Dobrý večer! from Cesky Krumlov, Czech Republic! Ok that's enough Czech from me...
Section 8: Programming
So BioPerl and (I'm going to plug BioPython in here too--see below, PyCogent) are basically what they sound like, perl codes/scripts/modules (however is easier for you to think about it) and python code (Perl and Python being programming languages) geared toward applications in biological analysis.
Now my husband is a programmer turned bioinformatic programmer and his best advice is to jump right in and just keep using it. My main concern with that...aside from my inability to manifest a 36 hour day that would allow me to take on learning a computer langauge...is I don't use it every day in my job. This makes it difficult to say the least to retain all the commands in your head and even then--when in doubt 'Google!' The links above, the BioPerl one being suggested in the preparation materials for the workshop and the BioPython will give you an idea of the modules/programs that have been constructed using those languages and provide more links if you want to get further into the mire and meld programming with biological analysis. You will have to learn some basics of the language itself before jumping into the biological application of it just for functionality's sake.
Now that's all I'm going to say for the moment, but we'll come back to this...my husband who was trained as a computer scientist and is a programmer who just recently got thrown into the world of biology head first and is now programming (using Python) for bioinformatic analysis has a python tutorial and some advice to dispense to you all who aspire to move in that direction...but he has to write it up.
In the meantime, one thing you absolutely need to get comfortable with is the ominous black box called command-line. You simply have to learn how to navigate around your computer in command-line interface. The conference organizers have provided a helpful tutorial so we are going to go through that and I'll add as we go based on my own trial and error experiences.
Section 8: Programming
So BioPerl and (I'm going to plug BioPython in here too--see below, PyCogent) are basically what they sound like, perl codes/scripts/modules (however is easier for you to think about it) and python code (Perl and Python being programming languages) geared toward applications in biological analysis.
Now my husband is a programmer turned bioinformatic programmer and his best advice is to jump right in and just keep using it. My main concern with that...aside from my inability to manifest a 36 hour day that would allow me to take on learning a computer langauge...is I don't use it every day in my job. This makes it difficult to say the least to retain all the commands in your head and even then--when in doubt 'Google!' The links above, the BioPerl one being suggested in the preparation materials for the workshop and the BioPython will give you an idea of the modules/programs that have been constructed using those languages and provide more links if you want to get further into the mire and meld programming with biological analysis. You will have to learn some basics of the language itself before jumping into the biological application of it just for functionality's sake.
Now that's all I'm going to say for the moment, but we'll come back to this...my husband who was trained as a computer scientist and is a programmer who just recently got thrown into the world of biology head first and is now programming (using Python) for bioinformatic analysis has a python tutorial and some advice to dispense to you all who aspire to move in that direction...but he has to write it up.
In the meantime, one thing you absolutely need to get comfortable with is the ominous black box called command-line. You simply have to learn how to navigate around your computer in command-line interface. The conference organizers have provided a helpful tutorial so we are going to go through that and I'll add as we go based on my own trial and error experiences.
