20 March 24 March. Relational Databases. Reading SQL. Perl DBI. SQL Tutorial or SQL Course MySQL tutorial

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1 20 March 24 March Relational Databases Reading SQL SQL Tutorial or SQL Course MySQL tutorial Perl DBI Database programming with Perl Appendix A and B Ch 1-5 Biol Practical Biocomputing 1

2 Database Design Entity Relationship approach Identify the entitites in your data: genes, sequences, citations, users, predictions, methods Make a preliminary layout of each as a table, list the attributes (columns) that define each entity Make sure each table has a primary key (unique) Identify one-to-many relationships. Make sure the "many" table has a foreign key pointing to the "one" table Identify many-to-many relationships For each, create an index table Check against use cases and try to write SQL for the use cases Review information for redundancy and consider breaking redundant information into separate tables Repeat Biol Practical Biocomputing 2

3 Database Design Formal Process Use cases Requirements Schema Design Implementation Testing Deployment Return to use cases Do you need a formal design process Is it just you for yourself? Do you have customers? Do you have deliverables? Biol Practical Biocomputing 3

4 Database Design Why design? Bad designs Lead to difficult queries May generate misleading results Generate inconsistent data/results Require redundant or excessive data entry Are difficult to change or extend May have poor performance Biol Practical Biocomputing 4

5 Database Design Use cases use cases are descriptions of the kinds of queries that you expect the database will have to perform Help prevent mission/function creep Used to define data Used to define tables and relationships Biol Practical Biocomputing 5

6 Database Design EcoliHub use cases Searches Find all the regulatory genes (i.e. all the genes in a functional class) Find all the regulatory genes for which there are/are not mutants, expression data, localization data, etc Find genes with particular combinations of protein motifs Find the genes that belong to any operon Find the genes that belong to any regulon Find the genes that have a particular phenotype when mutated Find the proteins that are found in a particular subcellular compartment Find groups of genes that are up or down regulated in an experiment Find evidence in the literature supporting assertions in the database Analyses For any of the above, find the neighboring genes to the initially identified set For any of the above, find/design primers for a certain gene For any of the above, find all the clones/kos for those genes Find commonalities in function in the genes that are up or down-regulated in a given experiment Find genes with similar behavior across sets of different experiments Given a gene name, find all the available info about this gene (motif, clones, mutants and relevant construction information, e.g., for making the mutants or the clones) For a gene, segment of DNA, operon/regulons, pathway, find all the available information Biol Practical Biocomputing 6

7 Database Design Requirements What will the user queries look like (use cases)? What will the reports look like? Translate use cases into tables What is the data needed to support the use cases What are the SQL queries needed What indices are needed Biol Practical Biocomputing 7

8 Database Design Considerations Archival vs current/encyclopedic Archival databases are much simpler because they don t need to be constantly updated Private vs public Controlling who has access to what adds a lot of overhead, including validation of users and timed release of information Data provenance Evidence codes Computational vs experimental Error recovery Timestamping Rollbacks and backups Biol Practical Biocomputing 8

9 Database Design Biggest Issues for biological databases Unique Identifiers Data updates Granularity and format of annotation Metadata for experiments Provenance Private Data status publication date privileges (owner, group,project,public,admin) Biol Practical Biocomputing 9

10 Database Design Reuse existing schema if possible Public Data Definitons MAGE/MIAME microarraysgene expression mmcif 3-dimensional structure De facto Standards FASTA EMBL/SWISS-Prot GENBANK ASN.1 CHADO General tools XML RDF OWL (replaces DAML/OIL) Biol Practical Biocomputing 10

11 DBI.pm Perl DBI Database Interface Provides a consistent interface to MySQL, MSSQL, Oracle, Informix, Sybase, ODBC etc. Makes Perl scripts (relatively) platform independent Biol Practical Biocomputing 11

12 DBI.pm Perl Application DBI Module DBD::Oracle DBD::Informix DBD::Other Oracle Server Informix Server Other Server Biol Practical Biocomputing 12

13 DBI.pm DBI works in four stages Make a database connection get a database handle (usually called $dbh) Set up a specific query in SQL done through a statement handle (usually called $sth) Execute the query Examine the results Biol Practical Biocomputing 13

