Final Project - mestato/EPP622_2024 GitHub Wiki

Final projects are due December 3rd, 2024 before 12pm.

(Other than the presentation which will be whatever time slot you are assigned)

Description

Each student will prepare a final project. This project requires that the student identify a bioinformatics research goal and appropriate dataset, execute the project, and prepare a written report with supporting data, analysis methods, code and other documentation. Final project grades are based on a 100 point scale:

One page project proposal – 10 points
Final oral presentation – 10 points
Final written report – 30 points
Code and methodology documentation ("lab notebook") – 30 points
Grade from peers – 20 points

An additional 14 points of your final grade is for providing feedback for other student’s projects

Grading rubric

For the one page project proposal (10 points)

Describe your question, dataset, and general methodology plan. This should be equivalent in scope to one of our tests (not too big, not too small, doable in about 3 weeks). You may do something similar to our course labs (variant calling, genome assembly, etc) or something new (RNASeq differential gene expression). If you do not have your own data or an idea of where to get some, let me know and we can find some.

For the final written report (30 points)

(Thanks go to this GA tech rubric for inspiration)

Final reports will be examined for plagiarism and/or copied text via iThenticate. Evidence of academic misconduct will result in a 0 score for the final project.

Minimum Requirements (10 points)

Student made reasonable progress toward the stated goal from the proposal. If the project is not completed, there should have been a solid attempt with significant effort put forth to make progress, and an explanation of the problem given in the document. Because we have 4 in class sessions and I am available for meetings during the project time period, small bugs or easily solvable impediments will not be considered sufficient for not completing the project.
At least one page, single spaced (figures and tables can be added as extra pages, text can go over if you want)
Proper scientific citations for the data (if published), any preliminary/background information, and all software/bioinformatics approaches
Scientific language used throughout (this should read like a manuscript, not a set of bullet points or a casual email)
Proper grammar. If you need help with this, there is a Student Writing Center.
Sections should include Background, Methods, Results and Conclusions/Further Work

Organization and Formatting (5 points)

5 - Excellent - points are ordered within sections, flow of logic for the project is clear
3 - Good - points are mostly well ordered, flow of logic for project is present but not completely clear
1 - Poor - an attempt at logic and order was made, but is difficult to understand
0 - No Points - Points are totally unordered, it is impossible to understand logic

Background - Goals, Rationale, Starting Data (5 points)

5 - Excellent - The project's goals and rationale are clearly stated, the student's motivation for the project is clear, supporting details/prior work relative to the subject are present and cited. Source of data is given and data is described in enough detail to evaluate methodology and whether it supports goals/rationale.
3 - Good - The goals and rationale are mostly clear (some minor confusion only), support details/prior work have largely been appropriately incorporated with only minor exceptions. Data source is given, may be slightly vague.
1 - Poor - Goals and rationale are present but not clear, supporting details/prior work are present but not cited or not relevant to the project, data is not well described or cited appropriately
0 - No Points - At least one of goals, rationale, supporting details/prior work, data description is not present

Methods including Experimental Design (5 points)

5 - Excellent - The project's experimental design and methods are clearly described in a logical order with proper citations, are comprehensive. The experimental design is appropriate and well-designed to the goals of the project and the data available
3 - Good - The experimental design and methods are mostly clear (some minor confusion only or some out of order or some missing citations). Experimental design is mostly appropriate and somewhat aligned with the goals
1 - Poor - Experimental design and methods are present but not clear (confusing, out of order, missing most or all citations), experimental design is not appropriate to the data or not aligned with the goals
0 - No Points - Experimental design or methods not present

Results and Conclusions (5 points)

5 - Excellent - Clear and thorough interpretation of results, presenting not just raw data but some interpretation. Conclusions tie the initial goals/rationale and the results together to tell a story
3 - Good - Thorough analysis of results but some questions remain, results are mostly complete, conclusions attempt to draw links between goals/rationale and results but are not entirely successful
1 - Poor - Results are present but are not clear, conclusions are present but do not draw links between goals/rationale and results
0 - No Points - Results and/or conclusion missing

