CS101 Introduction to Bioinformatics Programming

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==Objectives==
==Objectives==
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This course teaches biologists how to use programming as a way to automate biological data analysis and develop algorithms or workflows, and how to manage vast amounts of data using database technologies. Data could be DNA or amino acid sequences, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information. Perl programming and database management will be covered.  (This course is a combination of [[CS101A Perl for Biologists, Level 1]] and [[CS101C MySQL for Biologists, Level 1]].)
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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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No database experience is required, just a need to learn how to work with databases. No programming experience is required, just a need to learn how to program.
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==Instructor==
==Instructor==
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==Syllabus==
==Syllabus==
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The course is divided into 8 sessions, roughly 1-1.5 hours each, and 2 sessions are held every 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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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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* Session 1: Fundamentals of databases and deciding what to store. How to install a database management system (MySQL).
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; Session 1
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* Session 2: Database concepts, such as creating and designing a database, and populating the database with sample data.
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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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* Session 3: Data retrieval and manipulation concepts using SQL queries (Select, Update, Delete, Insert).
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; Session 2
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* Session 4: Additional topics, such as interfacing the database with the Microsoft Access front end and mining the data using a Perl database interface.
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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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* Session 5: Installation issues and a simple exercise that illustrate how to create and execute simple Perl programs. The Perl environment will be introduced.
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; Session 3
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* Session 6: Fundamentals of programming 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.
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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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* Session 7: Functions/subroutines, hash arrays and regular expressions.
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; Session 4
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* Session 8: 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.
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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.
{{Course footer
{{Course footer
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|hours=6
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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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