CS101 Introduction to Bioinformatics Programming

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==Objective==
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==Objectives==
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Taught in the context of biological research, this course helps biologists learn how to use the scripting language Perl to automate certain tasks and how to use the database management system MySQL to store, manage and query biological information.
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This course is a consolidation of courses covering four major programmatic technologies used in bioinformatics. It teaches IT specialists, entry level bioinformaticians, and biologists how to leverage the Linux shell, Perl, R, MySQL and various other open-source bioinformatics tools to perform computations in biological research and create information from data. Examples in this course use data from DNA and amino acid sequences, microarray profiles, images, mass spectrometry, LIMS, and biological annotations.
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==Course outline==
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==Instructor==
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* [[Shailender Nagpal]]
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==Course schedule==
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==Syllabus==
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This course has been offered several times. 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.
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The on-line version of the course is divided into 4 sessions, 1 session per day. The course is completed in 4 days, with the 5th day being reserved for project discussion and any other issues the students may want to discuss.
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* [http://edu.bioinformatics.org/GGA Course GGA (online), September 8-12, 2008, 15:30-17:30 GMT]
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; Session 1
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* [http://edu.bioinformatics.org/CS101A Site license login]
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Fundamentals of the Linux OS and shell -– filesystem, access and basic commands; navigation of the filesystem and basic file operations -– reading, writing, merging, copying, moving and setting permissions of files and directories
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==Registration==
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; Session 2
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Registration is done in two steps. First, if you haven't already done so, [https://edu.bioinformatics.org/login/signup.php 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 [http://edu.bioinformatics.org/download/registration_form.pdf 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.
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Fundamentals of scripting with Perl, such as scalars, arrays, variable interpolation, operators (mathematics, conditional, logical), file input/output, printing, loops (if-then-else, for, while), list operations, etc.; functions/subroutines, hash arrays and regular expressions; the installation of Perl packages, and some examples of using the famous package BioPerl for manipulating sequences, automating BLAST queries, etc. A project will be assigned that uses BioPerl and the Perl Database interface.
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Registration deadline: When full
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; Session 3
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==Tuition & discounts==
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Installing and running R, the R environment, help system, commands; basics of R –- data objects (vectors, matrices, data frames), plotting; creating R scripts, working with data files, statistics with R, functions; working with the Bioconductor package
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The fee for this course is $995 USD (commercial, government)
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; Session 4
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Discounted rates are available, as follows:
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Fundamentals of MySQL databases and deciding what to store, and how to install a database; creating and designing a database; populating the database with sample data; data retrieval and manipulation concepts using SQL queries (Select, Update, Delete, Insert); additional topics, such as interfacing the database with the Microsoft Access front end; mining the data using Perl database interface. A project will be assigned.
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* Academic and non-profit research organizations, $664
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* Students paying for themselves (not getting reimbursement) and unemployed individuals (verification required), please inquire.
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* [[Membership|Professional members]] get an additional 20% discount.
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* Limited scholarships may also be available for those in low-income economies.
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==Logistics==
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{{Course footer
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|hours=6
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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 90 to 120 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.
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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 [http://www.adobe.com/products/flashplayer/ Adobe Flash plugin].  A microphone and webcam are not required for this course.  The necessary software, lecture notes and exercises will be provided.
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==Certification==
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This course is certified by the [[Bioinformatics Organization|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.
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==Additional information==
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If you have any questions, please send a message to [http://edu.bioinformatics.org/message/discussion.php?id=100003 J.W. Bizzaro] (login required) or call +1 978 562 4800.
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==See also==
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* [[Educational services|Educational services at Bioinformatics.Org]]
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Latest revision as of 05:39, 28 November 2012

Contents

Objectives

This course is a consolidation of courses covering four major programmatic technologies used in bioinformatics. It teaches IT specialists, entry level bioinformaticians, and biologists how to leverage the Linux shell, Perl, R, MySQL and various other open-source bioinformatics tools to perform computations in biological research and create information from data. Examples in this course use data from DNA and amino acid sequences, microarray profiles, images, mass spectrometry, LIMS, and biological annotations.

Instructor

Syllabus

The on-line version of the course is divided into 4 sessions, 1 session per day. The course is completed in 4 days, with the 5th day being reserved for project discussion and any other issues the students may want to discuss.

Session 1

Fundamentals of the Linux OS and shell -– filesystem, access and basic commands; navigation of the filesystem and basic file operations -– reading, writing, merging, copying, moving and setting permissions of files and directories

Session 2

Fundamentals of scripting with Perl, such as scalars, arrays, variable interpolation, operators (mathematics, conditional, logical), file input/output, printing, loops (if-then-else, for, while), list operations, etc.; functions/subroutines, hash arrays and regular expressions; the installation of Perl packages, and some examples of using the famous package BioPerl for manipulating sequences, automating BLAST queries, etc. A project will be assigned that uses BioPerl and the Perl Database interface.

Session 3

Installing and running R, the R environment, help system, commands; basics of R –- data objects (vectors, matrices, data frames), plotting; creating R scripts, working with data files, statistics with R, functions; working with the Bioconductor package

Session 4

Fundamentals of MySQL databases and deciding what to store, and how to install a database; creating and designing a database; populating the database with sample data; data retrieval and manipulation concepts using SQL queries (Select, Update, Delete, Insert); additional topics, such as interfacing the database with the Microsoft Access front end; mining the data using Perl database interface. A project will be assigned.

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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