For the code and/or methodology documentation ("lab notebook") (30 points)

We discussed reproducible research in class. For your final project, I want to see the principles of reproducibility being followed. This means turning in the same type of Github "lab notebook" we used for Tests 2 and 3:

Student made reasonable progress toward the stated goal from the preproposal (see above)
an organized document that could be followed by you or someone else to complete the project in exactly the same way in the future
all steps used to process the data
a general description of where the analysis took place. For example, you might state: "ISAAC was used for all computational steps. The raw data is located in the folder /nics/d/home/mstaton1/xxx and all analysis steps were completed in the folder /nics/d/home/mstaton1/xxx."
all command lines used to execute software, process data or run a script (its not necessary to put all the cd and ls commands, but anything that would be needed to recreate the analysis should be present)

Grades will be determined by this rubric:

30 - Excellent - all of the above present, I feel confident I could take your raw data and recreate the analysis
25 - Very Good - 80% of the above present, I am confident that with some help from you or reading software manuals, I could create the analysis
20 - Good - 60% of the above, the majority of the analysis steps are there, but I would definitely need help to recreate
15 - Fair - 40% of the above, major gaps in analysis logic and many missing command lines
10 - Poor - 20% of the above, very little documentation, definitely could not be recreated or published.
0 - No Points - no code or methodology given

For the oral presentation (10 points)

Your oral presentation may be in advance of the project due date. If you are not done, please give a presentation based on the project you selected, the planned methods, the work you have accomplished so far, and any difficulties you have encountered.

You should aim for 6 minutes to present, 2 minutes for 1-2 questions.

10 - Excellent - Clear, logical explanation of the project, including brief background, methods, results and conclusions. Eye contact with audience, good use of slides as visuals without reading from them, slides do not contain grammatical errors. Poised, clear voice. Answers questions fully, demonstrates knowledge of subject. Good use of time.
7 - Good - Explanation of the project is mostly understandable, and all sections are present. Occasional eye contact, some but not extensive reading from slides, very few errors on slides. Clear voice. Provides general answers to questions but not necessarily totally thorough. Up to 2 minutes too long or too short.
4 - Poor - Explanation of the project is confusing, sections are missing. Little to no eye contact, reading from slides only. Many errors on slides. Cannot provide answers to questions. Well under or over time.
0 - No Points - No presentation given.

Peer grading process (20 points)

20 of the points for your final project will be taken from the grades your peers give you. They will be averaged to provide this final point value.

Your participation in grading peers is also part of your final grade (14%). When you arrive in class, you will be given a google form to fill out for the presentations that day. You will provide a score based on the oral presentation rubric for each. For full credit you will need to provide at least one constructive comment about each presentation. "Nice job" and "good job" do not count. Comments that could count might include "The results were a bit confusing, it might help to explain what GBS is" or similar. But also be nice, the goal is to provide constructive feedback.

10 - Provide feedback for all presentations
5 - Provide feedback for half the presentations (attend one of two days)
0 - Provide feedback for less than half the presentations

Presentation time slots

6 minutes to present, 2 minutes for 1-2 questions

**Tuesday November 26th

2:30 MENGLING HE
2:38 HANNAH TEDDLETON
2:46 SANSKRITI ACHARYA
2:54 SERENITY JONES
3:02 ERIN VAN BERKEL
3:10 JAMES ULMER
3:18 CHARLES DAWE
3:26 ANDREW REED

**Tuesay December 3rd

2:30 MARISSA NUFER
2:38 STEFANIE MENEZES DE MOURA
2:46 ALINA POKHREL
2:54 MAKHALI VOSS
3:02 MARIA CABALLERO ARAGON
3:10 KATIE WOOD
3:18 REBECCA KRAUS
3:26 PATRICK SISLER
3:34 ADITI