1. Introduction to bioperl

2. What is perl? Production Engineering Research Laboratory Practically Everything Really Likeable Pre-positioned Equipment Requirement List Principal Exchange Rate Linked Pathologically Eclectic Rubbish Lister Practical Extraction and Report Language

3. Perl is – Practical Extraction and Report Language (or Pathologically Eclectic Rubbish Lister) (written by Larry Wall in 1986) – An interpreted programming language that resembles both a real programming language and a shell – A language for easily manipulating text, files, and processes – Providing more concise and readable way to do jobs formerly accomplished using C or shells. What is perl, really?

4. 0’s and 1’s Low-level language, assemble needed High-level language, compilation needed High-level language, compilation NOT needed

5. Why use Perl? Easy to use – Basic syntax is C-like – Lazy memory management – A small amount of code goes a long way Fast – Perl has numerous built-in optimization features which makes it run faster than other scripting language. Portability – One script version runs everywhere (unmodified).

6. Why use Perl? Efficiency – More efficient than C to perform the same task Correctness – Perl fully parses and pre-”compiles” script before execution. Free to use – Comes with source code

7. To learn perl Take a perl class! Reading books – “Learning Perl, 5th Edition” by Randal Schwartz, Tom Phoenix, and brian d foy – “Programming Perl (3rd Edition)” by Larry Wall, tom Christiansen, and Jon Orwant Reading perl documentations Practice, practice, practice……

8. What’s Bioperl? Bioperl is not a new language It is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.

9. Perls script Perl Interpreter Perl Modules Bioperl Modules output input Bioperl and Perl

10. Why bioperl for bioinformatics? Perl is good at file manipulation and text processing, which make up a large part of the routine tasks in bioinformatics. Perl language, documentation and many Perl packages are freely available. Perl is easy to get started in, to write small and medium-sized programs.

11. Bioperl Project It is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research Started in 1995 by a group of scientists tired of rewriting BLAST and sequence parsers for various formats Version 0.7 was released in 2000 Bioperl 1.0 was released in 2002 A paper about bioperl was published in October 2002 (Satjich et al., 2002. The bioperl toolkit: perl modules for the life sciences. Genome Research 12: 1611-1618.) Current stable release 1.6.0 was made available in January 2009

12. Bioperl toolkit Core package (bioperl-live) – THE basic package and it’s required by all the other packages Run package (bioperl-run) – Providing wrappers for executing some 60 common bioinformatics applications DB package (bioperl-db) – Subproject to store sequence and annotation data in a BioSQL relational database Network package (bioperl-network) – Parses and analyzes protein-protein interaction data Dev package (bioperl-dev) – New and exploratory bioperl development

13. Installing bioperl on a Windows computer On Windows – Install ActivePerl – Install bioperl using PPM (Perl Package Manager) On cygwin (Linux-like environment in Windows) – Install cygwin – Install required perl modules – Install bioperl using source code Route 1 Route 2

14. Installing bioperl on a Windows computer On Windows – Install ActivePerl – Install bioperl using PPM (Perl Package Manager) On cygwin (Linux-like environment in Windows) – Install cygwin – Install required perl modules – Install bioperl using source code Route 1 Route 2

15. Installing bioperl on Windows www.bioperl.org http://www.bioperl.org/wiki/Main_Page Route 1 Downloads

16. Installing bioperl on Windows Route 1

17. Installing bioperl on Windows Route 1 Following the instructions

18. Easy installation process Works well No good if to parse the results of other linux- base applications Not recommended Installing bioperl on Windows Route 1

19. Installing bioperl on a Windows computer On Windows – Install ActivePerl – Install bioperl using PPM (Perl Package Manager) On cygwin (Linux-like environment in Windows) – Install cygwin – Install required perl modules – Install bioperl using source code Route 1 Route 2

20. Where to get bioperl www.bioperl.org http://www.bioperl.org

24. Small size

25. ~ stands for the home directory (..) To move one level up to the parental directory The parental directory is /home

26. There is one folder “XiaodongBai” in /home Attributes : First position: -regular file ddirectory (folder) llink Other positions: -not (readable|writeable|executable) rreadable wwriteable xexecutable

27. mkdir to make a directory called “programs” Now there are 2 folders in /home

28. Change directory to “programs” /cygdrive/c/Biodownloads/BioPerl-1.6.0.tar.gz Location of the downloaded bioperl file

29. gunzip -c /cygdrive/f/Downloads/BioPerl-1.6.0.tar.gz | tar -xvf - Commands to decompress and untar the bioperl file Designate your drive (usually C) and directory

30. All Bioperl files are in this folder now

31. Change directory to “BioPerl-1.6.0” All the files in the directory Read “INSTALL” for detailed instructions when you have time

32. perl Makefile.PL Check prerequisites required for bioperl installation Press “return” to accept the default “yes” and continue.

34. Prerequisites were installed successfully. Enter “a” and press “enter” to accept the default option and continue. Press “enter” for all questions along with way

35. Information about the installation of prerequisites Ignore the errors for now since these modules are optional Press “return” to accept the default options [a] for all, and continue.

36. First step done! Type “make” and press “enter” to start building

37. Second step done! Type “make test” and press “enter” to start testing

38. Testing in progress…

39. All tests are passed! Ignore any non- passed tests for now! Type “make install” and press “enter” to start installing

40. Bioperl is successfully installed! Congratulations!

41. Time to run a test to see whether bioperl works

42. Type “clear” and press “return” to clear the screen

43. Use “cp” command to copy the test script “bioperl_installation_test.pl” to the current directory (.)

44. Check if the file is executable (x in fourth position). If not, type “chmod +x bioperl_installation_test.pl” and press “enter”. Check it again to make sure that it is executable.

45. To run a perl script, type $./bioperl_installation_test.pl Or $perl bioperl_installation_test.pl

46. If you see “It works!!”, it works! If you see something else, the installation failed in the sense that the modules are not being loaded correctly. See the instructors for troubleshooting individually.

47. Bioperl reading materials Bioperl tutorial: http://www.bioperl.org/wiki/Bptutorial.pl http://www.bioperl.org/wiki/Bptutorial.pl HOW-TOs http://www.bioperl.org/wiki/HOWTOshttp://www.bioperl.org/wiki/HOWTOs Example code, in the scripts/ and examples/ directories of a bioperl installation Online course written at the Pasteur Institute. http://www.pasteur.fr/recherche/unites/sis/form ation/bioperl. http://www.pasteur.fr/recherche/unites/sis/form ation/bioperl

48. Troubleshooting: If “FATAL ERROR” is encountered early in the installation through cygwin, double check the firewall settings on your computer (allow). If this does not permit installation, see www.bioperl.org “Installing BioPerl on Windows” If you are running the WINDOWS VISTA OS, you will need to follow instructions for downloading at www.bioperl.org “Installing BioPerl on Windows” MAC OS X users should also refer to instructions at www.bioperl.org Make uses “build” not “make”