CS111A Introduction to Genome Browsers
From Bioinformatics.Org Wiki
Contents |
Objective
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. This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 10 "Continuing Scientific Education" (CSE) credits (one credit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.
Course outline
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.
- Day 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.
- Day 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).
- Day 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.
- Day 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.
- Day 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.
Course schedule
This course has been offered once. Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues. If you are interested in an upcoming course, register using instructions below.
Registration
Registration comprises of two steps. First, create an online account to access the educational section of our website. Second, register for this course by making a payment using either the online registration form (click on the scheduled course above; use this form only for credit card payments via secured PayPal), or by sending in the mail-in registration form (~150 kB PDF, use this form if paying by US checks, credit card or corporate purchase order). Please check the tuition rates and discounts below.
Registration deadline: When full
Tuition discounts
- Returning student discount: A 20% (rounded up) discount applies for students who have paid the base tuition (without a similar discount) for a course at Bioinformatics.Org that does not fall in the CS101 range (e.g., CS102A/B) (please use the mail-in registration form rather than PayPal if taking this discount).
- Cluster course discount: A 50% (rounded up) discount (cannot be combined with the 20% discount) applies for students who have paid the base tuition for a course that does fall in the CS101 range (please use the mail-in registration form rather than PayPal if taking this discount).
Tuition (all prices USD):
| Base tuition | If taken with another course at base tuition | |
| Commercial | $595 | $397 |
| Non-profit/academic | $476 | $318 |
For full-time students and the unemployed, please inquire about an additional discount (verification required).
Logistics
Online courses are offered via an online meeting system. Access information will be provided prior to the start of the course. Each lecture will last 45 to 90 minutes, depending on the topics covered. For those who cannot attend the lectures at those times, the lectures will be recorded and placed on the course website as Flash videos (resolution reduced by 30%) each day, within one day. Students will also be able to communicate with the instructor and other students via the course forums. Lecture attendance is therefore not required.
Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and the Adobe Flash plugin. A microphone and webcam is not required for this course. The necessary software, lecture notes and exercises will be provided.
Additional information
If you have any questions, please send a message to J.W. Bizzaro (login required) or call +1 978 562 4800.
