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GEGE2X01: Practical Report – Genome Assembly & Genomics
This assessment is worth 25% of your final grade. Submit one word document (.doc or .docx) file
via Canvas, due 4th November 23:59.
Report Guidelines
You will write a written report of the Virus Detectives exercises in practicals conducted in weeks 5-6
“Bioinformatics and Genomics: Genome Assembly and Interpreting Genomic Data”. Note that
this includes Week 5, Part 2 – Virus Detectives, Week 6, Part 1a – Identification and analysis
of protein coding genes and Week 6 Part 1b – Identification of restriction sites. The report does
not include Part 1 of Week 5 (Simulating a genome assembly) or Parts 2 and 3 of Week 6 (reading
DNA from chromatograms and the donkey coat colour case study).
Your aim is to write up the practical in the form of a brief scientific journal article, containing the
sections: Introduction, Methods, Results, Discussion and Supplementary Information.
For more information on the structure of a scientific journal article, see the “Research
Manuscript Template” from the journal PeerJ, available at:
https://peerj.com/about/author-instructions/
Note that you do not need to include an abstract or acknowledgements section. Your
conclusions should be contained within the Discussion.
This is a written report, so all sections should be in sentence form (no dot points or lists). Like
all journal articles, you should come up with an appropriate title for your report. Throughout the
report you can use subheadings followed by paragraphs, and present key information such as
your results in tables and figures that have a table/figure caption explaining the item. You must
include relevant references from the peer-reviewed scientific literature. Your report should be
no more than 1500 words (excluding figures, tables, references and supplementary information).
Aim: To use high-throughput sequence data to identify
an unknown pathogen and characterise its genome.
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Report Sections
Title: Provide a brief title that describes the report or the main findings. See scientific journal articles
for examples.
Introduction: Briefly describe the background and put the research into context. Think about the use
and importance of bioinformatics for genome assembly and virus identification, and about some of
the background terms that you will need to introduce. Include relevant references from the peer-
reviewed scientific literature by citing them in text where appropriate and including them in your
reference list. Consider the bigger picture – why is this work important? Finish this section by clearly
stating the aims.
Methods: Give a brief overview of the methods, starting with the Genome Assembly and finishing
with the Identification of Restriction Sites. Include all necessary information someone else would need
to repeat the analysis. Methods should be written in sentence form, not as a list or protocol.
Results: Use your results from the Week 5 & 6 Practicals (do not include the donkey coat colour case
study). Summarise the key results into table/s and figure/s, and describe the results in text. Tables and
figures should be presented with a table/figure caption that explains the content, and should be cited
within the main report, e.g. “Treatment A was more successful than Treatment B (Table 1)”.
Additional analyses or extra tables or figures that are not the main focus of your article should be
included in the Supplementary Information section (this is similar to an appendix). See examples from
the peer-reviewed literature for help with the type of things that should be included in the results
section.
Discussion: Interpret your results (use the questions from the practicals to guide you for some ideas
on where to start). Integrate your results with the available literature and discuss their biological
significance. Some points to consider include: What is the significance of the virus you have identified?
How are genomic and bioinformatic approaches useful in disease management? Given your results,
what recommendations would you make to public health officials? What are some future directions?
Word Count: State word count (excluding figures, tables, references, and supplementary
information).
References: Relevant peer-reviewed scientific literature must be cited in text where appropriate and
provided in a reference list. Only sources cited in the report should be included in the reference list.
References to non-scientific websites should be avoided. Do not use footnotes or end-notes. See the
University of Sydney Library website for guidelines for referencing:
https://libguides.library.usyd.edu.au/citation
There are many different referencing styles. Author-date styles are commonly used in scientific
publications. The PeerJ website (link on page 1) also contains details on referencing style. Whichever
style you choose, make sure that all sources are credited and that your formatting is consistent
throughout.
Supplementary Information: Include here any additional tables/figures that you produced but that
were not the main focus of your article. Supplementary Information is similar to an appendix. All tables
and figures should include a caption, and should be cited within the main report.
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Assessment Criteria
This assessment is worth 25% of your final mark for this unit of study. The marking rubric is provided
on the following page.
Criteria Weighting %
Context: Analysis is placed into context in the title, Introduction and throughout
the report. Relevant background information on the use and importance of
bioinformatics for genome assembly and virus identification is provided. Aims are
stated clearly.
20%
Reproducibility: Methods are described clearly and accurately, such that they are
easily understood and could be repeated by someone else.
10%
Technical accuracy: Results are presented in a clearly and succinctly, including
technically accurate tables, figures and Supplementary Information, as well as
clear figure and table captions.
