CS101E Python for Biologists, Level 1

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==Objective==
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==Objectives==
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This course aims at teaching biologists how to use Python as a programming language to automate routine data management tasks in biological research and solve difficult data-related computational problems. Data could be DNA or amino acid sequence, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information.
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This course teaches biologists how to use Python as a programming language to automate routine data management tasks in biological research and solve difficult data-related computational problems. Data could be DNA or amino acid sequence, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information.
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==Instructors==
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==Instructor==
* [[Shailender Nagpal]]
* [[Shailender Nagpal]]
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==Course outline==
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==Syllabus==
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The course is divided into 4 sessions. The 5th session is reserved for project discussion and any other issues the students may want to discuss. There will be quizzes and homework assignments after every lecture.
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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. There will be quizzes and homework assignments after every lecture.
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* Day 1: Installation issues and simple exercises that illustrate how to create and execute simple Python programs using variables and the print statement. The Python interpreter and editor will be introduced.
* Day 1: Installation issues and simple exercises that illustrate how to create and execute simple Python programs using variables and the print statement. The Python interpreter and editor will be introduced.
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* Day 2: Fundamentals of programming with Python, such as operators (mathematical, conditional, logical), file input/output, loops (if-then-else, for, while), etc.
* Day 2: Fundamentals of programming with Python, such as operators (mathematical, conditional, logical), file input/output, loops (if-then-else, for, while), etc.
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* Day 3: Functions, hashes and object oriented programming.
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* Day 3: Functions, hashes and object oriented programming
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* Day 4: Cover the installation of Python packages such as iPython, NumPy (Numeric Python), and Biopython. Some basic tasks in these packages will be covered. Project discussion.
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==Course schedule==
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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.)
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* [http://edu.bioinformatics.org/CTT Course CTT (online), June 30-July 4, 2008, 15:30-16:30 GMT]
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* [http://edu.bioinformatics.org/AGA Course AGA (online), December 10-14, 2007, 16:30-18:00 GMT]
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* [http://edu.bioinformatics.org/CS101E Site license login]
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==Registration==
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Registration is comprised of 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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Registration deadline: When full
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==Tuition & discounts==
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The fee for this course is $595 USD (Commercial, Government)
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Discounted rates are available, as follows:
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* Academic and non-profit research organizations, $397 (USD)
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* Students paying for themselves (not getting reimbursement) and unemployed individuals (verification required), $198
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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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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.
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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 is 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 '''5''' "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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* Day 4: Installation of Python packages such as iPython, NumPy (Numeric Python), and Biopython. Some basic tasks in these packages will be covered. Project discussion.
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* [[Educational services|Educational services at Bioinformatics.Org]]
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Latest revision as of 04:39, 5 November 2011

Contents

Objectives

This course teaches biologists how to use Python as a programming language to automate routine data management tasks in biological research and solve difficult data-related computational problems. Data could be DNA or amino acid sequence, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information.

Instructor

Syllabus

The course is divided into 4 sessions. The 5th session is reserved for project discussion and any other issues the students may want to discuss. There will be quizzes and homework assignments after every lecture.

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 an hour, 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 3 "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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