Summer Bioinformatics Program 2021

June 14th - August 17th, 2021

Overview

After the success of the 2020 Summer Bioinformatics Program the RNA Institute will again host a bioinformatics program, this year with opportunities for both in-person wet lab and virtual bioinformatics components. This summer program is designed to teach a bioinformatics approach to the analysis of biological research data.  Researchers are increasingly expected to have the bioinformatics skills necessary to effectively process, manage and utilize complex sets of data. This program will provide students with the skillset and tools that are a vital component for advanced degrees and careers in any STEM field.

Students will learn the basics of a UNIX operating system, how to manage data on a high performance computer (HPC) cluster, coding with the data and visualization program R and the analysis of next-generation sequencing data. Using these skills, students will tackle projects using large biological datasets related to the most common form of muscular dystrophy as well as other ongoing research programs at the RNA Institute. Throughout this process, students will learn the computational pipelines used for bioinformatics and how to present these large data sets in figures and graphs. As a new addition to this year’s program, students will also engage in professional development seminars and activities that will focus on preparing students for graduate school and a career in research.

This program is based on previously successful programs launched at the University of Oregon and the University of Florida.

 

Program Structure

In the first week, summer research students will attend mandatory remote classroom sessions in the mornings taught by course leaders and RNA Institute faculty. During the remainder of the day, students will research and learn independently with remote assistance provided by RNA Institute leaders or perform wet lab work within the RNA Institute. Students will meet up again remotely as a group at the end of the day for a Question and Answer session and for instructors to check in on their learning and research progress during the day. During this first week, students will learn the basics of UNIX operating system, the R programming language and bioinformatics pipeline.

In the following three weeks, summer research students will maintain this schedule of shorter mandatory remote morning classroom sessions, independent study and end of the day Q&A and check-in session while analyzing myotonic dystrophy data sets. For the remaining six weeks students will focus on applying the bioinformatics skills they have learned to an independent research topic developed with the help of their RNA Institute faculty member. The schedule of topics for each week (see schedule below) are designed to take students through the fundamentals of RNA science and the bioinformatics pipeline.

Students in the summer program must commit to attending these twice daily sessions and to performing independent learning and research during the rest of the day.

Course Resources
Schedule

Click to view Bioinformatics Summer Course 2021 Schedule

Project 1

Date 11am Lecture 4pm Afternoon Session
14-Jun   All - Introduction to the command line
15-Jun   Check concepts from CodeAcademy and have RStudio and terminal downloaded
16-Jun   Get students on HPCC; flag those whose credentials do not work yet
17-Jun Prokaryotic Lecture  
18-Jun What is bioinformatics/HPCC/sequencing history/RNA-Seq Download miniconda and STAR
Week 2    
21-Jun DM1 Lecture DM1 concepts
22- Jun Overview of sequencing pipeline and intro to DMSeq.org All students Q&A with Planco family - @3:15pm
23-Jun Run first test job / Background to STAR alignment Visit and tour DMSeq.org
24-Jun STAR Alignment Checkpoint: running STAR alignment (and FASTQC)
25-Jun STAR Alignment Output files and Intro to DESeq Checkpoint: running STAR alignment (and FASTQC)
Week 3    
28-Jun DESeq/RStudio/Mapping network drive Configure RStudio to run DESeq2
29-Jun Differential gene expression analysis  
30-Jun Condepts: Alternative splicing vs differential gene expression Download rMATS and configure RStudio to run maser
1-Jul Alternative splicing analysis  
2-Jul Figure generation from differential gene expression analysis  
Week 4    
6-Jul Figure generation from alternative splicing analysis Checkpoint: any programs not working?
7-Jul Gene ontology enrichment analysis [New lecture]  
8-Jul Expectations for project 2, questions from project 1  
9-Jul Introductory lectures to biology for project 2 by group leaders in individual small groups Introduction to biological concepts for project 2

Project 2 - Bioinformatics cohort

12-Jul Different sequencing technologies: nanopore, single cell seq, SHAPE-MaP  
13-Jul See project 2 full cohort Final presentations in small groups for project 1
14-Jul See project 2 full cohort Check students have access to data for project 2 and help to identify the research question and tools/pipeline to address their question
15-Jul Presentations on plan for project 2  
16-Jul Presentations on plan for project 2  
15-12 Jul   Small group meetings twice a week from 15th July to 12th August

