assignment3.Rmd

---
title: "Assignment3 - The Platinum Age of Virus Discovery"
output:
  html_document:
    fig_caption: true
---

## Preamble
Please mark the following boxes with an X as appropriate:
```
- [ ] Completed the Request for Evaluation by Artem
- [ ] Answers assisted with generative AI (please indicate where)
```

# Assignment 3 =================================================================
# ==============================================================================
```
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..==             ░ The Platinum Age of Virus░Discovery  ░                   ==..

At the dawn of the Molecular Genetics, Max Delbruck lead a loose collection of
geneticists known as the "Phage Group". They were amongst the first to pick up
the reciever when the Molecular Revolution was calling. They had two unifying
philosophies:

(1) Hard Physics-style Scientific Inquiry
(2) They studied viruses, because that's the simplest model organism to do
    cool science in.
    
I think Computational Biology is having that kind of moment today. And the way
to realize it is by choosing a strong model genome; Viruses!

Guidance from the Elders: https://www2.clarku.edu/faculty/pbergmann/SCEP/Platt%201964.pdf

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```

## Learner Objectives
```
By the end of this assignment, you will have taken the plunge into a real
research problem, there is risk and no certainty of "success", but as the old
saying goes, "If you can't fatally kill your hypothesis, then it was never alive
to begin with." Risk begets Reward.

It is up to you to find and guide the direction of the project, these questions
only give you a generic scaffold. As such, (and with the bonus marks) it will
be possible to do a technically good job and you'll do fine on the assignment.
A subset of you will rise to the occasion and knock it out of the park, that 
will reflect the 99% grades.
```

## Assignment Objectives
```
For this assignment you're going to compile all the components for a short
"Genome Announcement" style scientific paper, describing and naming a new virus
species which you have been randomized. You do not need to re-write the answers
into a seperate paper, this assignment  serves as the paper template. You will
know by the end if it's worth formalizing.

The goal here is *Data Exploration*, you are not expected to have every analysis
work and be super insightful. Most analyses will be difficult or impossible to 
interpret we often don't know the difference between these two. If you are able to
justify (hypothesis) the reason you performed a given analysis, and it's
inconclusive, you will recieve full marks for trying. You will be deducted marks
if and only if you include an analysis and it's not justified, or if you
misinterpret the analysis results. That is the feedback/learning mechanism of
peer review, meant to guide you in the future.

Please include the work when you judge you can make a *moderate* or *high* 
confidence conclusion, even if the conclusion is that it is inconclusive.
```

## Logistics
```
Inclusive in this document should be all supporting code, scripts, and/or 
software settings used to answer any questions in the assignment. If you use or
generate a data-object, such as .fasta, .pdb, .sto, .csv, etc..., include this
in your submission repository.

For Written portions please use block text like this and you can include 
references simply as square brackets [Babaian. 2023].
```

## Virus Assignment
```
You are randomly assigned a Virus. 

## `a3/data/virusAssignments.csv` 
  Gives the assignment of your virus. Each virus has a unique identifier (sOTU)
  as well as some summary statistics about where this virus was "found" in the
  SRA. You're also given a link to the assembly file from the "index run" which
  should contain your virus sequence.

## `virusRunObservations.csv`
  This file  contains a list of all SRA "runs" in which these  viruses were 
  reliably detected. You can use the sOTU identifier to get an  estimate overview
  for your virus. The final column in this file contains the  barcode sequence
  detected in that particular run.