14 DBI.pm Opening a database connection use DBI; use strict; $dbh = DBI->connect( $dsn, $user, $password, { RaiseError => 1, AutoCommit => 1 } ); DBI->connect( dsn, user, pass, { parameters } ) dsn - data source name the database name and connection information user - your username pass - your password hash of parameters RaiseError - report errors AutoCommit - makes changes permanent automatically Database connections are usually reused multiple times Biol Practical Biocomputing 14

15 DBI.pm Identifying the database data source name ($dsn) DBI:DriverName: database_name DBI:DriverName: database_name:hostname:port DBI:DriverName:database=database_name;host=hostname;port=port Drivername is mysql (lower case) would be different for other DBMS Host is thr.genomics.purdue.edu Port is 3306 (MySql standard port) installations can choose other ports $dsn = 'DBI:mysql:test:thr.genomics.purdue.edu:3306'; Biol Practical Biocomputing 15

16 DBI.pm Simple example #!/usr/bin/perl # ddbi.pl use DBI; use strict; my $dsn = 'DBI:mysql:test:thr.genomics.purdue.edu:3306'; my $user = "gribskov"; my $password = "mysql"; my $dbh = DBI->connect( $dsn, $user, $password ) or die $DBI::errstr; my $sth = $dbh->prepare( "show tables" ); $sth->execute; while ( = $sth->fetchrow_array ) { print "@result\n"; } $sth->finish; $dbh->disconnect; thr(~/scripts)-40% ddbi.pl employee project testaa testad Biol Practical Biocomputing 16

17 DBI.pm database handle methods prepare - set up and possibly optimize an SQL statement returns a statement handle do - prepare and execute a single SQL command last_insert_id - Returns a value 'identifying' the row just inserted, if possible. Usually a value assigned by the database server to a column with an auto_increment type. Returns undef if the driver can't determine the value. disconnect - undef the database handle and disconnect from the database ping - check if the database is responding Biol Practical Biocomputing 17

18 DBI.pm Statement handle methods execute - execute a single SQL command fetchrow methods - get one row of results from the statement handle and return it as an array (list), array reference, or hash reference fetchrow_array fetchrow_arrayref fetchrow_hashref (preferably use this) fetchall methods - get all of the results from a statement handle and return an array of array or hash references fetchall_arrayref fetchall_hashref rows - number of rows in the result finish - release the statement handle (statement handle will no longer be used clears the results of SQL) Biol Practical Biocomputing 18

19 DBI.pm #!/usr/bin/perl #ddbi.pl use DBI; use strict; my $dsn = 'DBI:mysql:gribskov:descartes.genomics.purdue.edu:3306'; my $user = "gribskov"; my $password = "mysql"; my $dbh = DBI->connect( $dsn, $user, $password ) or die $DBI::errstr; my $sql = qq{ SELECT name,phone FROM employee WHERE age > 30 } my $sth = $dbh->prepare( $sql ); $sth->execute; while ( = $sth->fetchrow_array ) { print "@result\n"; } $sth->finish; $dbh->disconnect; thr(~/scripts)-59% ddbi.pl Edgar Poe 666 Usher House sales Elmer Fudd 27 Pigsty Rd admin Bugs Bunny 1 Rabbit Hole Dr research Daffy Duck 43 Pond St sales Biol Practical Biocomputing 19

20 DBI.pm use DBI; use strict; my $dsn = 'DBI:mysql:gribskov:descartes.genomics.purdue.edu:3306'; my $user = "gribskov"; my $password = "mysql"; my $dbh = DBI->connect( $dsn, $user, $password ) or die $DBI::errstr; my $sql = qq{ SELECT * FROM employee WHERE age > 30 }; my $sth = $dbh->prepare( $sql ); $sth->execute; while ( my ($name,$address,$phone,$age,$dept) = $sth->fetchrow_array ) { printf "%-15s %-20s %-10s %-4d %-10s\n", $name,$address,$phone,$age,$dept; } What happens if I add a column to the employee table? $sth->finish; $dbh->disconnect; thr(~/scripts)-66% ddbi.pl Edgar Poe 666 Usher House sales Elmer Fudd 27 Pigsty Rd admin Bugs Bunny 1 Rabbit Hole Dr research Daffy Duck 43 Pond St sales Biol Practical Biocomputing 20

21 DBI.pm Results fetchrow_array requires that you know the order of the columns in a table If you add columns to the table, scripts that rely on this order will fail fetchrow_hashref is much safer Biol Practical Biocomputing 21

