Course Offering: RNAseq analysis tools for the wet-lab biologist

The Center for Informatics and Graff Library is offering the following course:

RNAseq analysis tools for the wet-lab biologist: Using open-source programming languages Linux, R, and Python

The course is offered in four parts from 9 to 11 am, on August 6, 10, 13, and 17, in Conference Room G112, Graff Library. Register for the course here. Please note that you will need to register for each of the four classes in the course separately.

COURSE DESCRIPTION

Using real-world examples from publicly available “big” datasets, the objective of this course is to teach participants how to evaluate, process, analyze, interpret, and report information generated in the lab. The tutorial begins with the basic overview and use of a command line interface, i.e. a way to directly tell your computer what you want it to do by writing your own commands. From there, users will be introduced to Linux, R, and Python; open-source programming languages that are used world-wide by the scientific community to address a variety of data analysis, statistical, and graphical needs. With this information, and using either a local or cloud-based computing resource, participants will step through a high-throughput data analysis pipeline from an RNA sequencing experiment, starting with data uploading and finishing with visualization of results.

LESSONS

1. All about the shell: what is it, how do you get to it, and basic commands.
2. Programming languages used in the course: introduction, syntax, basic commands.
3. Computing environments and getting set up for the analysis.
4. RNAseq – take a raw data file and convert it to analyzable data (data upload, pre-alignment quality check, alignment, quantify reads, normalization, visualizations).
5. Statistical analysis and data visualizations.

INSTRUCTORS

Omar Khalid, PhD, ORIEN Informatics, Center for Informatics
John Kaddis, PhD, Diabetes and Cancer Discovery Science, Diabetes Metabolism Research Institute
Denis O’Meally, PhD, Center for Gene Therapy, Hematologic Malignancies and Stem Cell Transplantation Institute
Allen Mao, High Performance Research Computing Center, Center for Informatics

Upcoming Database Search Training in the Library

The Lee Graff Library is offering introductory training on searching two of the major research literature databases, Scopus and the Web of Science. Join us and learn how to stay current with the literature in your field of research.

Introduction to Scopus
Thursday, May 17, 12:30 to 2:00 pm, Lee Graff Library, Room G112
Learn to search and analyze the biomedical and health sciences research literature using the Scopus database. This training is provided by Elsevier Science.

Introduction to the Web of Science and Incites
Wednesday, June 6, noon to 1:30 pm, Lee Graff Library, Room G112
Learn to search and analyze the biomedical and health sciences research literature using the Web of Science and Incites databases. This training is provided by Clarivate Analytics.

Register for these and other Library classes.

 

The Infinite Library: Presentation and Training on March 29th

Do our 16,000+ books and 40,000+ journals cover everything our patrons need? Certainly not. Thankfully, there is interlibrary loan.

Interlibrary loan is a service whereby a user of one library can borrow books or receive copies of documents that are owned by another library. Through our networks, we are able to supplement our collection to provide our patrons with nearly everything they need: hence the idea of the Infinite Library.

Learn more at our 45-minute hands-on session. The basics of accessing electronic resources, an introduction to interlibrary loan and document delivery, and an overview of related copyright laws will be covered. You will leave this session with tips and tricks for how to better access our online journals and books as well as how to place requests using ILLiad, our online document delivery and interlibrary loan system.

The session is scheduled for March 29th at 2:00pm in the Graff Library (Room G112). Laptops will be provided. Please visit here to register.

For more information, contact Brian Chambers at bchambers@coh.org or ext. 88614.

Library Services Staff Participated in LPDW

Learning and Personal Development Week (LPDW) took place January 25-29 and the Library Services team supported the culture of learning at City of Hope by being involved in a variety of ways. Library Director Andrea Lynch was involved in the planning phases as a LPDW Advisor and Library Assistant Heather Lanctot volunteered as an Ambassador, helping to increase awareness, promoting staff registration, and hosting and photographing classes and sessions.

Library Services Offers Classes During LPDW

Library Services is offering a variety of classes and sessions during Learning and Personal Development Week. To register for any of the classes listed below, go here. We look forward to seeing you next week!