The philosophy of ‘BCH709 Introduction to Bioinformatics’ is to teach researchers basic concepts, skills, and tools for working with data so that student can get their own bioinformatics work done without pain. This illustrates the concept of bioinformatics analysis and Next Generation Sequencing for genomics including hands-on bioinformatics, understanding genomics through bioinformatics, use of command-line in multiple platforms, use of command-line tools to analyze sequencing data, and connecting to and using cloud computing.
Class Schedule
MonWed 9:00AM - 10:15AM
Aug 29, 2023 - Dec 18 2023
Modes of Instruction
This course will be accommodated in-person. This semester we will not offer Online or Alternative HyFlex course model
Class Room location
Classroom was changed to Fleischmann Agriculture Building room 234 (FA234)
FA234
Course description
As contemporary biologists we have entered an age where the use of computers in our daily work has become all but essential. The manipulation and analysis of DNA, RNA, and protein data by electronic means has become a routine task. Further, the amount of DNA, RNA and protein sequence data we are putting into databases every day is expanding at a geometric rate, and with coming advances in sequencing technology, this rate is only expected to increase. With all this new data, analysis by individual humans is simply not possible. Thus, in the past 15 years, computational biology has emerged as a field concerned with storage, manipulation, and extraction of valuable information from all this new data. However, because computational biology is an emerging field, organized courses are generally saved for higher-level study, and often are not required parts of an undergraduate curriculum. We seek to fill this void in education and create a course that will introduce students to bioinformatics at an earlier point in their education. This knowledge will prove to be not simply useful, but essential, for any student considering a degree in any area of biology and medical science.
Syllabus
Please read our Syllabus.
Rubric
Please read our Rubric.
Tentative Course Schedules
| 8/28/2023 | M | Week1 | 8/28/2023 | Monday | Introduction |
|---|---|---|---|---|---|
| 8/30/2023 | W | Week1 | 8/30/2023 | Wednesday | Introduction to Bioinformatics |
| 9/4/2023 | M | Week2 | 9/4/2023 | Monday | Labor Day |
| 9/6/2023 | W | Week2 | 9/6/2023 | Wednesday | Linux Environment and command line |
| 9/11/2023 | M | Week3 | 9/11/2023 | Monday | Linux Environment and Cloud |
| 9/13/2023 | W | Week3 | 9/13/2023 | Wednesday | Conda, Compile & Software Installations |
| 9/18/2023 | M | Week4 | 9/18/2023 | Monday | GitHub and server |
| 9/20/2023 | W | Week4 | 9/20/2023 | Wednesday | Sequencing methods and strategies |
| 9/25/2023 | M | Week5 | 9/25/2023 | Monday | Sequencing methods and strategies |
| 9/27/2023 | W | Week5 | 9/27/2023 | Wednesday | Sequence manipulation |
| 10/2/2023 | M | Week6 | 10/2/2023 | Monday | RNA-Seq |
| 10/4/2023 | W | Week6 | 10/4/2023 | Wednesday | Transcriptome assembly |
| 10/9/2023 | M | Week7 | 10/9/2023 | Monday | Transcriptome algorithms |
| 10/11/2023 | W | Week7 | 10/11/2023 | Wednesday | Introduction of R & R plotting (Tong Zhou PhD) |
| 10/16/2023 | M | Week8 | 10/16/2023 | Monday | RNA-Seq R in RNA-Seq / DESeq2 / EdgeR |
| 10/18/2023 | W | Week8 | 10/18/2023 | Wednesday | Review |
| 10/23/2023 | M | Week9 | 10/23/2023 | Monday | Midterm Exam |
| 10/25/2023 | W | Week10 | 10/25/2023 | Wednesday | Viral variant identification in NGS data (Richard Tillet, Ph. D) |
| 10/30/2023 | M | Week10 | 10/30/2023 | Monday | R in RNA-Seq / DESeq2 / EdgeR BLAST search and gene alignment |
| 11/1/2023 | W | Week11 | 11/1/2023 | Wednesday | Gene family analysis and phylogenetics (David Alvarez-Ponce, PhD) |
