BF528 - Applications in Translational Bioinformatics
Welcome to the homepage of BF528. CURRENTLY UNDER REVISION.
Semester: Spring 2024
Meeting time: TBA
Location: TBA
Office hours: By appointment and weekly as determined in class
Contents:
Learning Objectives
- Gain conceptual understanding of the assays and tools used in modern bioinformatics studies from how they function on a molecular level to the major computational analysis steps
- Develop proficiency in creating bioinformatics workflows with an emphasis on reproducibility and portability
- Practice analyzing bioinformatics results and interpreting them in the context of the underlying research question to draw meaningful biological conclusions
Below you will find a selection of some of the prominent biological and computational topics that will be covered in the course:
- High Throughput Sequencing Technologies (RNAseq, ChIPseq, scRNAseq) and various omics technologies (Proteomics, Metabolomics, etc)
- Computational Workflow Tools (snakemake, nextflow)
- Reproducibility and Replicability Tools (Git, Docker, Conda)
- Bioinformatics Databases and File Formats
Course Description
The objective of this course is to expose students to modern bioinformatics studies with a specific focus on the analysis of next generation sequencing data. The course lectures will cover a mix of both biological and computational topics necessary for the technical and conceptual understanding of current high-throughput genomics techniques. This will include brief discussions of the molecular mechanisms of the assays, basic data analysis workflows, and translating these results into biological conclusions.
Students will get hands-on experience developing computational workflows that perform an end-to-end analysis of sequencing data from ubiquitous NGS technologies including RNA-sequencing, ChIP-sequencing, and Single Cell RNA-sequencing. The course emphasizes the importance of reproducibility, portability, and replicability in modern bioinformatics.
Classes will be traditional lectures exploring the variety of topics regarding next generation sequencing and labs will focus on practical activities meant to give you experience working with the tools and technologies needed for our analyses.
Projects are split into weekly tasks but the majority of your evaluation will be the final report produced for each project.
Course Values and Policies
Everyone is welcome. Every background, race, color, creed, religion, ethnic origin, age, sex, sexual orientation, gender identity, nationality is welcome and celebrated in this course. Everyone deserves respect, patience, and kindness. Disrespectful language, discrimination, or harassment of any kind are not tolerated, and may result in removal from class or the University. The instructors deem these principles to be inviolable human rights. Students should feel safe reporting any and all instances of discrimination or harassment to the instructor, to any of the Bioinformatics Program leadership, or the BU Equal Opportunity Office
Everyone brings value. Each of us brings unique experiences, skills, and creativity to this course. Our diversity is our greatest asset. Collaboration is highly encouraged. All students are encouraged to work together and seek out any and all available resources when completing projects in all aspects of the course, including sharing both ideas and code as well as those found on the internet. Any and all available resources may be brought to bear. However, consistent with BU policy, your reports should be written in your own words and represent your own work and understanding of the material.
Life happens. Your mental, physical and emotional health isfar more important than any class. Make sure to take care of yourself and reach out to someone you trust (mentor, family member, or friend) if you ever feel you need to talk to someone. BU offers a number of resources through Student Health Services for managing situations involving grief, anxiety and depression, stress, homesickness and other common issues. I am also always here to listen without judgment. On a related note, if you need to miss class because of private matters, you do not need to disclose anything you aren’t comfortable sharing, please just let me know and I will work with you to help you catch up when you return. Your family, friends, and health should always come first.
Prerequisites
Basic understanding of biology and genomics. Any of these courses are adequate prerequisites for this course: BF527, BE505/BE605. Students should have some experience programming in a modern programming language (R, python, C, Java, etc).
Instructor
Joey Orofino & Adam Labadorf
My pledge to foster Diversity, Inclusion, Anti-racism
This course is a judgement free and anti-racist learning environment. Our cohort consists of students from a wide variety of social identities and life circumstances. Everyone will treat one another with respect and consideration at all times or be asked to leave the classroom.
As instructor, I pledge to
- Learn and correctly pronounce everyone’s preferred name/nickname
- Use preferred pronouns for those who wish to indicate this to me/the class
- Work to accommodate/prevent language related challenges (for instance I will do my best to avoid the use of idioms and slang)
Project Overview
The three projects are as follows:
- [Nextflow Practice][Nextflow Introductory Project] [Transcriptional Profile of Mammalian Cardiac Regeneration with mRNA-Seq][Project 1: Transcriptional Profile of Mammalian Cardiac Regeneration with mRNA-Seq]
- [ChIPseq analysis of the human transcription factor Runx1][Project 2: ChIPseq analysis of the human transcription factor Runx1]
- [scRNAseq analysis of human liver][Project 3: scRNAseq analysis of human liver]
]
Grading and Assessment
Project 0 is an introduction to all the tools and technologies we will be utilizing throughout the semester. You will receive feedback on all your tasks, but it will not count as part of your assessment.
60% of your grade: Projects 1 and 2 have been split into weekly tasks. These tasks will be a mixture of computational or analysis tasks and some discussion questions meant to enhance your understanding of larger concepts or the rationale underlying certain tasks. These tasks and answers to the discussion questions will be due the week following their assignment. Myself and the TAs will provide feedback on if you successfully completed the tasks or answered the questions and you will then be allowed to resubmit your work the following week. As long as you successfully address the given feedback upon resubmission, you will receive full credit for each week.
