CS111 Introduction to Genome Browsers

This course will provide a general introduction to genome browsers to acquaint the researcher on the use and data available on several popular genome browsers such as the UCSC Genome Browser, Ensembl, NCBI Map Viewer and Integrated Microbial Genomes (IMG). There are several publicly available genome browsers (see course outline) that allow researchers to access annotated data on a large number of genomes. These genome browsers are excellent resources for data discovery and analysis. This course is targeted towards researchers who are not acquainted with these genome browsers or who wish to learn to use these tools more effectively. The course will go over the basic use of each genome browser and some of the data and tools available to them. The user will also get a good overview of comparisons and contrasts between these browsers.

No experience is required, although prior experience with any other programming language will be helpful. Math skills will also be useful.

Each class is approximately 90 minutes long, each would include about 45 minutes of introduction (where attendees can follow along on the browser) and another 45 minutes of hands-on project exercises.

Session 1

Introduction: General overview of genome browsers and characteristics.

UCSC Genome Browser: Introduction to the UCSC (University of California, Santa Cruz) Genome Browser, a comprehensive database of human and dozens of other species genomic data. These data are presented in easy to understand graphical interface with annotated data from sources from around the world.

Session 2

An introduction to some advanced topics of the UCSC Genome Browser will include several useful analysis tools such as the Gene Sorter and a powerful advanced search (Table Browser).

Session 3

Ensembl: Ensembl Genome Browser is an extensive browser with a large number and variety of genomes. A joint project of the European Bioinformatics Institute (EBI) and the Sanger Institute, Ensembl gives the user the ability to browse an annotated graphical display of the genome, add user generated data for viewing and research, complete an advanced search (BioMart) of the data and much more.

Session 4

Map Viewer: Map Viewer is a genome viewing browser from the NCBI. Map Viewer organizes and displays dozens of species genomes, and provides additional context with appropriate annotations for the genomic sequences. Extensive integration with other NCBI tools enables researchers to link quickly to relevant additional details.

Session 5

Integrated Microbial Genomics (IMG): A data management platform for analyzing microbial genomes, and integrates data from not only the Joint Genome Institute projects but many other public information resources as well. At the IMG system, you can search for genes by keyword or BLAST searches, you can search for genes phylogenetically among many organisms, and you can browse for information by organism. From search results, you can follow links to various data ranging from protein functions to taxonomic lineages.

Conclusion: General summary and a compare and contrast of genome browsers.

This course is taught by Warren Lathe.

Registration

Registration for courses at Bioinformatics.org takes two steps:

Step 1

If you haven't already done so, create an on-line account to access the educational section of our website. Please note that the registration for our educational system is separate from that of the main website; you will require another account.

Step 2

Register for this course by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).

On-demand course held on-line

This course might be taught on-demand, on-line. Please check the list of on-demand courses to see if this course can be taken as such.

An on-demand version provides pre-recorded video lectures. Once registered, you may begin by viewing the first lecture video, and if you have any questions, you may then email the instructor.

Slides are available with both on-demand and live of courses, and many also have examples (such as data and scripts). Assignments are also provided for your edification but are not graded. And, when finished, you may request a certificate of attendance.

On-demand course tuition:

• For-profit & government: $600 USD
• Non-profit & self-pay: $400 USD
• See below for additional discounts.

Students who've taken the on-demand version of this course can access the course page here.

Live course held online

This course might also be taught live, on-line. Please check the calendar to see if it will be held in the near future.

Live, online course tuition:

• For-profit & government: $1,000 USD
• Non-profit & self-pay: $600 USD
• See below for additional discounts.

Registration deadline: When full

Students who've taken the live course can continue to access their course pages here. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)

Live course held on-site

We can come to your facility to teach this course. Please contact us for additional information.

Discounts

Additional discounts are available as follows:

• Professional members: 20% discount
• Limited scholarships may also be available for those residing in low-income economies (please inquire).

Certification

This course is certified by Bioinformatics.org, one of the oldest and largest international affiliations in the field, and it will count as 6 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within Bioinformatics.org. Students completing the course will receive a certificate attesting to that.

Refund policy

For any course type, if a student is not satisfied with the conduct or content of a course, they may request a full refund within the first two days of lecture. After two days but within a week, a 50% refund will be granted. After one week, a 100% credit toward another course will be granted. No refunds or credits apply beyond those stated here.

Additional information

Please contact us for questions or additional information.

See also

• Educational services at Bioinformatics.org