CS102A Perl for Biologists, Level 2

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==Objective==
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==Objectives==
Taught in the context of biological research, this course shows biologists how to use the scripting language Perl to automate certain tasks. It is a continuation of [[CS101A Perl for Biologists, Level 1]] and covers advanced topics and projects.
Taught in the context of biological research, this course shows biologists how to use the scripting language Perl to automate certain tasks. It is a continuation of [[CS101A Perl for Biologists, Level 1]] and covers advanced topics and projects.
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==Course outline==
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==Instructor==
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Day 1
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* [[Shailender Nagpal]]
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* Perl basics (a quick review):
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==Syllabus==
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** How to use Perl commands in scripts and functions
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** Good programming practices
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** Specials notes, shortcuts, basic commands you may have forgotten
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* Case study: Automating BLAST
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** Downloading sequences and formating them for querying using the “formatdb.exe” program
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** Creating FASTA file with sequences on which to use BLAST
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** Writing a program to call “blastall.exe”, finding the best hits
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* Case study: Gene expression analysis
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** Reading ~20000 gene scores in a text file corresponding to 8 samples, and a gene information file
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** Performing thresholding and normalization for this data
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** Calculating fold change, difference, t-statistics, p-value, confidence intervals, etc.
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** Outputing the filtered results, sorted by lower confidence interval, and removing Affymetrix control genes
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Day 2
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* Day 1: Perl basics (a quick review):
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*** How to use Perl commands in scripts and functions
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* Creating and using modules, namespaces and packages
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*** Good programming practices
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*** Specials notes, shortcuts, basic commands you may have forgotten
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* References and object-oriented programming
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** Case study: Automating BLAST
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*** Downloading sequences and formating them for querying using the “formatdb.exe” program
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Day 3
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*** Creating FASTA file with sequences on which to use BLAST
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*** Writing a program to call “blastall.exe”, finding the best hits
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* The Perl DBI and DBD for the MySQL DBMS
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** Case study: Gene expression analysis
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*** Reading ~20000 gene scores in a text file corresponding to 8 samples, and a gene information file
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* Using BioPerl for sequence analysis
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*** Performing thresholding and normalization for this data
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*** Calculating fold change, difference, t-statistics, p-value, confidence intervals, etc.
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Day 4
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*** Outputing the filtered results, sorted by lower confidence interval, and removing Affymetrix control genes
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* Day 2: Creating and using modules, namespaces, packages. References and object-oriented programming
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* Project: Microarray database with sequence information
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* Day 3: The Perl DBI and DBD for the MySQL DBMS. Using BioPerl for sequence analysis
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* Day 4: Project: Microarray database with sequence information
** Use SantaLucia rules to calculate the delta-G value of all 25-mer Perfect Match (PM) probe sequences.
** Use SantaLucia rules to calculate the delta-G value of all 25-mer Perfect Match (PM) probe sequences.
** Create tables in a database using Perl to accommodate the data.
** Create tables in a database using Perl to accommodate the data.
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* Day 5: Project discussions
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Day 5
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{{Course footer
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|hours=3
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* Project discussions
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}}
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==Logistics==
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http://edu.bioinformatics.org/images/asap_logo.png
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Locale: This course is offered on the ASAP online meeting system.  Access information will be provided prior to the start of the course.
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Dates & times: Please see the course schedule below for the next time that this course will run. 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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For an additional USD $49, students who attend this course may order data discs containing full-resolution lecture videos and extra copies of the slides, scripts and data files.
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Technical Requirements: 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].  Please [[ASAP requirements|check the specific system requirements for your computer]].  A microphone and webcam is not required for this course.  The necessary software, lecture notes and exercises will be provided.
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==Prerequisites (entry conditions)==
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Students should have taken [[CS101A Perl for Biologists, Level 1]] or have equivalent experience.
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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 '''8''' "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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==Course schedule==
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* [http://edu.bioinformatics.org/TG/site Course TG, September 24-28, 2007, 15:30-17:00 UTC]
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==Registration==
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===[[Tuition discounts]]===
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* Returning student discount: A 20% (rounded up) discount applies for students who have paid the base tuition (without a similar discount) for a course at Bioinformatics.Org that does '''''not''''' fall in the CS101 range (e.g., CS102A/B) (please use the mail-in registration form rather than PayPal if taking this discount).
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* Cluster course discount: A 50% (rounded up) discount (cannot be combined with the 20% discount) applies for students who have paid the base tuition for a course that '''''does''''' fall in the CS101 range (please use the mail-in registration form rather than PayPal if taking this discount).
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Tuition (all prices USD):
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        <td style="border-right: solid 1px black; padding: 0.5em;"></td>
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        <td style="border-right: solid 1px black; padding: 0.5em;">Base tuition</td>
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        <td style="border-right: solid 1px black; padding: 0.5em;">If taken with a non-CS101<br />course at base tuition</td>
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        <td style="padding: 0.5em;">If taken with another CS101<br />course at base tuition</td>
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        <td style="border-right: solid 1px black; padding: 0.5em;">Commercial</td>
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        <td style="border-right: solid 1px black; padding: 0.5em;">$595</td>
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        <td style="border-right: solid 1px black; padding: 0.5em;">$476</td>
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        <td style="padding: 0.5em;">$298</td>
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        <td style="border-right: solid 1px black; padding: 0.5em;">$397</td>
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        <td style="border-right: solid 1px black; padding: 0.5em;">$318</td>
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        <td style="padding: 0.5em;">$199</td>
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For full-time students and the unemployed, please inquire about an additional discount (verification required).
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Registration deadline: When full
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Please [https://edu.bioinformatics.org/login/signup.php create an account] before registering, if you haven't already done so.  The educational website at Bioinformatics.Org requires a separate username and password.
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Available payment methods:
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# Online registration form (account required; please use the link in the course schedule above)<br />''Use this form only for credit card payments (via secured PayPal)''.
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# [http://edu.bioinformatics.org/download/registration_form.pdf Mail-in registration form] (~150 kB PDF)<br />''Use this form if paying by check (US bank accounts only), credit card or corporate purchase order''.
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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 +1 508 890 8600.
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''ASAP is a trademark of Convoq, Inc.<br />Other names are trademarks of their respective owners.''
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Latest revision as of 20:11, 19 May 2011

Contents

Objectives

Taught in the context of biological research, this course shows biologists how to use the scripting language Perl to automate certain tasks. It is a continuation of CS101A Perl for Biologists, Level 1 and covers advanced topics and projects.

Instructor

Syllabus

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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