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The coursework involves writing a technical report (90%) and developing an application (10%) using Hadoop and MapReduce in the context of a Bioinformatics use case. Listing five AWS modules that you complete from the AWS Academy Cloud Foundations course will contribute 20% as part of the report. You DO NOT need previous Bioinformatics knowledge for this coursework. Input files are provided in plain text and are tab-delimited in Cloud Computing.

Background for the application

A biopharmaceutical company requires a computational analysis platform to compare various bacterial organisms based on their features. Your task is to investigate how cloud resources can be utilised to develop a scalable application to efficiently analyse several organisms as and when required. As the lead developer, you have been given seven example files (see the Appendix). Once developed, the application can be used to compare and analyse thousands of organisms.

Each line in these files includes an identifier for a protein in the second column and information about the protein’s function in the fifth column (Figure 1). A protein’s function is specified via a related Gene Ontology (GO) term. Figure 1 shows example rows for the P0A9Q1 protein. The GO:0003677 term in the “GO ID” column (5^th column) indicates the “DNA binding” function. Hence, it can be concluded that the P0A9Q1 protein can bind to DNA.

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1.1 Part I – Application (10%)

You will create an application using Hadoop and MapReduce for the following task using the Java programming language. You will use the files provided as input (see the Appendix for these files). You are allowed to use Python 3.

The GO:0030420 term (“establishment of competence for transformation”) and its subterms are used to indicate whether a bacteria can have the competence feature, which is about being transformed to take up exogenous genetic materials. Identify which organisms (using the provided seven input files) may exhibit “competence” as a physiological state. Hint: In the context of this coursework, the existence of the GO:0030420 term, and its subterms, in a file suggests that the corresponding organism may exhibit the competence feature. Therefore, you can count the number of GO assignments for the GO:0030420 term and related subterms for each file.

1.1  Part II – Technical report (90%)

For part two of this coursework, your task is to produce a report of approximately 2500 words. The report will cover the following topics.

1. Design a native cloud application for an image web service (50%). This item will include your design and report from the AWS workshop (Workshop 2). You can only refer to AWS resources covered in the AWS Academy Cloud Foundations course.
   1. Describe how IaaS, PaaS, SaaS concepts are related to the application you will develop when using the AWS resources. Explain the IaaS, PaaS and SaaS concepts by giving real-world examples from existing cloud providers and the literature.
   1. Provide an overview diagram of your design.
   1. Describe your design for the image web service and its REST interface for different access and search options.
   1. Describe how you plan to integrate different AWS products for this image web service considering cloud-related characteristics (e.g. storage, scalability and so on).
2. Describe and evaluate the bioinformatics application (see section 1.1) that you will develop

(10%).

• Describe your source and output files and folders and how they should be used.
  • Critically evaluate design aspects related to your solution, present and evaluate your findings (see section 1.1).
• Analysis and discussion for future cloud integration of the bioinformatics application (see section 1.1) (10%). Identify and describe an existing cloud-based and distributed file processing system. Explain how you can integrate the bioinformatics application you will develop (see section 1.1) with this cloud-based system in the future. Discuss the advantages and disadvantages of migrating your application to the cloud.
• AWS Academy Cloud Foundations course (20%). List five AWS modules that you complete from the online AWS Academy Cloud Foundations course, together with your score for each module. The course is accessible from the link below. Invitation emails were sent at the beginning of the semester. To successfully complete an AWS module, your score must be 80% or more. https://awsacademy.instructure.com/courses/12799

Input files

Table 1. List of bacterial organisms and corresponding input files. The files are available from the KLE assessment page.

	Organism	Input File
1	Escherichia coli K-12	Escherichia_coli_K-12_ecocyc_83333.gaf
2	Bacillus subtilis 168	Bacillus_subtilis_168-224308.gaf
3	Bacillus amyloliquefaciens FZB42	Bacillus_amyloliquefaciens_FZB42-326423.gaf
4	Bacillus licheniformis ATCC 14580	Bacillus_licheniformis_ATCC_14580-279010.gaf
5	Bacillus megaterium DSM 319	Bacillus_megaterium_DSM_319-592022.gaf
6	Geobacillus kaustophilus HTA426	Geobacillus_kaustophilus_HTA426-235909.gaf
7	Geobacillus thermodenitrificans NG80	Geobacillus_thermodenitrificans_NG80_2-420246.gaf

File format

Data are available in the Gene Annotation File (GAF) format, which defines tab-delimited columns to represent information, as shown below.

Table 2. The flat-file format is comprised of 17 tab-delimited fields. More details can be found at http://geneontology.org/docs/go-annotation-file-gaf-format-2.0.

Column	Content	Required?	Cardinality	Example
1	DB	required	1	UniProtKB
2	DB Object ID	required	1	P12345
3	DB Object Symbol	required	1	PHO3
4	Qualifier	optional	0 or greater	NOT
5	GO ID	required	1	GO:0003993
6	DB:Reference (|DB:Reference)	required	1 or greater	SGD_REF:S000047763
7	Evidence Code	required	1	IMP
8	With (or) From	optional	0 or greater	GO:0000346
9	Aspect	required	1	F
10	DB Object Name	optional	0 or 1	Toll-like receptor 4
11	DB Object Synonym (|Synonym)	optional	0 or greater	hToll
12	DB Object Type	required	1	protein
13	Taxon(|taxon)	required	1 or 2	taxon:9606
14	Date	required	1	20090118
15	Assigned By	required	1	SGD
16	Annotation Extension	optional	0 or greater	part_of(CL:0000576)
17	Gene Product Form ID	optional	0 or 1	UniProtKB:P12345-2

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