Course Development: Gen 712/812

 

 

 

 

UNH

*Graduate school

*Genetics Program

*Hubbard Center for Genome   

 Studies

 

The course development has many aspects:

Preparation of detailed PowerPoint based lectures

System administration of a dedicated server on which all bioinformatics work was conducted.

Tuning accessory software: APACHE, MySQL,

Lecture encompassed: Linux/Unix, Perl Fundamentals, Perl-CGI, MySQL, HTML authoring and APACHE web server configuration.

Linux/Unix Operating System:

As most bioinformatics software is based on the Linux/Unix Operating Systems, students were first introduced to this platform. This entailed

1.       the preparation of a crash course on the system

2.       the preparation and use of secure shell for remote login

Perl Fundamentals

·         All the major perl programming concepts

·         The frills (Comments, whitespace, indentation)

·         Variables (Scalars, Arrays, Hashes,)

·         Operators (String, Numeric operators)

·         Quotations in perl (single, double, back tics, qq, qw, q, qx)

·         Conditionals (if, if-else, if-elsif-else)

·         Loops (for, foreach, while, do-while, until)

·         Regular Expressions (Simple to intermediate)

·         Functions (String, numeric, list, array, hash, file handling …)

·         File Handles and I/O (Open, Close, <STDIN>, read)

·         Subroutimes (@_, shift, references)

·         Special Variables ($_, @_, @ARGV, __DATA__, __END__)

·         References and anonymous data structures

Perl-CGI

                CGI programming was used for:

·         Serving static and dynamic pages (CGI.pm)

·         Interacting with remote databases (NCBI)

·         Interacting with local databases (MySQL)

Database MySQL

                For creating custom databases

                Interrogating them from perl scripts

HTML authoring

                Web services require knowledge of HTML authoring so students were instructed in basic HTML scripting and writing HTML output from CGI scripts using CGI.pm functions.

APACHE Configuration

                As my course required that students work in web services, I had to configure one of the servers at the HCGS so that every student got their own web pages complete with cgi-bin directories.  This was a very interesting introduction into Linux System administration as I had to create user accounts, manage disk quotas, create user directories for web services etc,.