CS201 High Performance Computing

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==Objectives==
==Objectives==
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This course aims at teaching Biologists how to implement High Performance Computing (HPC) strategies for data management and analysis tasks in biological research and resolve difficult BIG DATA related problems. Data could be DNA or Amino acid sequences, Microarray or NGS data, Images, Mass spectrometry data, text articles or any other kind of biological information.
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This course teaches biologists how to implement High Performance Computing (HPC) strategies for data management and analysis tasks in biological research and to resolve difficult Big Data related problems. Data can be DNA or amino acid sequences, microarray or NGS data, images, mass spectrometry data, text articles, or any other kind of biological information.
==Instructor==
==Instructor==

Revision as of 04:31, 6 November 2013

Contents

Objectives

This course teaches biologists how to implement High Performance Computing (HPC) strategies for data management and analysis tasks in biological research and to resolve difficult Big Data related problems. Data can be DNA or amino acid sequences, microarray or NGS data, images, mass spectrometry data, text articles, or any other kind of biological information.

Instructor

Syllabus

The course is divided into 4 sessions, roughly 1-1.5 hours each. The 5th session is reserved for project discussion and any other issues the students may want to discuss.

Session 1

Session 1 will cover basic architectures and methods for implementing HPC on powerful servers, clusters and the cloud

Session 2

Session 2 will cover various multi-threaded applications for sequence search and read alignment, as well as basic usage of multiple cores simultaneously using linux processes

Session 3

Session 3 will cover cluster computing using job managers such as SGE, LSF and PBS

Session 4

Session 4 will cover cloud computing and how to use the Amazon web service to request resources (instances) at will, add datasets and run applications

Scheduled courses

If you are interested in an upcoming course, register using instructions below. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)

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 the course by making a payment using either the on-line registration form (click on the name of the course where it appears in the list of upcoming courses; use this form only for PayPal payments and credit card payments via secured PayPal), or by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).

Please also check the course tuition rates and discounts.

Registration deadline: When full

Tuition & discounts

Live instruction held on-line
Live instruction held on-site
On-demand instruction held on-line

Additional discounts are available as follows:

Logistics

The necessary software, lecture notes and exercises will be provided.

Live instruction held on-line

On-line/live courses use the WebEx on-line meeting system. Access information will be provided prior to the start of the course. Unless otherwise noted, each lecture begins at 16:00 GMT and runs for about two hours, 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 AVI video files 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 Java. A microphone and webcam are not required but may be used.

Certification

This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 6 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within the Organization. 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

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