22 DBI.pm with $sth->fetchrow_hashref #!/usr/local/bin/perl use DBI; use strict; my $dsn = 'DBI:mysql:gribskov:descartes.genomics.purdue.edu:3306'; my $user = "gribskov"; my $password = "mysql"; my $dbh = DBI->connect( $dsn, $user, $password ) or die $DBI::errstr; my $sql = qq{ SELECT * FROM employee WHERE age > 30 }; my $sth = $dbh->prepare( $sql ); $sth->execute; while ( my $result = $sth->fetchrow_hashref ) { foreach my $column ( keys %$result ) { print "$column => $$result{$column}\n"; } print "\n"; } $sth->finish; $dbh->disconnect; descartes(~/scripts)-61% ddbi.pl department => sales name => Edgar Poe address => 666 Usher House age => 45 phone => department => admin name => Elmer Fudd address => 27 Pigsty Rd. age => 65 phone => department => research name => Bugs Bunny address => 1 Rabbit Hole Dr. age => 35 phone => department => sales name => Daffy Duck address => 43 Pond St. age => 35 Biol Practical Biocomputing phone =>

23 DBI.pm Error messages database and statement handles can be interrogated about possible error status of previous calls $h->err - returns error number $h->errstr - returns descriptive message $h->state - returns a five digit SQLSTATE code, most importantly returns 0 if successful my $dbh = DBI->connect( $dsn, $user, $password ) or die $dbh->errstr; Biol Practical Biocomputing 23

24 DBI.pm Trapping errors my ( $sth ); my $sql = qq/ SELECT FROM TableName WHERE Field = 'value' /; eval { $sth = $dbh->prepare( $sql ); $sth->execute; }; if ( $@ ) { print "Error in the database: $@"; exit; } $@ has the last error message Biol Practical Biocomputing 24

25 DBI.pm Trapping errors eval executes a bit of code in its own context, as if it was a small separate script $i = 10; $zero = 0; thr(~/scripts)-95% error.pl Illegal division by zero at error.pl line 6. $result = $i / $zero; with eval - error message is $@ (special variable) $i = 10; $zero = 0; thr(~/scripts)-103% error.pl Error: Illegal division by zero at error.pl line 7. eval{ $result = $i / $zero; }; Biol Practical Biocomputing 25

26 DBI.pm Placeholders If a statement is to be reused repeatedly it need only be "prepared" once the position of the changing data is filled with a placeholder also called "bind value" placeholder sql executes much faster because you only prepare once prevents SQL injection attacks $sql = "INSERT into users (name, phone, ) values (?,?,?)"; $sth = $dbh->prepare( $sql ); while ( $line = <> ) { ( $name, $phone, $ ) = split " ", $line; $sth->execute( $name, $phone, $ ); } Biol Practical Biocomputing 26

27 SQL Left and right joins Include the rows of a table that do not satisfy the join condition RIGHT [OUTER] JOIN show all rows of second table LEFT [OUTER] JOIN show all rows of first table SELECT columns FROM table1 RIGHT JOIN table2 ON table1.id=table2.id conditions mysql> SELECT * -> FROM employee -> RIGHT JOIN project ON employee.name=project.name; name address phone age department number title name Jane Doe 127 Elm St sales 1 database Jane Doe Edgar Poe 666 Usher House sales 2 database Edgar Poe Elmer Fudd 27 Pigsty Rd admin 3 database Elmer Fudd Richard Roe 915 W. State St sales 4 space shuttle Richard Roe Bugs Bunny 1 Rabbit Hole Dr research 5 space shuttle Bugs Bunny Road Runner 177 Mesa Canyon Rd admin 6 space shuttle Road Runner Bugs Bunny 1 Rabbit Hole Dr research 7 nation building Bugs Bunny Daffy Duck 43 Pond St sales 8 nation building Daffy Duck rows in set (0.00 sec) Biol Practical Biocomputing 27

28 SQL Left and right joins mysql> SELECT * -> FROM employee -> LEFT JOIN project ON employee.name=project.name; name address phone age department number title name Jane Doe 127 Elm St sales 1 database Jane Doe Richard Roe 915 W. State St sales 4 space shuttle Richard Roe Edgar Poe 666 Usher House sales 2 database Edgar Poe Elmer Fudd 27 Pigsty Rd admin 3 database Elmer Fudd Bugs Bunny 1 Rabbit Hole Dr research 5 space shuttle Bugs Bunny Bugs Bunny 1 Rabbit Hole Dr research 7 nation building Bugs Bunny Daffy Duck 43 Pond St sales 8 nation building Daffy Duck Road Runner 177 Mesa Canyon Rd admin 6 space shuttle Road Runner Atom Ant 1 Deep Chamber research NULL NULL NULL rows in set (0.00 sec) Useful for finding missing data that should join Biol Practical Biocomputing 28

