the lack of available subjects, and tissue quantities, limited the number of experiments that could be performed.
After months of work a small number of proteins were identified that showed a significant difference in protein spot intensity 'spot'. Unfortunately, it was only possible to retrieve reliable and consistent data between the lean and poorly controlled diabetic patients. These data, in the form of RefSeq protein IDs, are available in the following file.
Your task
Using the RefSeq protein IDs data in the file you should carry out a bioinformatics analysis to produce a set of results, from which you draw a hypothesis and then suggest possible experiments to explore the hypothesis.
Some handy hints:
  1. make use of all your bioinformatics skills
  2. use the bioinformatics skills from this module - you should be able to use all of them
  3. use the bioinformatics skills you learnt in the second year - site
  4. don't forget to use the help, and guidance, provided by this website
  5. don't forget the stats...
  6. keep a detailed journal/record (think of it like a lab book) of the searches and research that you do - OneNote will be ideal for this (and don't forget that Dr Morris can see what you put in OneNote if it is in your class notebook)
  7. make use of the collaborative tools in Microsoft Teams
  8. follow the report guidelines given above
  9. don't panic
  10. think...
  11. break the task down in to small pieces and tackle them one at a time
  12. there is no one right answer...
Finally, good luck with the above. If you have any questions please feel free to email me (n.j.morris@ncl.ac.uk) or contact me via the Micrsoft Team, and as usual if the question is potentially of interest to the rest of the class, I will respond to the whole group.
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