## `virusRdRp_detected.fa`
  This file contains _ALL_ RdRp and RdRp-like sequences which were detected in
  the "index runs". From within this file, you should recover your assigned
  RdRp sequence (using sequence from virusRunObservations.csv).

```

## Example "Virus Announcement" references
(emulate these)

- [Bornaviruses](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8321990/)
- [Pepino Mosiac Virus](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6952647/)
- [Lancehead filovirus](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8498845/)
- [Perch filovirus](https://journals.asm.org/doi/10.1128/mra.00028-23)
- [Locarnaviruses](https://link.springer.com/article/10.1007/s00705-023-05908-1)
- [Odysseus Narnavirus](https://www.biorxiv.org/content/10.1101/2023.09.17.558162v1)

# ==============================================================================

## Question 1 : Framing the story `(10 points)` --------------------------------
(do second last)
**Q.** `(1 point)` Write a title for your paper which describes your one key finding.

**A.** TODO

**Q.** `(bonus point)` Include a pun in your title which relates to a theme or motif
used throughout your paper.

**A.** TODO

**Q.** `(1 point)` Give your virus a latin binomial name, and explain the etiology
of the name and how it relates to the story of your virus.

**A.** TODO

**Q.** `(8 points)` For any given paper, 90% of the readership will only read your
abstract. How many people go on to read the rest of your paper will depend
on your ability to capture peoples interest in the abstract. (hint: write the
abstract last)

Read *How to Construct a Nature summary paragraph* and write a short abstract
closely following this structure.

Link: https://www.nature.com/documents/nature-summary-paragraph.pdf

**A.** TODO

## Question 2 : Digital Virus Ecology  `(15 points)` ---------------------------

In brief, ecology is the relationship of an organism to biotic and abiotic
factors. Consider the the sample source for this virus and describe the
specifics (e.g. run accessions, study authors, associated species, ...) and
generics (e.g. type of ecosystem, country/continent, common associated host
class like Mammals). 

All viruses should occur in more than one dataset (SRA run), compare and contrast
the ecology of your index case, and the broader ecology of all virus-containing
datasets. What commonalities, if any, emerge in the data?

Guiding questions:
- Is there an associated publication with your index case?
- Which dataset(s) is the virus found in?
- What is the origin(s) of these dataset(s)
- Can you observe a common factor which links these datasets together and
  may explain the presence of the virus?

Write your answer in themed paragraphs (subsections), as it were to go into the
first *results* section of your paper.

**A.** TODO

## Question 3 : Interrogate the Virus `(20 points)` ----------------------------

**Q.** `(10 points)` Research and identify what are at least 20 *features* of
the viruses related to the one you have found.

List or write short sentences describing those features here. Examples are:
```
# Example Answer
- Narnaviruses have an RNA genome
- Narnaviruses have a single-stranded genome
- The typical genome length is between 2,200 - 3,200 nucleotides long
- Narnaviruses typically encode for a single protein, RdRp
- Narnavirus RdRp are typically 800-1000 amino acids long
- ...
```
**A.** TODO

**Q.** `(10 points)`  Create a figure(s) visualizing your virus genome (see 
papers for examples/inspiration). The figure should capture the *key genomic*
*features* of the virus which includes (but is not limited to):
- Open reading frames, and note if they are not CDS complete
- Annotation of every ORF
- A scale legend in nucleotides and amino acids for ORFs

In addition consider virus-family specific features, such as
- RNA secondary structures
- Conserved sequence motifs
- Frameshifting sites
- Evidence of poly-A or splicing
- Additional known (or unknown) protein domains

In addition consider additional measurements, such as
- TPM / RPKM for the virus within your dataset
- Additional viral segments/viral contigs
- Coverage profile of reads mapped to your contig
- Single Nucleotide Variants present in the mapping data

- `(6 points)` Figure (technical)
- `(2 points)` Figure (aesthetic)
- `(2 points)` Figure legend

**A.** TODO

**Q.** - `(bonus 2 points)`
  - Run the RdRp and/or open reading frame through AlphaFold2 ( https://github.com/sokrypton/ColabFold )
  - Add a figure of the RdRp with motifs A (blue), B (green), and C (red) visualized.
    See: `Odysseyus Narnavirus` example paper. Try PyMol.

**A.** TODO

## Question 4 : `(5 bonus points max)` -----------------------------------------

**Q.** `(bonus 5 points)` 
  Do something creative or cool with the viral genome.

**A.** TODO

-- OR --

**Q.** `(bonus 5 points)`
  Generate a multiple sequence alignment of the RdRp sequence, and either 
  (i) all RdRp of viruses in the same family or
  (ii) all BLAST hits with >80% query coverage and >40% amino acid identity
  Visualize it in (e.g. Jalview) and include a figure.
  
  Generate a phylogenetic tree (e.g. IQTree) of the multiple sequence alignment
  above, visualize it (e.g. Dendroscope) and include a figure.

**A.** TODO

## Question 5 : Discussion `(5 points)` ----------------------------------------

Discuss for your reader what you have learned from this virus, or what novel
biological insights does characterizing this genome offers to the reader. What
facts did you find the most fascinating about your kind of virus, and did your 
virus share these traits? Even more interesting is if it _doesn't_ have a trait
known to that virus. It's always fun to push against the textbook definitions.

**A.** TODO

## Question 6 : References `(10 points)` ---------------------------------------

Add at least **10 relevant references** throughout your report. Be sure to 
reference both software papers, biology papers, and the paper from which the
data was generated (if available).

## Question 7 : `(5 points)` ---------------------------------------------------

**Q.** Respond to this email (Do this last):

```
Subject: Inquiry Regarding Your Fascinating Research Paper

  Dear Dr. XXXXXXXX,
  
  I hope this message finds you well. My name is April O-Neil, and I am a reporter
  with the CBC. Recently, I came across your research paper on EurekAlert!,
  and I must express my sincere appreciation for the compelling work you've done.
  
  Your paper provided a deep and insightful exploration into virus discovery,
  and to be honest I'm not an expert in it but  I found the methodology and 
  results particularly intriguing. I believe that our readers would benefit
  greatly from a more in-depth understanding of your research.
  
  To that end, I am writing to request a brief 100-word summary of the main
  findings of your paper. This summary will be used to pitch the story to my 
  editor with the intention of conducting a more comprehensive interview with
  you. I am confident that such an article would not only shed light on the
  importance of your work but also inspire a broader audience.
  
  If you could provide the summary at your earliest convenience, along with a 
  suitable time for a follow-up interview, I would be immensely grateful. 
  Your expertise and insights would undoubtedly contribute to a compelling 
  feature that highlights the significance of your research.
  
  Thank you for your time and consideration. I look forward to the possibility
  of discussing your work in greater detail.
  
  Best regards,
  
  April O-Neil
  Senior reporter. CBC
```

**A.** TODO