29 SQL Left and right joins What employees do not have projects assigned? mysql> SELECT employee.name -> FROM employee -> LEFT JOIN project ON employee.name=project.name -> WHERE project.number IS NULL; name Atom Ant row in set (0.00 sec) Biol Practical Biocomputing 29

30 SQL Functions (partial list) Mathematical Functions Trigonometry and logarithm sin, cos, tan, cot, asin, acos, atan, ln, log10, log2, exp, pi, radians, degrees Comparison/conversion floor, ceiling, abs, truncate, round Other sign, rand, mod, pow, sqrt, format Date and Time curdate, curtime, now Day, dayofmonth, dayofweek, dayofyear, dayname, from_days String (very partial list) Length password, encrypt, compress, uncompress Bit functions & (and), (or), ^(xor), << (shift left), >> (shift right), ~ (invert) Biol Practical Biocomputing 30

31 SQL Bit functions Sometimes a convenient way to perform multiple tests simultaneously Particularly useful when the data belongs to overlapping groups Example: PlantsP, PlantsT, PlantsUbq Three resources one database Biol Practical Biocomputing 31

32 SQL Bit masks Use a column and store a comma delimited list of which database a datum belongs to requires time consuming parsing if list is big susceptible to spelling errors (use enum datatype) verbose Another solution use one boolean column for each database, simply mark each row as true or false with a 1 or 0 requires altering table to extend large numbers of choices make tables swell alarming Bit solution use one bit per option a zero bit means false, a one bit means true easily extensible can be included in SQL queries Biol Practical Biocomputing 32

33 SQL Bit masks bit mask query mysql> SELECT sequence -> FROM sequence_genomic -> WHERE dbmask & 4; PlantsP PlantsT PlantsUbq integer value 101 P and U T and U T only U only P only 4 Biol Practical Biocomputing 33

34 SQL Counting and grouping mysql> SELECT d.department AS dept,p.title AS project, count(*) -> FROM department d,employee e,project p -> WHERE d.department=e.department -> AND e.name=p.name -> GROUP BY project; dept project count(*) sales database 3 research nation building 2 sales space shuttle rows in set (0.00 sec) mysql> SELECT d.department AS dept,p.title AS project, count(*) -> FROM department d,employee e,project p -> WHERE d.department=e.department -> AND e.name=p.name -> GROUP BY project -> ORDER BY count(*) DESC; ERROR 1111 (HY000): Invalid use of group function Biol Practical Biocomputing 34

35 SQL Counting and grouping mysql> SELECT d.department AS dept,p.title AS project, count(*) AS number -> FROM department d,employee e,project p -> WHERE d.department=e.department -> AND e.name=p.name -> GROUP BY project -> ORDER BY number DESC; dept project number sales database 3 sales space shuttle 3 research nation building rows in set (0.00 sec) Biol Practical Biocomputing 35

36 SQL Functions with GROUP BY sum max, min std, variance mysql> SELECT student_name, MIN(test_score), MAX(test_score) -> FROM student -> GROUP BY student_name; Biol Practical Biocomputing 36

37 SQL Performance DBMS have sophisticated searching mechanisms that make them fast (much faster than sequential searching) Fast searching requires indexing Primary Key columns are indexed Other columns can be indexed as you wish In general, make an index on any column that you will use in looking things up (especially in making joins) Index when you CREATE TABLE Index later with ALTER TABLE files vs blobs store the complete text of large images, or just save the location of the file? Do you need to search the content? MySQL now allows compression using compress function Biol Practical Biocomputing 37

38 Database Design Unique IDs Every table row must have a unique primary key Can use data columns, e.g. gene name, person name, etc., but must be sure that it will be unique Often you cannot guarantee this so a unique number is used In MySQL this can be an autoincrementing number column Unique IDs once generated should not be re-used for a new object! Biol Practical Biocomputing 38

