Project Guidelines

Coding Guidelines

  • Include a script named project.m that when executed, is able to generate most/all of the results you present in your project. Any additional files required to run project.m should be included in your project folder.
  • Publish your project.m script as project.pdf.
  • If you work in a programming language other than matlab, you need to include a comparable project master file and have a pdf file of its execution.
  • If you are using data files, don't use full-paths to access them. Others downloading your project files should be able to execute regardless of where they place the project files. Make as few assumptions as possible regarding the file system your code is running and specify these assumptions in a README.TXT file.
  • Keep large data files (e.g., image files, GEO files) in a separate location on your computer than the project files.
  • If you are getting data from the web, get it on-demand within your code (i.e., download if it has not been downloaded before). Store these files in a temporary folder or in a data folder.
  • Be mindful of what information is “leaking”. E.g., if you are committing files to a github or other online repository, exclude any journal and conference papers that are not in the public domain (provide a URL for such publications).
  • Don't use full-paths. Others downloading your project files should be able to execute regardless of where they place the project files. Make as few assumptions as possible regarding the file system your code is running and specify these assumptions in a README.TXT file.

Project Presentation

  • Create your presentation in a file named presentation.pptx. If you use Google Docs, export it as presentation.pptx. If you are using a slideshow editor that cannot export as a powerpoint file, then export it as presentation.pdf.
  • You are to give a 10-15 minute presentation of your project. Your presentation will be graded based on how well you accomplish the following sections.
  • Title page [5%, 0min]
    • Title, your name(s) (last names are recommended/optional).
    • If your project is based on a publication, include its reference.
  • Introduction - Problem description, Motivation [5%, 1min, very brief]:
    • Why are we studying this problem? What is the biomedical need? Public health stats, if available.
  • Introduction - Biology/Physiology [15%, 3min]
    • Describe the underlying biology/physiology.
    • Find figures illustrating the system (remember to cite the sources).
  • Introduction - Goals [15%, 2min]
    • What do you/authors hope to find/accomplish with this study?
    • If successful, how will your findings/result influence our understanding or medical practice?
  • Experiments and Methods [20%, 3min]
    • Describe the experiment(s) that produced the datasets you are analyzing in your project.
    • Describe your analysis workflow. e.g, normalization, types of statistical tests, thresholds, etc.
    • Describe the methods and software you used. If we covered it in the course, you do not need to go into detail.
  • Results [20%, 3min]
    • Show your main findings.
    • Use figures (e.g., bar charts) instead of tables to present your results.
    • Compare your results to those from publications using these datasets.
  • Discussion [20%, 2min]
    • Do your results make sense biologically? Find studies that support your findings. (E.g., you found 10 genes in your Alzheimer's dataset analysis, check literature to see if these genes are known for their involvement in Alzheimer's).
    • What are the limitations of your study?
    • What follow up studies can be performed to improve upon your findings?

Project Report

  • Submit a 2 to 3-page report.docx file. Use the template file to write your report. The template file describes the sections you need to include in your report.
  • If you use Google Docs or other editor to write your report, please export your report as a Word document.
  • The break-down of the grading of the report will be similar to the presentation.

index.yml Summary File

Create a file named index.yml and enter your project's information (title/author/abstract). The projects may become publicly available. For author information, your first name(s) is required; last name(s) is recommended/optinal. When entering abstract in multiple lines, place two spaces in each of the lines after the first. See below for contents of an example index.yml file.

title: Pathway based functional analysis of IBD patients using metagenomic analysis of human gut microbiome
author: Dhruv Sakalley
abstract: Each of the additional lines of the abstract should be indented with 2 spaces.
  The abstract should be ASCII-only, e.g., if you copy-paste from Word, replace smart-quotes
  with regular quotes. Replace non-ASCII special characters and symbols with ASCII characters.
  Human Gut Microbiome contains collection of diverse species which help carry
  out various functions for the proper functioning of the human body. However, IBD
  is a condition where the diversity of this microbiome is significantly altered.
  Little is known about the causes and effects of these variations in the present
  literature. The next generation sequencing techniques provide suitable data for
  Metagenomic analysis leading to identification of uncluttered microorganisms, and
  make it possible to get detailed functional insights into the functional footprint
  of these altered microorganisms. This study uses of KEGG pathways for mapping functionality
  of the diverse gene sets in order to better understand function level changes caused
  due to the altered microbiome in case of IBD.

Project thumbnail

Create an image file thumb.png that can be used as a cover image for your project.

proj/project.txt · Last modified: 2017/11/13 15:07 by Ahmet Sacan