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Final Review

Lec 1 Review of Molecular Biology Central dogma Proteins DNA Reading frames Perl topics: Running perl variables: scalars, arrays, hashes while loops Scalar and list context string operations printing substitution: s/x/y/ translation: tr/abc/def/. Lec 2 Input / output

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Final Review

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  1. Lec 1 Review of Molecular Biology Central dogma Proteins DNA Reading frames Perl topics: Running perl variables: scalars, arrays, hashes while loops Scalar and list context string operations printing substitution: s/x/y/ translation: tr/abc/def/ Lec 2 Input / output String operations concatentation, quoting String functions length, split, join, substr, index, sprintf, uc, lc, chomp Array Functions Conditionals Logical operators Loops Finding motifs Counting nucleotides Final Review BINF 634 Fall 2013 - Lecture 14 Review

  2. Lec 3 Perl Shortcuts Declaring variables and Scope Subroutines Array References Programming Methods Top Down Design Bottom Up Coding and Testing Pseudocode Reading manuals and help pages Debugging POD Lec 4 Logical expression string functions: substr and index Random numbers and mutation Hashes Transcription, translation, genetic code Implementation using hashes Final Review BINF 634 Fall 2013 - Lecture 14 Review

  3. Lec 5 Regular expressions Meta-characters Controlling patterns |, *, +, {N,M}, ? Capturing matches $`, $&, $' $1, $2 … ($x, $y) = $s =~ /(…) … (…)/ g modifier Lec 6 Data Structures and Efficiency /usr/bin/time head, tail, diff, cmp Hashes for effiecient lookup and counting Intersection Unique items in two lists Counting items Sorting using BLOCKS using user-defined subroutines sort LIST sort BLOCK LIST sort USERSUB LIST Final Review BINF 634 Fall 2013 - Lecture 14 Review

  4. Lec 7 Functions on arrays splice, grep, map Two-dimensional arrays Processing Printing Transposing Using Hashes to Pass Parameters to subroutines Lec 8 Perl Modules Module Getopt::Std Range Operator Restriction Maps Parsing Rebase File Final Review BINF 634 Fall 2013 - Lecture 14 Review

  5. Lec 9 CGI.pm Creating HTML pages with Perl Forms processing A general Web front end for Perl programs Security in CGI Programming Taint mode -T Untainting user supplied data Using external programs Permissions issued cgi-bin directory Using temporary directories Lec 10: SQL and MySQL Tables Column Types and Properties Keys, Indexes, and AUTO_INCREMENT The mysql client Creating databases and tables Inserting records Selecting data Using conditionals Using LIKE and NOT LIKE Sorting query results Limiting query results Updating data Deleting data Using functions Perl DBI Final Review BINF 634 Fall 2013 - Lecture 14 Review

  6. Lec 11 Data Visualization GD::Graph gnuplot Lec 12 Advanced SQL for Multiple Table Databases JOINS Objected Oriented Perl Objects Attributes Methods Classes Instances Intro to BioPerl Bio::Seq Bio::SeqIO Bio::DB::GenBank Bio::Perl Final Review BINF 634 Fall 2013 - Lecture 14 Review

  7. Lec 13 Adding links to CGI script Command Line Perl perl -e perl -ne perl -ane BEGIN {}, END {} Environmental variables and the ENV hash Files and Directories opendir, readdir, closedir, mkdir, rmdir, chdir File test operators -r -w -x -o -e -s -f -d Recursion XML Lec 14 Final Review Course readings: Tisdall: Chapters 1-12 Appendix B Wall: Chapters 1, 5, 26 pp 579-584 Ch 24: Common Practices (recommended) Final Review BINF 634 Fall 2013 - Lecture 14 Review

  8. Final Review • Take Home Final Exam • No collaboration allowed on the exam. • Due to me via email by 7:15 pm Monday 12/16/13 • No extensions will be given • Good Luck! • Barplot in GD (See Visualization Lecture) • Barplots in GD on a Directory Structure (See Cmd Line Recursion Lecture) • Shaded Pattern in GD (See http://search.cpan.org/~lds/GD-2.46/GD.pm, think about the order that you draw things in) • PubMed XML Processing (See the Cmd Recursion Record) • File extraction and conversion with Bioperl (See Bioperl Lecture) • LWP (See http://search.cpan.org/~gaas/libwww-perl-6.03/lib/LWP.pm) • Bioperl Sequence Manipulations (See BioPerl Lecture) • Barplots in PDL see hint and visualization lecture • Piecharts in R see tonight’s lecture • Please try to provide me answers based on your real needs when possible. BINF 634 Fall 2013 - Lecture 14 Review

  9. Additional Reading • Mastering Perl for Bioinformatics [Paperback] • James D. Tisdall (Author) • Building Bioinformatics Solutions: with Perl, R and MySQL [Paperback] • Conrad Bessant (Author), Ian Shadforth (Author), Darren Oakley(Author) BINF 634 Fall 2013 - Lecture 14 Review

  10. Thanks to each and everyone of you to taking this course with me! Perseverance is the hard work you do after you get tired of doing the hard work you already did. Newt Gingrich Read more at http://www.brainyquote.com/quotes/quotes/n/newtgingri107062.html#Ayx6LpiuIl4lAZfR.99 BINF 634 Fall 2013 - Lecture 14 Review

  11. Advertisement for Spring 2012 • BINF702 – RESEARCH METHODS (3 Credit Hours) • Noncalculus-based biostatistics • Statistical analysis and programming with R • MONDAY 7:20 pm – 10:00 pm • Has a distance learning section • BINF704-COLLOQUIUM (1 Credit Hour) • Tuesday 4:30-6:00pm • BINF705-RESEARCH ETHICS (1 Credit Hour) • Tuesday 6:00 pm – 7:00 pm • BINF734-ADVANCED BIOINFORMATICS PROGRAMMING (3 Credit Hours) • Tuesdays 7:20 pm – 10:00 pm • Jason Kinser BINF 634 Fall 2013 - Lecture 14 Review

  12. Course Evaluation • Evaluate my course by using the MyMason Portal listed below.   • http://myMason.gmu.edu/ • Closing dates • 12/10/11 regular sections • 12/9/11 distance learning section • Training slides are provided at the url below • https://crserating.gmu.edu/CourseEvaluation.ppt • The evaluations are important to me and the university. • You must must use their Mason Net ID and password to access the system. • The survey is not available between 6 pm on Sundays and 6 am on Mondays due to server maintenance. BINF 634 Fall 2013 - Lecture 14 Review

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