39 Database Design Problems with Unique IDs Not mnemonic If your database generates keys on the fly, you must guarantee that a race condition does not develop and give the same key to multiple events, e.g. Process 1 queries UID table for highest existing key (1 SQL query) Process 2 queries UID table for highest existing key Process 1 assigns new UID as highest + 1 and inserts into UID table Process 2 assigns new UID and tries to insert into UID table (fails due to non-unique primary key) Lock table can be used to prevent this Or catch error on process 2 insert and try again Biol Practical Biocomputing 39

40 Database Design Complicated fields one strategy Initially defined as a text block Add XML markup When data model is stable, convert to tables/columns mutation <Mutation> <Reference_sequence>... <Reference_sequence> <Sequence_position>... <Sequence_position> <Sequence_change>... </Sequence_change> <Begin>...</Begin> <End>... </End> <Difference>... </Difference> </Mutation> Biol Practical Biocomputing 40

41 Web Server CGI Scripts Html pages go in htdocs xampp -> htdocs localhost/mypage.html cgi scripts go in cgi-bin localhost/cgi-bin/plot.cgi localhost/blast.cgi Biol Practical Biocomputing 41

42 Web Server htdocs Index.php is default Biol Practical Biocomputing 42

43 Web Server Scripts CGI scripts are executed by server Conventionally stored in cgi-bin env.cgi #!perl use CGI; my $cgi = new CGI; print $cgi->header; print $cgi->start_html; print qq{ <pre>\n}; foreach my $symbol ( sort keys %ENV ) { print "$symbol\t$env{$symbol}\n"; } print "</prep>\n"; print "</body>\n"; print "</html>\n"; exit 0; Biol Practical Biocomputing 43

44 Web Server Biol Practical Biocomputing 44

45 Web Server Path Problems How do you find an executable? In unix, when I type the name of a program, the OS looks in a defined set of directories called the "path" my path looks like echo $PATH /cbio/server/software/bin:/home/gribskov/scripts:/usr/local/bin:/usr/local/perl/bin:/usr/local/genome/bin:/opt/csw/mysql5/ bin:/opt/csw/apache2/sbin:/opt/csw/bin:/opt/csw/sbin:/usr/bin:/usr/local/emboss/bin:/usr/x11/bin:/usr/ccs/bin:/usr/dt/bin: /usr/openwin/bin:/usr/ucb:/usr/sfw/bin:/usr/local/mummer:/usr/sbin:. Especially on UNIX, the web server often has an impoverished path such as path:/usr/sbin:/usr/bin Need to use complete path to executables Biol Practical Biocomputing 45

46 Web Server Path Problems Executable must be in the path to work #!perl use CGI; use strict; my $exe = "/usr/local/msatcommander/msatcommand.py"; my $cgi = new CGI; print $cgi->header; print $cgi->start_html; print qq{ <pre>\n}; my $command = $exe." test.fa"; print "command:$command\n"; system( $command ); command:/usr/local/msatcommander/msatcommand.py test.fa Traceback (most recent call last): File "/usr/local/msatcommander/msatcommand.py", line 15, in? import seqsearch File "/usr/local/msatcommander/seqsearch.py", line 13, in? from Bio.Seq import Seq ImportError: No module named Bio.Seq Biol Practical Biocomputing 46

47 Web Server Path Problems Add necessary directories to path #!/usr/bin/perl use CGI; use strict; my $exe = "/usr/local/msatcommander/msatcommand.py"; $ENV{PYTHONPATH} = "/usr/local/python:/usr/local/python/lib/python2.7/site-packages"; my $path = $ENV{PATH}; my $cgi = new CGI; print $cgi->header; print $cgi->start_html; print qq{ <pre>\n}; my $command = $exe." test.fa"; print "command:$command\n"; print "path:$path\n"; system( $command ); Biol Practical Biocomputing 47

48 Web Server Path Problems Output Biol Practical Biocomputing 48

49 CGI scripts See Web Development with Perl, Fenwick et al. some useful examples of CGI + database Don't forget your HTML HTML tutorial - HTML tag reference - really basic tutorial - Biol Practical Biocomputing 49

50 CGI scripts Package CGI.pm Major purpose Get parameters from html forms via both get and post write html web pages Additional escaping characters creating/managing cookies preserve state Functional vs object-oriented CGI.pm supports both a functional and object oriented interface. I am used to the OO one so that s what I ll show in examples. see the documentation for more information Biol Practical Biocomputing 50