The other 40% of your grade: Projects 1 and 2 were designed with scaffolding and instructions meant to aid you in developing these nextflow pipelines. The remaining 40% of your grade will be based on project 3.
For project 3, you will be asked to develop a pipeline from scratch, using all of the principles and techniques we’ve utilized throughout the semester. We will provide minimal guidance and a list of analyses and questions you will need to answer. This project will involved generating a nextflow pipeline and analysis workflow that will process a scRNAseq experiment from raw data to biological analysis.
Course Schedule
| No. | Day | Date | Primary Topic | Project Assigned/Due |
|---|---|---|---|---|
| 1 | Fri | 1/19/2024 | Introduction | |
| 2 | Mon | 1/22/2024 | Genomics, Genes, and Genomes & [conda] | Assignment 0 Assigned |
| 3 | Wed | 1/24/2024 | Computational Pipeline Strategies | |
| 4 | Fri | 1/26/2024 | Snakemake pt2, Git and Miniconda setup | |
| 5 | Mon | 1/29/2024 | 2nd Gen Sequencing & Data Formats | Wk 1 - P1 Assigned |
| 6 | Wed | 1/31/2024 | Working with Git, Vscode, snakemake on SCC | |
| 7 | Fri | 2/2/2024 | Sequence Analysis Fundamentals | |
| 8 | Mon | 2/5/2024 | Project 1 - Week 1 Review | Wk2 - P1 Assigned / Wk 1 - P1 Due |
| 9 | Wed | 2/7/2024 | Sequence Analysis - RNA-Seq 1 | |
| 10 | Fri | 2/9/2024 | Sequence Analysis - RNA-Seq 2 | |
| 11 | Mon | 2/12/2024 | Project 1 - Week 2 Review | Wk3 - P1 Assigned / Wk 2 - P1 Due |
| 12 | Wed | 2/14/2024 | SCC Cluster Usage & terminal multiplexers | |
| 13 | Fri | 2/16/2024 | Replicability vs Reproducibility Strategies | |
| Mon | 2/19/2024 | No Class | Wk4 - P1 Assigned | |
| 14 | Wed | 2/21/2024 | Project 1 - Week 3 Review | Wk3 - P1 Due |
| 15 | Fri | 2/23/2024 | Gene Sets and Enrichment | |
| 16 | Mon | 2/26/2024 | Project1 - Week 4 Review | Wk5 - P1 Assigned / Wk4 - P1 Due |
| 17 | Wed | 2/28/2024 | Putting it all together - snakemake | |
| 18 | Fri | 3/1/2024 | Sequence Analysis - ChIP-Seq | |
| 19 | Mon | 3/4/2024 | Sequence Analysis - ATAC-Seq | Wk1 - P2 Assigned / P1 Report Due |
| 20 | Wed | 3/6/2024 | Genome Browsers | |
| 21 | Fri | 3/8/2024 | Project 1 Final Review | |
| 22 | Mon | 3/11/2024 | No Class | |
| 23 | Wed | 3/13/2024 | No Class | |
| 24 | Fri | 3/15/2024 | No Class | |
| 25 | Mon | 3/18/2024 | Project 2 - Week 1 Check-in and Review | Wk2 - P2 Assigned / Wk2 - P1 Due |
| 26 | Wed | 3/20/2024 | Biological Databases | |
| 27 | Fri | 3/22/2024 | Genomic Variation and SNP Analysis | |
| 28 | Mon | 3/25/2024 | Project 2 - Week 2 Check-in and Review | Wk3 - P2 Assigned / Wk2 - P2 Due |
| 29 | Wed | 3/27/2024 | Microbiome: 16s | |
| 30 | Fri | 3/29/2024 | Microbiome: Metagenomics | |
| 31 | Mon | 4/1/2024 | Project 2 - Week 3 Check-In and Review | Wk4 - P2 Assigned / Wk3 - P2 due |
| 32 | Wed | 4/3/2024 | Proteomics | |
| 33 | Fri | 4/5/2024 | Metabolomics | |
| 34 | Mon | 4/8/2024 | Project 2 - Week 4 Check-In and Review | Wk5 - P2 Assigned / Wk4 - P2 Due |
| 35 | Wed | 4/10/2024 | Docker | |
| 36 | Fri | 4/12/2024 | Single Cell Analysis Part 1 | |
| 37 | Mon | 4/15/2024 | No class | Final Project Start|P2 Report due |
| 38 | Wed | 4/17/2024 | Single Cell Analysis Part 2 | |
| 39 | Fri | 4/19/2024 | Single Cell Analysis Part 3 | |
| 40 | Mon | 4/22/2024 | Single Cell Analysis Workshop Pt. 1 | |
| 41 | Wed | 4/24/2024 | Project 3 Check-In | |
| 42 | Fri | 4/26/2024 | Single Cell Analysis Workshop Pt. 2 | |
| 43 | Mon | 4/29/2024 | Spatial Transcriptomics | |
| 44 | Wed | 5/1/2024 | Course Feedback and Discussion | |
| 45 | Wed | 5/08/2024 | Final projects due | P3 Report Due |