CS102A Perl for Biologists, Level 2

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==Course outline==
==Course outline==
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Day 1
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* Day 1: Perl basics (a quick review):
 +
*** How to use Perl commands in scripts and functions
 +
*** Good programming practices
 +
*** Specials notes, shortcuts, basic commands you may have forgotten
 +
** Case study: Automating BLAST
 +
*** 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
 +
*** Writing a program to call “blastall.exe”, finding the best hits
 +
** Case study: Gene expression analysis
 +
*** Reading ~20000 gene scores in a text file corresponding to 8 samples, and a gene information file
 +
*** 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
 +
* Day 2: Creating and using modules, namespaces, packages. References and object-oriented programming
 +
* Day 3: The Perl DBI and DBD for the MySQL DBMS. Using BioPerl for sequence analysis
 +
* 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.
 +
** Create tables in a database using Perl to accommodate the data.
 +
* Day 5: Project discussions
-
* Perl basics (a quick review):
+
==Course schedule==
-
** How to use Perl commands in scripts and functions
+
-
** Good programming practices
+
-
** Specials notes, shortcuts, basic commands you may have forgotten
+
-
* Case study: Automating BLAST
+
-
** Downloading sequences and formating them for querying using the “formatdb.exe” program
+
-
** Creating FASTA file with sequences on which to use BLAST
+
-
** Writing a program to call “blastall.exe”, finding the best hits
+
-
* Case study: Gene expression analysis
+
-
** Reading ~20000 gene scores in a text file corresponding to 8 samples, and a gene information file
+
-
** Performing thresholding and normalization for this data
+
-
** Calculating fold change, difference, t-statistics, p-value, confidence intervals, etc.
+
-
** Outputing the filtered results, sorted by lower confidence interval, and removing Affymetrix control genes
+
-
Day 2
+
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.
-
* Creating and using modules, namespaces and packages
+
* [http://edu.bioinformatics.org/TG/site Course TG, September 24-28, 2007, 15:30-17:00 UTC (Registration Open)]
 +
* [http://edu.bioinformatics.org/CT/site Course CT (online), May 28 - June 2, 2007]
 +
* [http://edu.bioinformatics.org/AQ/site Course AQ (online), April 2-6, 2007]
 +
* [http://edu.bioinformatics.org/AJ/site Course AJ (online), February 12-16, 2007]
 +
* [http://edu.bioinformatics.org/AE/site Course AE (online), January 29 - February 2, 2007]
 +
* [http://edu.bioinformatics.org/AB/site Course AB (online), January 8-12, 2007]
 +
* [http://edu.bioinformatics.org/AA/site Course AA (onsite), September 19, 2007]
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* References and object-oriented programming
+
==Registration==
-
Day 3
+
Registration comprises of two steps. First, [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.
-
* The Perl DBI and DBD for the MySQL DBMS
+
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.
-
* Using BioPerl for sequence analysis
+
Registration deadline: When full
-
Day 4
+
===[[Tuition discounts]]===
-
* Project: Microarray database with sequence information
+
* 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).
-
** Use SantaLucia rules to calculate the delta-G value of all 25-mer Perfect Match (PM) probe sequences.
+
* 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).
-
** Create tables in a database using Perl to accommodate the data.
+
-
Day 5
+
Tuition (all prices USD):
 +
<table style="background-color: white; border: solid 1px black;">
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    <tr style="background-color: #666666; border-bottom: solid 1px black; color: white; font-weight: bold;">
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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>
 +
        <td style="border-right: solid 1px black; padding: 0.5em;">If taken with a non-CS101<br />course at base tuition</td>
 +
        <td style="padding: 0.5em;">If taken with another CS101<br />course at base tuition</td>
 +
    </tr>
 +
    <tr>
 +
        <td style="border-right: solid 1px black; padding: 0.5em;">Commercial</td>
 +
        <td style="border-right: solid 1px black; padding: 0.5em;">$595</td>
 +
        <td style="border-right: solid 1px black; padding: 0.5em;">$476</td>
 +
        <td style="padding: 0.5em;">$298</td>
 +
    </tr>
 +
    <tr>
 +
        <td style="border-right: solid 1px black; padding: 0.5em;">Non-profit/academic</td>
 +
        <td style="border-right: solid 1px black; padding: 0.5em;">$397</td>
 +
        <td style="border-right: solid 1px black; padding: 0.5em;">$318</td>
 +
        <td style="padding: 0.5em;">$199</td>
 +
    </tr>
 +
</table>
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* Project discussions
+
For full-time students and the unemployed, please inquire about an additional discount (verification required).
-
==Logistics==
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==Additional information==
-
http://edu.bioinformatics.org/images/asap_logo.png
+
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.
-
 
+
-
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.
+
-
 
+
-
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.
+
-
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.
 
==Course schedule==
==Course schedule==

Revision as of 00:36, 24 August 2007

Contents

Objective

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.

Course outline

Course schedule

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.

Registration

Registration comprises of two steps. First, 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 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.

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.

Registration deadline: When full

Tuition discounts

Tuition (all prices USD):

Base tuition If taken with a non-CS101
course at base tuition
If taken with another CS101
course at base tuition
Commercial $595 $476 $298
Non-profit/academic $397 $318 $199

For full-time students and the unemployed, please inquire about an additional discount (verification required).

Additional information

If you have any questions, please send a message to J.W. Bizzaro (login required) or call +1 508 890 8600.




Course schedule

Registration

Tuition discounts

Tuition (all prices USD):

Base tuition If taken with a non-CS101
course at base tuition
If taken with another CS101
course at base tuition
Commercial $595 $476 $298
Non-profit/academic $397 $318 $199

For full-time students and the unemployed, please inquire about an additional discount (verification required).

Registration deadline: When full

Please create an account before registering, if you haven't already done so. The educational website at Bioinformatics.Org requires a separate username and password.

Available payment methods:

  1. Online registration form (account required; please use the link in the course schedule above)
    Use this form only for credit card payments (via secured PayPal).
  2. Mail-in registration form (~150 kB PDF)
    Use this form if paying by check (US bank accounts only), credit card or corporate purchase order.

Additional information

If you have any questions, please send a message to J.W. Bizzaro (login required) or call +1 508 890 8600.

ASAP is a trademark of Convoq, Inc.
Other names are trademarks of their respective owners.

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