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Andy Kudlicki Office: BSB 547 Phone: 772-2253, 771-1011 cell a.kudlicki@utmb

BMB 6216 – Algorithms for Biology - Class 1. Andy Kudlicki Office: BSB 547 Phone: 772-2253, 771-1011 cell a.kudlicki@utmb.edu. BMB 6216 – Algorithms for Biology. Welcome! Imagine doing science without computers? It can (almost all) be done: Paper file folders Xeroxing

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Andy Kudlicki Office: BSB 547 Phone: 772-2253, 771-1011 cell a.kudlicki@utmb

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  1. BMB 6216 – Algorithms for Biology - Class 1 Andy Kudlicki Office: BSB 547 Phone: 772-2253, 771-1011 cell a.kudlicki@utmb.edu

  2. BMB 6216 – Algorithms for Biology • Welcome! • Imagine doing science without computers? It can (almost all) be done: • Paper file folders • Xeroxing • Photographs on film • Actually going to the library to browse journals • Abstract collections • Telephone, Snail-mail, Telegrams • Typewriters

  3. BMB 6216 – Algorithms for Biology The one exception: Science is quantitative, and has always been.

  4. BMB 6216 – Algorithms for Biology • This course: • Using computers for computing. • Aspects useful in biology / bioinformatics • Simple tasks ( 2 * 71.12 = ? ) • Simple repetitive tasks (few or many repetitions) • Somewhat complicated tasks • Typical problems of high complexity • BLAST, genome assembly, motif discovery, ...

  5. BMB 6216 – Algorithms for Biology • This course: • Using computers for computing. • Aspects useful in biology / bioinformatics • Simple tasks ( 2 * 71.12 = ? ) • Simple repetitive tasks (few or many repetitions) • Somewhat complicated tasks • Typical problems of high complexity • BLAST, genome assembly, motif discovery, ... spreadsheets ( Solved, software available )

  6. BMB 6216 – Algorithms for Biology – Class 1 Course Overview Class 1     Introduction to the course and to the Perl programming language Class 2     Computational complexity and numerical stability of algorithms Class 3     Data Structures and Containers in PERL and other languages 1.     Tables, lists, queues, hashes and when to use them 2.     When PERL is not enough: A quick look at R and C++ Class 4     Matrix operations; Principal Component Analysis; ICA Class 5     Network / graph algorithms 1.     Interaction Networks 2.     Regulation networks 3.     Graphs for enumerating hypotheses

  7. BMB 6216 – Algorithms for Biology Course Overview Class 6     Strings and Regular Expressions 1.     In silico enzyme digestion 2.     Gene translation Class 7     Randomization and Monte Carlo simulations 1.     Randomization by permutation 2.     Modeling the null-hypothesis probability distribution Class 8     Custom vector graphics: generating SVG from your data 1.     Create and re-create the killer graph for your paper Class 9     Visualization of multidimensional data Class 10     Web tools 1.     The components of a web page, elements of HTML. 2.     Extracting data from webpages and other documents. 3.     Connect to GenBank using BioPerl

  8. BMB 6216 – Algorithms for Biology Course Overview Class 11     Cgi-bin: Creating dynamic web-based tools for data analysis. Class 12     Relational databases and SQL 1.     Relational Model, normalization 2.     Basic SQL 3.     Examples: Experimental results, Class 13     Databases and WWW Class 14     Clustering 1.     Hierarchical 2.     K-means 3.     friends-of-Friends Class 15     Timecourses and spectral analysis; Convolution.

  9. BMB 6216 – Algorithms for Biology Format: Mixed – lecture with hands-on assignments. Computer environment: Linux Perl, also C/C++, R, shell, awk, sed, ..., when needed Supplementary reading: Larry Wall et al: Programming Perl Wing-Kin Sung: Algorithms in Bioinformatics James Tisdall: Beginning Perl for Bioinformatics James Tisdall: Mastering Perl for Bioinformatics Stroustrup: The C++ Programmming Language Special requests: Welcome !

