Bioinformatics.org
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  • CS101 Introduction to Bioinformatics Programming

    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.

    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.

    This course is taught by Shailender Nagpal, M.S.

    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

     

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