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

July 13, 2018

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.


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.


  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.


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


Stem Cell Research News July 02, 2018

July 9, 2018

The July 2nd issue of Stem Cell Research News has been posted.

BioCentury July 02, 2018

July 9, 2018

The week of July 02, 2018 issue of BioCentury has been released.

Holiday Notice:

BioCentury will not be published next week, July 9th, in observance of the Independence Day holiday in the U.S. Both will return the week of July 16.

The Cancer Letter July 06, 2018

July 9, 2018

The July 06, 2018 issue of Cancer Letter has been posted and now includes The Clinical Cancer Letter Section.

Staff Training for New Integrated Library System, July 9th to 11th

July 5, 2018

Graff Library is beginning the process of migration to a new integrated library system (the Library Catalog).  The new system will increase the Library’s ability to efficiently provide access to our collections, both electronic and print. Library staff will receive training to prepare for the migration Monday to Wednesday, July 9th through the 11th. Library operations will continue as usual on these days, although we may not be able to respond to your questions and assist you as quickly as we normally do.

If you have any questions or concerns, please contact Keir Reavie (82980,


The Cancer Letter June 29, 2018

July 2, 2018

The June 29, 2018 issue of Cancer Letter has been posted and now includes The Clinical Cancer Letter Section.

Graff Library will be Closed on Independence Day

June 28, 2018

In observance of Independence Day, the Library Services team will not be staffing the Graff Medical and Scientific Library on Wednesday, July 4, 2018. We will respond to your questions and process any interlibrary loan and document delivery requests when we return on July 5.

Please remember that the City of Hope community can access the library anytime. Although the Graff Library is staffed Monday through Friday from 8 a.m. to 6 p.m., the building is available 24/7, 365 days of the year, via badge access at our back egress (near the Hilton building). For more information, refer to the Library After Hours brochure.

Please contact Keir Reavie, Director of Library Services, at, or extension 82980 if you have any questions, concerns, or comments.