  10. BMB 6216 – Algorithms for Biology Format: Mixed – lecture with hands-on assignments. Computer environment: Linux • * Rich in standard tools, mostly open-source • * Industry standard • * Very similar to MacOS, Android, iOS, BSD, ChromeOS, etc. • Has many flavors created for specific purposes

  11. BMB 6216 – Algorithms for Biology Using your laptop in class: To get a *nix environment: * linux laptop (or unix console on Mac) • Live CD distribution * cygwin * virtual machine * remote session (preferred, guaranteed to work)

  12. Remote session: Use • “Remote Desktop Connection” from win* • Server: 129.109.88.185 • From mac – install “Remote Desktop Connection Client for Mac” • From Linux “rdesktop 129.109.88.185” Also works from off campus • (mycitrix.utmb.edu -> remote desktop session) Other options: • ssh (puTTY on windows) , no graphics though, only on-campus • NX NoMachine

  13. BMB 6216 – Algorithms for Biology Login to: 129.109.54.80 Username: Password:

  14. BMB 6216 – Algorithms for Biology Unix / linux shell / command line: • List files: ls ls -a ls -1 ls -l ls -lrt • Directory: cd pwd • Copy, move, delete, link: cp mv rm ln • Machine status: ps w uptime top df du whoami /sbin/ifconfig date • Text editors: joe nano emacs (c-x c-f) vi • Pager: more less; also: cat, head, tail, tac • Misc: echo tr sed man wc chmod

  15. BMB 6216 – Algorithms for Biology Simple data flow / spreadsheet-like • Find in file : grep [grep -v; grep -f; egrep] • Select top/bottom lines from file: head, tail • Select columns: awk awk '{print $2, $3, $5+$6}' • Merge lines: cat • Merge columns: paste • Sort • Data flow: > >> < | tee tac

  16. BMB 6216 – Algorithms for Biology Exercise: The file /data/students/classes/remastercycle.csv contains gene expression data arranged as time-series in columns. (affy-id, name, gene-id, data*36) • How many named genes are there? • What is the average expression at timepoint 1? In how many genes it is above average? • What is the average expression at t1 of named genes, unnamed genes, non-genes? (genes have systematic names like YLR405W) • List 200 named genes that have the highest (t7+t19+t31)-(t1+t13+t25)

  17. BMB 6216 – Algorithms for Biology Log in to your account (on 129.109.88.185) • Make a fresh directory, e.g. mkdir bmb6216 cd bmb6216 mkdir class_1; cd class_1 cp /data/students/classes/hello.pl . * Cat it. * Less it. * Run it. • Backup: cp hello.pl hello-0.pl • Edit it: vi hello.pl

  18. BMB 6216 – Algorithms for Biology Editing with vi • I / i (insert) • A / a (append) • X / x / dd (delete) • R (eplace) / r (eplace 1 character) • {n} W / w / B / b / hjkl -move around • [ESC] – back from insert to command • ZZ / :w / :q / :wq / :x / :q! - exit / save / quit • xp – swap chars. ddp – swap lines

  19. BMB 6216 – Algorithms for Biology Exercise: The file /home/students/classes/Class_1/remastercycle.csv contains gene expression data arranged as time-series in columns. (affy-id, name, gene-id, data*36) • How many named genes are there? • What is the average expression at timepoint 1? In how many genes it is above average? • What is the average expression at t1 of named genes, unnamed genes, non-genes? (genes have systematic names like YLR405W), named genes also have a common name in column 2. • List 200 named genes that have the highest (t7+t19+t31)-(t1+t13+t25)

  20. BMB 6216 – Algorithms for Biology PERL Why PERL? Practical Extraction and Report Language Pathologically Eclectic Rubbish Lister • Versatile, portable • Widely used in bioinformatics and web applications • There's more than one way to do it • Not the most elegant language, great for dirty hacks • Easily integrated with anything

  21. BMB 6216 – Algorithms for Biology Warning: PERL6 ain't PERL

  22. BMB 6216 – Algorithms for Biology PERL HELLO WORLD: print ''Hello \n'';

  23. BMB 6216 – Algorithms for Biology PERL HELLO WORLD: > perl print ''Hello \n''; ^D

  24. BMB 6216 – Algorithms for Biology PERL HELLO WORLD: >perl -e 'print ''Hello \n'';'

  25. BMB 6216 – Algorithms for Biology PERL HELLO WORLD: hello.pl ================== #!/usr/bin/perl print ''Hello \n''; ================== > perl hello.pl Or > ./hello.pl (after chmod +x hello.pl)

  26. BMB 6216 – Algorithms for Biology VARIABLES: Scalar: $dna = 'ATTTGCCCTGCCCATT'; $mouse_tail_inches = 2.13; $RNA = ''GGGUUCAAUAUAUGGC''; $seven = -6; Default variable: $_ No need to declare variables. If not specified, $_ is assumed.

