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.

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

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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, kreavie@coh.org).

 


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 kreavie@coh.org, or extension 82980 if you have any questions, concerns, or comments.


Just Culture: Communicating, Collaborating and Thinking as a Team, the Reading List

June 5, 2018

Many of the books mentioned by Craig Clapper in his presentation on patient safety at the City of Hope on June 5, 2018, are available in the Graff Library, in print and electronic versions. The reading list can be found here.

The Library will add to this list as we obtain access to additional material related to this important topic.

If you have any questions about this or other topics, please contact the Library at library@coh.org, or 626-218-7497.

 


Graff Library will be Closed on Memorial Day

May 24, 2018

In observance of Memorial Day, the Library Services team will not be staffing the Graff Medical and Scientific Library on Monday, May 28, 2018. We will respond to your questions and process any interlibrary loan and document delivery requests when we return on May 29.

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 kreavie@coh.org, or extension 82980 if you have any questions, concerns, or comments.


Upcoming Database Search Training in the Library

May 1, 2018

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.

 


Library Catalog Testing, Monday, April 23.

April 17, 2018

The Lee Graff Library will be running some tests on the integrated library system Monday, April 23, from 5 to 7 pm. During this time the Library Catalog may not be available, or operate as expected. We apologize for any inconvenience. If you have any questions or concerns, please contact Keir Reavie via email, or at 626-218-2980.