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Student Projects

Interested in providing data for student projects? Contact Leslie Coonrod and Stacey Wagner.

Project Scope and Expectations

Students work on projects in groups of 3-4 over the course of 4 months while balancing additional coursework. On average, each student will dedicate ~5 hours per week to project work. Projects may result in publishable data, although many projects are exploratory, validation based, or primarily involve pipeline comparisons.

What is expected from groups that provide projects?

  • Identify a mentor to engage with students periodically (twice a month, on average) to answer questions about the project
    • Optional: mentor is experienced in bioinformatics/computational biology
    • BGMP faculty will provide technical mentorship when applicable
  • Provide a project description that:
    • Defines the goals of the project
    • Provides instructions for the students about how data can be accessed
    • Provides relevant papers from the field’s literature
  • Project data must be available NO LATER than Sept 3, 2020, please do not submit projects that have data “coming soon”

Learning outcomes for students

  • Define the biological background and explain relevance to technical and non-technical audiences
  • Demonstrate collaborative working skills
  • Evaluate data quality
  • Create and execute plan for data analysis
  • Write original scripts, employ HPC, and utilize bioinformatics software for analyses
  • Interpret data and employ appropriate statistical tests and concepts to support conclusions about data
  • Present conclusions with clear visuals through
    • talks
    • posters
    • write-ups

2020 Tentative Timeline

In addition to periodic “lab meeting” style project updates, following is a rough timeline for the projects:

Date Major checkpoint Details
Sept 3, 2020 Project description submission deadline Projects will be reviewed by BGMP staff to ensure that the scope of the project is appropriate for our class and that the data are available
Sept 10, 2020 Potential topics communicated to students Projects are discussed in class
Sept 29, 2020 Assign projects to student groups Student project preferences are considered, each group has ~3 students, projects with insufficient student interest may be dropped
Oct 13 & 15, 2020 Groups present project background and motivation Mentors welcome to attend
Nov 17 & 19, 2020 Groups present project to general audience/layperson Mentors welcome to attend
early-Dec 2020 Formal presentation of projects Final oral presentations, mentors invited
Jan/Feb 2020 Formal write-up of data/results Mentors can specify preferred format (ex: GitHub repo, poster, results section of paper, etc.)
Jan 29, 2021 Poster presentations Poster session at Genomics in Action meeting, wrap-up of projects

Examples of types of analyses from previous years

  • De novo transcriptome assembly and annotation
  • Genome assembly
  • Phage display analysis to determine peptide binding specificity to a protein
  • Microbiota community composition association with diet (16S amplicon)
  • Identification of adapted mutations within experimentally evolved gut bacterium (whole genome sequencing)
  • Differential gene expression analysis
  • Alternative splicing profiling in human disease
  • Single-cell RNA-seq

Student background

During the summer term, students undergo intensive training in basic programming in Python, Unix shell (Bash), and R. Students understand how sequencing technology works, experimental design, and how to solve common problems in computational biology. Specifically, students are practiced in:

  • Command line navigation
  • Reading, evaluating, and presenting scientific literature in many Life Science disciplines
  • Working on a shared computing environment (HPC) and job submission
  • Parsing sequencing and other types of data
  • Analyses of genomic data:
    • QC
    • genome assembly
    • transcriptome assembly
    • differential gene expression analysis
    • visualization of multivariate data
    • phylogenetics
    • 16S amplicon-based profiling of microbial communities
  • Biological statistics (courses during fall and winter terms)

Publishing

The standard conventions of authorship should be followed: if student contributions are written up in a publication, then authorship should be considered. 

Example Posters

Below are examples of posters project groups have created for past Genomics in Action meetings. Click the links below to view the posters.