51 CGI scripts fatalstobrowser with CGI::Carp qw(fatalstobrowser); Biol Practical Biocomputing 51

52 CGI scripts Getting parameters Forms include a method either get, or post these are fundamentally different ways to pass information from an web page with a form to a CGI script GET <form action= /cgi-bin/do_something.cgi method= get > parameters are passed in the url cpk POST <form action= /cgi-bin/do_something.cgi method= post > parameters are passed as part of the mime encoded message sent to the server cannot be seen by user CGI.pm uses a single syntax to get the values of parameters regardless of GET or POST Biol Practical Biocomputing 52

53 CGI scripts Getting Parameters when you create the CGI object (variable) it automatically fetches all input parameters if it is being run as a CGI script (through a web server) use CGI; my $query = new CGI; param function get a single parameter $value = = $query->param( 'name' ); # only if parameter has list of values Vars function get all parameters %params = $query->vars; Delete function not usually needed $query->delete('foo','bar','baz'); $query->delete_all(); Biol Practical Biocomputing 53

54 CGI scripts Debugging Offline mode lets you enter parameters in tag-value form for testing, i.e., name=john use CGI qw(-debug); #!/usr/bin/perl use strict; use CGI qw(-debug); my $cgi = new CGI; my %params = $cgi->vars; foreach my $k ( keys %params ) { print "k => $param{$k}\n"; } (offline mode: enter name=value pairs on standard input; press ^D or ^Z when done) name=john x=6 len=50 k => 50 k => john k => 6 Biol Practical Biocomputing 54

55 CGI scripts Debugging Sometimes you just want to know what the parameters passed to the script are so you can confirm your form is right dump function prints any parameters entered through a get or post print $cgi->dump;make sure to use FatalsToBrowser Biol Practical Biocomputing 55

56 CGI scripts URL encoding Certain characters are not allowed in URLs space + CGI.pm provides a function to convert a string to the URL encoded form - escape #!/usr/bin/perl use strict; use CGI; my $string = qq{xyz.cgi?name="john wilbur"&eq="1+3" }; print "original string $string \n"; my $ustring = $cgi->escape( $string ); print "url encoded string $ustring \n"; original string xyz.cgi?name="john wilbur"&eq="1+3" url encoded string xyz.cgi?name%3d%22john%20wilbur%22%26eq%3d%221%2b3%22%20 Biol Practical Biocomputing 56

57 CGI scripts Uploaded files Many websites let you upload a file instead of cutting and pasting something into a box <html> <head> <title>upload a file</title> </head> <body> <h1>upload a file</h1> <p> Please choose a file to upload: </p> <form action="cgi-bin/upload.cgi" method="post" enctype="multipart/formdata"> <input type="file" name="filename"> <input type="submit" value="ok"> </form> </body> </html> Biol Practical Biocomputing 57

58 CGI scripts Uploaded files upload function gets a value that is the name of the file also can be used as a filehandle my $cgi = new CGI; my $filename = $cgi->upload( filename ); while( <$filename> ) { # do something with file contents } Biol Practical Biocomputing 58

59 CGI scripts Using CGI.pm to write HTML Not recommended - I don't find this very useful since you need to remember the HTML anyway, but your taste may differ HTML written by CGI.pm is often very hard to figure out since it doesn't contain newlines and indentation Several features are useful (even for me) header function prints an http format header line print $cgi->header; same as print "Content-type: text/plain\n\n"; start_html function prints an HTML header (or XHTML) print $cgi->start_html; end_html closes the HTML elements opened in start_html print $cgi->end_html; <?xml version="1.0" encoding="iso "?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" " <html xmlns=" lang="en-us" xml:lang="en-us"> <head><title>hello World</title> </head><body> </body></html> Biol Practical Biocomputing 59

60 CGI scripts Using CGI.pm to write HTML Anchors (links) print $cgi->a( {-href=>" "purdue university" ) print qq{<a href=" university</a>}; Lists use CGI; my $cgi = CGI->new(); print $cgi->start_ul; foreach my $name (qw/jacob Jeremy Jacinta Jenni Jack/) { print $cgi->li($name); } print $cgi->end_ul; <ul><li>jacob</li><li>jeremy</li><li>jacinta</li><li>jenni</li><li>jack</li></ul> print qq{<ul>\n}; foreach my $name (qw/jacob Jeremy Jacinta Jenni Jack/) { print qq{ <li>$name<\li>\n"; } print qq{</ul>}; <ul> <li>jacob</li> <li>jeremy</li> <li>jacinta</li> <li>jenni</li> <li>jack</li> </ul> Biol Practical Biocomputing 60