  27. BMB 6216 – Algorithms for Biology VARIABLES: No need to declare variables. Risky though: $my_variable = 51; $something = $my_variable + 3; $something_else = $myvariable + 4; use strict;

  28. BMB 6216 – Algorithms for Biology OPERATIONS: String: $dna = “ATAGAGGTA” . “CATATC”; $at_repeat = “AT” x 50; substr() sub-string length() Binding: print $dna if $dna =~ /ATA/; chop (last char) chomp (end of line) Special characters: \t \n

  29. BMB 6216 – Algorithms for Biology The different quotations $x=6; print ''x= $x \n''; print 'x= $x \n';

  30. BMB 6216 – Algorithms for Biology OPERATIONS: Arithmetic: $a + $b $a - $b $a * $b $a % $b $a ** $b

  31. BMB 6216 – Algorithms for Biology OPERATIONS: Incrementation (C-like) $a ++ $a *= 4 $repeat = 'AT'; $repeat x=36;

  32. BMB 6216 – Algorithms for Biology LISTS/TABLES: @a = (4, 6, 3.21, 7, 'cat', ''dog''); $a[0] = 6; $#a address of last element @a + 0 size of array OPERATIONS: * join / split * push / pop / shift / unshift

  33. BMB 6216 – Algorithms for Biology LISTS/TABLES: @a = (4, 6, 3.21, 7, 'cat', ''dog''); $a[0] = 6; $#a address of last element @a + 0 size of array OPERATIONS: * join / split * push / pop / shift / unshift

  34. BMB 6216 – Algorithms for Biology HASHES: The most important data type in biology! $expression{''RPS16''} = 4.65; %expression = ( RPL12 => 1.23, CDC28 => 5.31, STAT1 => ''experiment gone south” );

  35. BMB 6216 – Algorithms for Biology FLOW CONTROL: if ( $a > 4 ) { print sqrt ($a), “\n”; }; while ( $x > 0 ) { print --$x , “\n”}; $x>0 or $x = 6; for $z (1..333) {print $z, ' ';}; for ($i=0; $i<=1000; ++$i) { next unless $a[$i] > 0 };

  36. BMB 6216 – Algorithms for Biology TRUE or FALSE false strings: • ''0'' • '''' Every other string is true! ''0.00'' is true ''0.00'' + 0 is false • if ( 'Elvis is alive' ) { print 4+5, “\n”; }; • undef() is false

  37. BMB 6216 – Algorithms for Biology SUBROUTINES sub addit { my ($x1, $x2) = @_; return $x1 + $x2; };

  38. BMB 6216 – Algorithms for Biology Input / Output: while (<>) { chomp; $sum += $_; };

  39. BMB 6216 – Algorithms for Biology Input: open BLABLA, “data.csv”; $firstline = <BLABLA>; @headers = split “\t”, $firstline; while (<BLABLA>) {something}; close BLABLA;

  40. BMB 6216 – Algorithms for Biology Output: • print $x, ''\n''; • printf ''format'', $x; • print + join '' '', @list; open BLABLA, “>outdata.csv”; print BLABLA $x, $y, ''\n''; #no comma!!! close BLABLA;

  41. BMB 6216 – Algorithms for Biology Exercises: 1. repeat in PERL the awk/sort exercise from last hour 2. a-S_cer_TANAY_1000upstream.fasta contains the sequences out UTRs of genes. What is the correlation between the position of GATGAGA sequence and avg expression of the gene?

  42. BMB 6216 – Algorithms for Biology Simple data flow / spreadsheet-like • Find in file : grep [grep -v; grep -f; egrep] • Select top/bottom lines from file: head, tail • Select columns: awk awk '{print $2, $3, $5+$6}' • Merge lines: cat • Merge columns: paste • Sort • Data flow: > >> < | tee tac

  43. BMB 6216 – Algorithms for Biology C / C++ -> for total control =========================== Hello.C ====== #include <iostream> using namespace std; int main () { cout << "Hello :) " << 5+4 << endl; };

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