Project 2 Full cohort

13-Jul Repeat expansion diseases - Hannah Shorrock Research Seminar 11am
14-Jul Interview technique and building a CV - John Cleary and Tammy Reid Professional Development - 11am
20-Jul Prokaryotic - Spencer Bruce Research Seminar 11am
21-Jul Rigor, reproducibility and ethics in science - Panel Discussion  Professional Development - 11am
27-Jul Developmental biology - Nicholas Moskwa Research Seminar 11am
28-Jul How to read and write a paper - Gaby Fuchs Professional Development - 11am
3-Aug COVID - Ryan Meng - tentative date Research Seminar 11am
4-Aug Next steps for undergraduate researchers - Panel Discussion Professional Development - 11am
10-Aug Computational biology - Sweta Vangaveti Research Seminar 11am
12-17 Aug Final presentations from every student on summer fellowship program Research Seminar 11am
Communication
Programming

Introduction to R and RStudio


Learn R: https://www.codecademy.com/learn/learn-r

 
Module 1 (Introduction): https://www.codecademy.com/learn/learn-r/modules/learn-r-introduction

 
Module 2 (Data Frames): https://www.codecademy.com/learn/learn-r/modules/learn-r-data-frames

 
Module 3 (Data Cleaning): https://www.codecademy.com/learn/learn-r/modules/learn-r-data-cleaning

 
Introduction to the Command Line


Linux Basics: The Command Line Interface https://www.edx.org/course/linux-basics-the-command-line-interface 

Unix Tutorial:

http://www.ee.surrey.ac.uk/Teaching/Unix/ 
https://www.tutorialspoint.com/unix/unix-directories.htm
 
Unix Cheat Sheet: 
http://www.mathcs.emory.edu/~valerie/courses/fall10/155/resources/unix_cheatsheet.html
 
R and RStudio Tutorial:
http://ncss-tech.github.io/stats_for_soil_survey/chapters/1_introduction/1_introduction.html#2_c ourse_overview 

 

Terminal

Windows 10 
Downloading: https://www.ssl.com/how-to/enable-linux-subsystem-install-ubuntu-windows-10/ 
Accessing: Use the start menu and navigate to the Ubuntu app or use the search bar to find the Ubuntu app

macOS 
Downloading: Terminal comes pre-loaded with macOS
Accessing: Open your Applications folder, followed by your Utilities folder, and select Terminal or press Command + spacebar to launch Spotlight and search for Terminal
 

R

Windows 10 
Open an internet browser and go to www.r-project.or g. 
Click the "download R" link in the middle of the page under "Getting Started." Select a CRAN location (a mirror site) and click the corresponding link.  
Click on the "Download R for Windows" link at the top of the page.  
Click on the "install R for the first time" link at the top of the page. 
Click "Download R for Windows" and save the executable file somewhere on your computer. Run the .exe file and follow the installation instructions.  
 
macOS
Open an internet browser and go to www.r-project.or g.
Click the "download R" link in the middle of the page under "Getting Started." Select a CRAN location (a mirror site) and click the corresponding link. 
Click on the "Download R for (Mac) OS X" link at the top of the page. 
Click on the file containing the latest version of R under "Files." 
Save the .pkg file, double-click it to open, and follow the installation instructions. Now that R is installed, you need to download and install RStudio. 

 

RStudio 

Windows 10
Go to www.rstudio.com and click on the "Download RStudio" button. 
Click on "Download RStudio Desktop." 
Click on the version recommended for your system, or the latest Windows version, and save the executable file.  Run the .exe file and follow the installation instructions. 

macOS 
Go to www.rstudio.com and click on the "Download RStudio" button. 
Click on "Download RStudio Desktop." 
Click on the version recommended for your system, or the latest Mac version, save the .dmg file on your computer, double-click it to open, and then drag and drop it to your applications folder. 
 