15%
Understanding, interpretation and extension: Demonstrate understanding and
interpretation of the results. Discussion of implications, relevance of research and
suggestions of future directions/experiments.
30%
Structure: Overall clarity, including appropriate scientific style, spelling, grammar
and overall document structure
10%
Word count: Word count stated and within limit 5%
References: Research and use of appropriate peer-reviewed scientific references 10%
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Marking Rubric
Criteria High Distinction
Exceptional
Distinction
Outstanding
Credit
Skillful
Pass
Requirements met
Fail Not Attempted
1 0.8 0.7 0.55 0.3 0
Context (20%) Creative and insightful
placing into a broader
genomics context,
providing excellent
level of background on
the use and
importance of
bioinformatics for
genome assembly and
virus identification.
Aims clearly stated.
Excellent description
of context and
genomics, providing
relevant background
on bioinformatics for
genome assembly
and virus
identification. Aims
clearly stated.
Context of analysis
was described
well, providing
some background
on the use of
bioinformatics for
genome assembly
and virus
identification.
Accurate aims.
An attempt to place
the analysis into
context, with some
background on the
use of
bioinformatics for
genome assembly
and virus
identification
provided. Aims
mentioned vaguely.
Analysis not placed
into context: no
connection to
background or
bigger picture,
incomplete/incorrect
attempt at aims or
aims not included.
No serious
attempt
Reproducibility
(10%)
Technically
outstanding
description of
methods, such that
they could be clearly
understood and
repeated by someone
else.
Methods described
correctly and
accurately. Details
required to repeat
the analysis are
clearly described.
Methods mostly
correct. May be
missing minor
details to repeat
the analysis.
Methods present
with some errors
and/or details
needed to repeat
the analysis missing.
Excessive errors in
recounting the
methods, and/or
substantial lack of
information such
that repeating the
analysis would be
impossible.
No serious
attempt
Technical
accuracy (15%)
Exceptionally clear and
succinct presentation
of results, figures and
tables, including the
graphics and the
figure/table captions.
Results, figures and
tables complete, well
presented, visually
clear and correct.
Necessary
information
presented
accurately in
figures and tables.
Tables and figures
presented
adequately.
Figure/table
captions vague or
incomplete.
Tables and figures
missing or presented
incorrectly. Key
results missing.
No serious
attempt
Understanding,
interpretation,
extension
(30%)
Exceptional level of
understanding of the
subject and results and
implications
Excellent
understanding of the
subject with clear and
coherent
Results
interpreted
correctly,
understanding of
Attempt to
interpret results at
a basic level with
lack of clarity and
Misunderstanding or
misinterpreting the
results, no attempt
No serious
attempt
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interpreted
insightfully. Skillful
suggestions for
relevant future
directions, showing a
high level of genetic
understanding.
interpretation of
results and
implications.
Relevant future
directions suggested
showing clear
understanding.
the subject clearly
shown. Good
attempt to suggest
future directions.
insight. Superficial
attempt to suggest
future directions.
to propose future
directions.
Structure
(10%)
Exceptional scientific
writing style, excellent
articulation of ideas
and concepts. Layout
clear and
comprehensive.
Excellent writing skill
and clear scientific
voice. Ideas and
concepts articulated
clearly. Layout clear
and correct.
Well written, good
scientific voice,
coherent layout.
Adequate writing
skill, some language
errors. Layout
sufficient.
Writing needs
improvement,
language unclear,
excessive errors.
No serious
attempt
Word count
(5%)
Word count is clearly
stated and is within
given limit (< or = 1500
words, excluding
figures, tables,
reference list and
supplementary
information).
N/A N/A N/A N/A Word count not
stated or is
above limit (>
1500 words,
excluding
figures, tables,
reference list
and
supplementary
information).
References
(10%)
Well researched, with
appropriate scientific
sources provided. In-
text citations and
reference list without
errors.
Good selection of
relevant scientific
sources provided. In-
text citations and
reference list with
minor errors or
inconsistencies in
style that do not
impact ability to
locate sources.
Generally well
researched, but
some cited
references missing
from reference list
(vice versa), or
occasional in-text
citations missing.
References
provided, some
relevant. Additional
referencing
required or multiple
non-academic
sources used.
Limited or no
referencing
throughout the
document or no
reference list
provided.
No serious
attempt
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Academic Honesty

While the University is aware that the vast majority of students and staff act ethically and honestly,
it is opposed to and will not tolerate academic dishonesty or plagiarism and will treat all allegations
of dishonesty seriously.
Further information on academic honesty, academic dishonesty, and the resources available to all
students can be found on the academic integrity pages on the current students website:
https://sydney.edu.au/students/academic-integrity.html

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学霸联盟