| 11/6/2023 | M | Week11 | 11/6/2023 | Monday | Database & file format |
| 11/8/2023 | W | Week12 | 11/8/2023 | Wednesday | RNA-Seq & BLAST Genome assembly & annotation & structure |
| 11/13/2023 | M | Week12 | 11/13/2023 | Monday | RNA-Seq & BLAST Genome structure |
| 11/15/2023 | W | Week13 | 11/15/2023 | Wednesday | RNA-Seq & BLAST Variant analysis |
| 11/20/2023 | M | Week13 | 11/20/2023 | Monday | RNA-Seq & BLAST Variant analysis Transcriptome analysis (Genome based) |
| 11/22/2023 | W | Week14 | 11/22/2023 | Wednesday | Nextday is Thanksgiving |
| 11/27/2023 | M | Week14 | 11/27/2023 | Monday | RNA-Seq & BLAST Genomics |
| 11/29/2023 | W | Week15 | 11/29/2023 | Wednesday | Enrichment analysis |
| 12/4/2023 | M | Week15 | 12/4/2023 | Monday | RNA-Seq mouse and human |
| 12/6/2023 | W | Week16 | 12/6/2023 | Wednesday | RNA-Seq mouse and human |
| 12/11/2023 | M | Week16 | 12/11/2023 | Monday | Class Review DEG |
| 12/13/2023 | W | Week17 | 12/13/2023 | Wednesday | Prepday |
| 12/18/2023 | M | Week17 | 12/18/2023 | Monday | Final Exam |
Prerequisites
- Computer with ethernet port or wifi (If in case you bring your desktop, please do not bring your monitor. we have a monitor in our classroom) Online introduction to Linux. Students must complete one of the following online tutorials (or both) before class begins.
- UNR affilated email <ID>@unr.edu or <ID>@nevada.unr.edu - How to Activate
- Setup your computer
- Setup Slack ID
- Setup Github ID
- Please register by using UNR email datacamp
- Please fill this form
Getting Started
This lesson assumes that learners have no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. Participants should bring their own laptops and plan to participate actively.
To get started, follow the directions in the Setup tab to get access to the required software and data for this workshop.
Optional Additional Meeting
Research Computing Hackathon (Hosted by HPC team)
Every Friday at 2:00pm to 4:00pm through SLACK
Hackathons provide a space for hands-on training and solution development within a Research Computing environment at the University. This is also a place to get clarification on questions/concerns regarding the HPC environment. Please bring problems to challenge the HPC team, the Office of Information Technology, and research colleagues. If you don’t need help, we still encourage you to attend and share your time and expertise with those in need of assistance. You don’t need to be an expert to attend a hackathon. Individuals at all computing skill levels are welcome! Won Yim will attend this hackathon.
Meeting
Office Howard Medical Science 216
I prefer to have online meeting through SLACK.
Optional Reading materials
Note: all reading material can be freely accessed and downloaded from the UNR internet.
Other Website
Plant Genomics Lab
Lecture website
Lecture Github
Frequently Asked Questions
Read our FAQ. Currently, this page is empty, but we will build it through the class.
Teaching Platform
This lecture was designed to be run on Unix-base system such as Ubuntu, mac, etc. All the software and data used in the class will be open source. All example data will be hosted on a Google Cloud Service. If you want to know how to use Unix-base system on your computer, please follow the directions in the Setup tab.
The website theme was adapted from the original by Data Carpentry. The infrastructure, including adventure-time and docker-browser-server, was built by @maxogden and @mafintosh. The setup of this app was based on the get-data adventure. This adventure app was made by Richard Smith-Unna. The lecture materials were crafted by Won Yim. This work is licensed under a Creative Commons 4.0 International License.