1. BF528 - Applications in Translational Bioinformatics
1/23/2019

2. Instructor Introductions
Instructor: Adam Labadorf
TAs:
Emma Briars
Dakota Hawkins
Zhe Wang

3. Course Overview Survey course in bioinformatics
Focus on high-throughput sequencing data, tools, and techniques
Focus on practical skills
Group work simulates real-world collaborative environment

4. Course Goals
Survey current bioinformatics techniques in translational studies
Give you hands-on experience working with high-throughput biological data and tools
Read and understand papers that use bioinformatics in translational studies
Develop shared vocabulary between biology and computation

5. Prerequisites Molecular and cell biology
BF527, BE505/605 or equivalent
Good-to-haves:
Basic statistics knowledge
Programming/linux cluster experience
But don’t panic...

6. Course Organization http://bf528.readthedocs.io
Wed/Fri 2:30-4:15 STH 318
Some online content early in semester
Online content limited to ~1 hr/class
Class period split into two segments:
Lecture or discussion of online material
Project group meeting and discussion

7. Course Organization cont’d
Students assigned into groups of 4
Each group has a primary TA
4 projects over the course of the semester
The last project is an individual project
No homeworks
No exams

8. Schedule of Topics Lecture Day Date Topic Project Assigned/Due 1 W
Jan 23
Introduction 2 F
Jan 25
Computational Skills Primer 3
Jan 30
Genomics, Genes, and Genomes 4
Feb 1
Array Technologies 5
Feb 6
Gene sets and enrichment 6
Feb 8
2nd Gen Sequencing 7
Feb 13
Sequence Analysis 1 - WGS/WES 8
Feb 15
Genomic Variation and SNP Analysis 9
Feb 20
Biological Data Formats 10
Feb 22
Databases
1/2 11
Feb 27
Sequence Analysis 2 - RNA-Seq 12
Mar 1
Biomarkers 13
Mar 6
Sequence Analysis 3 - ChIP-Seq 14
Mar 8
Phylogenetics
Spring Break

9. Schedule of Topics cont’d15 W
Mar 20
Replicability vs Reproducibility Strategies
2/3 16 F
Mar 22
Computational Environment Management 17
Mar 27
Computational Pipeline Strategies 18
Mar 29
Sequence Visualization 19
Apr 3
Microbiome: 16S 20
Apr 5
Microbiome: Metagenomics 21
Apr 10
Metabolomics 22
Apr 12
Proteomics/Mass Spectrometry
Apr 17
No class, schedule adjustment
3/4 23
Apr 19
Single Cell Techniques 24
Apr 24
Systems Biology 25
Apr 26
Integrative Genomics 26
May 1
The Future/In class group work

10. Projects Assigned into groups based on experience
Groups are for the entire semester
You will reproduce published findings from published manuscripts
Each project has a full writeup

11. Project Groups Group members will play one of four roles:
Data Curator - find, download, and organize data
Programmer - process data into analyzable form
Analyst - transform processed data into interpretable form
Biologist - understand paper and biological context, help interpret results
Roles rotate for each project
Structured class time to help facilitate group work and help each other!

12. Project Group Meeting : Wednesdays
Time allotted for groups to meet and discuss progress
“Stand-up” meeting structure:
“What did I work on since our last meeting?”
“What challenges did I encounter?”
“Are there any obstacles to completing my work?”
“What will I be working on for next meeting?”
Each group will make a brief status report at the end of class

13. Project Group Meeting : Fridays
Time allotted for roles to meet and discuss progress
Similar structure to Wednesdays
Share challenges and solutions among roles
Each role group will make a brief status report at the end of class

14. Project Report Organized like a published study
Sections (primary role):
Intro - background and motivation (Biologist)
Data - data description (Data Curator)
Methods - processing and tools (Programmer)
Results - findings (Analyst)
Discussion - interpret findings (Biologist)
Conclusion (all)

15. Assessment Each project is 25% of your total grade Broken down:
Intro, Conclusion - 2.5%
Data, Methods, Results, Discussion, 20%
Stand-up participation: 15%

16. Translational Bioinformatics

17. Biology as Data Science
DNA structure published in Nature
first genetic sequence determined, protein DataBank
Sanger sequencing, first genome sequenced
PCR technique invented
Human Genome Project begun
first bacterial genome sequenced, microarray technology first described
yeast genome on a microarray, sequencing by synthesis concept established
first multicellular eukaryote sequenced
first draft of human genome
Solexa Genome Analyzer released

18. “Big” Data Single Microarray dataset: ~500Mb
Single short read dataset: ~2Gb-300Gb
Human genome reference sequence: ~2Gb
One run of Illumina instruments:
HiSeq 2500: ~1Tb
NovaSeq 6000: ~6Tb
Gene Expression Omnibus (GEO):
2014: 1,237,138 samples, ~28 Tb
2018: 2,335,694 samples, ?? Tb

19. What is Bioinformatics?
“Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to study and process biological data.”
Wikipedia

20. Conceptual History of Bioinformatics
Biological sequences digitized
Biological databases needed to store sequences
Search tools needed for databases
Tools for analyzing data from searches
Computational tools required to analyze human genome
Sophisticated sequence analysis tools enable analysis of large amounts of sequencing data
Sequencing data volume explodes, requiring new tools
And here we are

21. The Biologist’s Tools
Wet lab biologists:
Bioinformaticians:

22. Sequence: The Fundamental Datatype
Computer Science
genome assembly, homology, phylogeny
Physics
DNA/RNA/protein structure, drug prediction
Statistics
gene expression, population genetics, biomarkers
Mathematics
metabolic modeling, synthetic biology, systems biology

23. Genbank Sequences

24. Translational Bioinformatics
“Translational Bioinformatics is an emerging field in the study of health informatics, focused on the convergence of molecular bioinformatics, biostatistics, statistical genetics, and clinical informatics.”
Wikipedia

25. Workshop 0. Basic Linux and Command Line Usage
For Next Time
Assignment: familiarize yourself with the material on basic command line usage found here:
Workshop 0. Basic Linux and Command Line Usage

26. SSH and SCC SCC - Shared Compute Cluster You all have accounts on SCC
You will need an ssh client program to connect:
Mac, Linux: Terminal (included)
Windows: MobaXTerm
Connect to: scc1.bu.edu with your BU username/password
Demonstration

27. 2019 Survey Results

28. Programming/Computer Skills

29. Statistics

30. Biology

31. Bioinformatics

32. Rank the following roles that you might play in a project in order of preference

33.
Rank the following roles that you might play in a project in order of preference

34. 2018 Survey Results

35. How comfortable are you with the following programming languages/concepts?

36. How comfortable are you with the following statistics concepts?

37. How comfortable are you with the following biology concepts?

38. How comfortable are you with the following bioinformatics concepts?

39. Rank the following roles that you might play in a project in order of preference

40. What do you hope to learn?

41. How do you plan to use what you learn?