 

 

Participants
Group 1
Emily Davey

Group Leader: Emily Davey, Research Assistant

Affiliation: University at Albany

Email: [email protected]

Bhumika Devkota

Bhumika Devkota, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Andy Berglund

Dana Rzek

Dana Rzek, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Andy Berglund

 

Morgan Williams, University at Albany

Email: [email protected]

Mentor: Tammy Reid

Subodh Mishra

Subodh Mishra, Postdoctoral Fellow, University at Albany

Email: [email protected]

Mentor: Andy Berglund

Asmar Aliyeva

Asmer Aliyeva , University at Albany

Email: [email protected]

Mentor: Tammy Reid

Amber Rieger

Amber Rieger, University at Albany

Email: [email protected]

Mentor: Tammy Reid

Labika Baral

Labika Baral, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Andy Berglund

 

Joseph Porter, Postdoctoral Fellow, University of Rochester

Email: [email protected]

Mentor:

Amy Mascorro

Amy Mascorro, University at Albany

Email: [email protected]

Mentor: Andy Berglund

Alyssa Kamara

Alyssa Kamara, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Andy Berglund

Kenneth Mensah

Kenneth Sarpong Mensah, Farmingdale State College

Email: [email protected]

Mentor: Andy Berglund

Demi Ishmael

Demi Ishmael, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Andy Berglund

 

Group 2
Jacob Schroader

Group Leader: Jacob Schroader, RNA Fellow

University at Albany

Email: [email protected]

Humphrey Omeoga

Humphrey Omeoga, Graduate Student, University at Albany

Email: [email protected]

Mentor: Tom Begley

Anwesha Sarkar

Anwesha Sarkar, Graduate Student, University at Albany

Email: [email protected]

Mentor: Tom Begley

Thomas Jambunathan

Thomas Jambunathan, Undergraduate Student, Cornell University

Email: [email protected]

Mentor: Kaalak Reddy

 

Forrest Gao, High School Student

Email: [email protected]

Mentor: Jia Sheng

Aiyana Carter

Aiyana Carter, SUNY Oneonta

Email: [email protected]

Mentor: Alan Chen, Ing Nang Wang

Jack Geary

John 'Jack' Geary, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Gaby Fuchs

 

Chetna Mathur, Graduate Student, University at Albany

Email: [email protected]

Mentor: Tom Begley

Christina Heil

Christina Heil, Postdoctoral Fellow, University of Rochester

Email: [email protected]

Mentor:

 

Group 3
Nicholas Moskwa

Group Leader: Nicholas Moskwa

 

Lydia Proskauer

Lydia Proskauer, Undergraduate Student, Colgate University

Email: [email protected]

Mentor: Prash Rangan

 

Jen Morrissey, Graduate Student, University at Albany

Email:[email protected]

Mentor: Mindy Larsen

Avik Paul

Avik Paul, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Bijan Dey

Kavi Palanivel

Kavipriya Kovai Palanivel, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Jason Herschkowitz / Ali Ropri

Annie Scully

Annalyse Scully, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Jason Herschkowitz / Ali Ropri

Sakthi Muthukrishnan

Sakthi Muthukrishnan, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Mindy Larsen

Nick Mathias

Nick Mathias, Graduate Student, University at Albany

Email: [email protected]

Mentor: Prash Rangan

 

Group 4
 

Group Leader: Spencer Bruce, Postdoctoral Fellow

University at Albany

Email: [email protected]

 

Group Leader: Maddy Turcotte

University at Albany

Email: [email protected]

Manuela Montoya Giraldo

Manuela Montoya Giraldo, Graduate Student, Universidad Libre Pereira

Email: [email protected]

Mentor: Cheryl Andam

Andrew Muñoz Gamba

Andrew Munoz Gamba, Graduate Student, Colombia

Email: [email protected]

Mentor: Cara Pager

Sevinj Mursalova

Sevinj Mursalova, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Cheryl Andam

Teresa Hnin

Thet (Theresa) Hnin, Graduate Student, University at Albany

Email: [email protected]

Mentor: Alex Valm

Farwah Narjis

Farwah Narjis, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Cheryl Andam

Marven Berlus

Marven Berlus, Undergraduate Student, University at Albany

Email: [email protected]

Mentor: Cheryl Andam

Gabrielle Roosevelt

Gabrielle Roosevelt, University at Albany

Email: [email protected]

Mentor: Cheryl Andam

Milan Pfister

Milan Pfister, University at Albany

Email: [email protected]

Mentor: Cheryl Andam

 

Kickoff Meeting - June 10, 2021

RNA Institute Summer Fellowship