Useful Links:
Textpad - a decent text editor for
programming.
Eclipse - a better programming editor ... but with a bit steeper learing curve (google for "eclipse perl" to
see how to set yourself up for perl coding)
ActivePerl - a perl installation for
Windows.
Cygwin - a Unix environment that runs in Windows (comes with
Perl - use either this or ActivePerl, not both)
Ohnline regex tester
MySQL on amadeus
| Week | Reading / Links | Lecture "notes" | Exercises | Extras |
| 1 | Intro to Excel |
class notes excel sheet that covers the kind of material discussed in class (and more) excel sheet for exercises |
name list numbers named numbers ranges genome annotation chart data 1 chart data 2 |
|
| 2 | Genomics resources/tools |
genomics resources bookmarks blast queries |
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| 3 |
Amadeus (the unix server) Unix tutorial (part 1: sections 1-5, 8, 10, 11) |
SSH secure shell Unix Crib Sheet Unix Essentials Another unix reference card |
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| 4 | Genomics resources/tools | |||
| 5 | "Beginning Perl" by Simon Cozens: | |||
| 6 | "Beginning Perl" | |||
| 7 | "Beginning Perl"
|
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| 8 | "Beginning Perl"
|
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| 9 | ||||
| 10 | "Beginning Perl" | |||
| 11 | "Beginning Perl" | |||
| 12 |
Chapter 10 -
modules A very simple intro to modules BioPerl docs Docs for v.1.2.3, the version on amadeus. Use "SearchIO" for blast file parsing. BioPerl wiki page |
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| 12 |
MySQL on amadeus |