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GEGE2X01 Genome Assembly

创建日期：2024-04-19 15:46:51

所属分类：计算机computer science

标签： GEGE2X01

Genome Assembly

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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
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.
2
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.
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.
3
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%
4

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1300A ENGG 1300 OLET1139 STAT 3503 STAT 206 FEM11149 ELEN 4720 COMP20003 SOLA1070 CS574 C11CS LINB29H3 MAST90083 ECON7200 STAT 610 LINB29 DSM-5 COMP3161 EEEN40010 MATH 4431 K353 STA 3386 IERG4300 COMS W4167 ENG5298 AMME 2302 CS3910 COMPSCI 320 STATS 369 GR5242 COSC 328 CSCI435 MGTS1301 INFS2200 COMP3900 CIS 375 Module AE03 COMP3121 CS260 HAM503 MGMT5050 INT3075 COSC 285 GEOL0029 GEGE2X01 STAT1201 MATH1061 MMF1941H STAT 5060 CS 520 COMP 4320 MSIN0104 000T FINS3648 ECMT2160 ECON4003 Phys 129L CSE 142 CS 3130 MGEB01 EECS 340 Finance (20443/20444) ECMM149 COMP5310 EEEN60180 CSC 111 AT2 CSCI 4430 STAB57 MA/CSC 427 MATH322 D100 CSCI544 CITS3004 CI6227 CSE 565 APCO 1P01 852L1 ELEC S411F COMP3207 STATS330 ECON7530 FIT5149 CSI4104 CMPT 371 COMP201 SEHS4696 FI4003 MATH6182 CG1 WS MATH401 MGT 205 QTM 110 COMP 0137 MACE12201 FIT5210 ECE 544 BISM7206 HUDM 6055 ECON3203 STATS 210 MSCI 570 MATH6173 COMPSCI4039 Accounting COM3503 AOE2024 ECON213 PSYC10004 Control Data 100/200A PHIL2617 PHYS3116 MIE250 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