1. CS 122: Last Lecture Tarik Booker California State University, Los Angeles

2. Last Lecture!!!  Final Exam  Tuesday, March 17 1:30PM – 4:30PM ET- A220  Today:  Goodies  Fun  Things to keep you busy until CS 422

3. Final Exam  Everything until last lecture  E-R Diagrams MAYBE Included on Final  Look at Final Review for More Examples  GOOD LUCK!!!

4. What we will cover today…  Fancy Stuff  LAMP / WAMP  Bioinformatics  Fun with databases  Public Databases  Applications for databases  Query Languages  Yahoo’s YQL  Facebook FQL  Google’s Freebase  Query Languages

5. Fancy Stuff  What’s the rule for fancy stuff?  Just checking…  MySQL Workbench  Command-line execution  Output formatting (HTML)

6. MySQL WorkBench  A Graphical User Interface (GUI) for MySQL  http://www.mysql.com/products/workbenc h/ http://www.mysql.com/products/workbenc h/  Contains interactive windows for MySQL server, E-R Diagrams, and SQL command interface.  Fun; easy; buggy.  Use at your own risk!

8. Command-Line Execution  You don’t need to open a direct client connection to access the database  Try this at the shell command line, not the mysql client :  >mysql –u root –e “show databases;” –D lyric  E stands for “execute”, D stands for database  Make sure the –D is capitalized.  >mysql –u root –e “select * from members;” –D lyric  >mysql –u root –e “Any SQL query” –D database_name

9. Output Formatting  Now try this:  >mysql –u root –e “show databases;” –D lyric –H  Again, CAPITAL “H”  You can specify mysql to output information as a table in a website!!  Our tables are already formatted!  >mysql –u root –e “select * from artists join xrefartistsmembers using (artistid) join members using(memberid);” -D lyric -H

10. Output Formatting (2)  The > operator in the windows shell will put the output of the command into a filename (of your choosing)  Called output redirection  Don’t confuse this with my prompt indicator(>)  Ex:  >dir > dir_out.txt  Let’s use these with our command-line mysql queries

11. Output Formatting (3)  >mysql –u root –e “select * from artists join xrefartistsmembers using(artistid) join members using(memberid);” -D lyric –H > ArtistMembersout.html  Now open this in a web browser!  Note: This file is in the directory mysql is in (unless you change the path)  >mysql –u root –e “select * from artists join xrefartistsmembers using(artistid) join members using(memberid);” -D lyric –H >../../ArtistMembersout.html  >mysql –u root –e “select * from artists join xrefartistsmembers using(artistid) join members using(memberid);” -D lyric –H |../../ArtistMembersout.html

12. LAMP/WAMP  Linux, Apache, MySQL, PHP  Typical model of web solutions  Completely free (buy your own computer, though)  Linux – open source operating system  Apache – open source server  MySQL – this class  PHP – web programming language  WAMP = Windows, Apache, MySQL, PHP

13. LAMP/WAMP (2)  Most (if not all) professional (and data intensive) web pages use databases  Wikipedia, IMDB, Google, PayPal, Ebay, etc.  LAMP makes creating your own site easy (and free)

14. Public Databases  Public MySQL Databases  Public Databases

15. Public MySQL Databases  If you are interesting in seeing the type of information used in databases, search for public mysql databases  Many are also PostgreSQL DBs (look up)  Many are for public analysis of interesting data  Bioinformatics – the study of processing biological data

16. Bioinformatics  The interdisciplinary study of developing methods and software tools for processing biological data.  Why? There’s a LOT of biological data  Viruses, Genome, etc.  Human Genome  Over 3 billion base pairs  Data must be structured, accessible, and computable

17. Bioinformatics (2) Only One Human X Chromosome:

18. Bioinformatics (3)  Different schools have bioinformatics  Cal State LA has a minor:  http://web.calstatela.edu/centers/cinqa/binf /minorinfo.php http://web.calstatela.edu/centers/cinqa/binf /minorinfo.php  And courses:  http://web.calstatela.edu/faculty/jmomand/ Bioinformaticscourse.html http://web.calstatela.edu/faculty/jmomand/ Bioinformaticscourse.html  Other schools have more resources…

19. UCSC Genome Bioinformatics  UCSC Genome  https://genome.ucsc.edu/index.html  Public MySQL Database  https://genome.ucsc.edu/goldenPath/help/mysql.html https://genome.ucsc.edu/goldenPath/help/mysql.html  Note “Conditions of Use:”  “Avoid excessive or heavy queries that may impact the server performance. Inappropriate query use will result in a restriction of access. If you plan to execute a query that you think may be excessive, contact UCSC first to avoid the possibility of having your access blocked.”  What SQL techniques should you NOT use ?

20. UCSC Genome Bioinformatics (2)  Contains a portal (site) of information on Ebola and other diseases  Can search database with biological information

21. UCSC Bioinformatics  To access the public database:  mysql --user=genome --host=genome-mysql.cse.ucsc.edu –A  Don’t do this in class!  Make sure you follow the rules of the database before you access!!!  Grants (public) access to many different biological data  Ebola is “eboVir3” database

22. UCSC Bioinformatics  Each database has large amounts of biological data  Can be downloaded separately  Up to you to determine what’s necessary

23. Other Bioinformatics Databases  There are also other databases out there for bioinformatics  ENSEMBL Database  http://uswest.ensembl.org/info/data/mysql. html http://uswest.ensembl.org/info/data/mysql. html  GO Database  http://geneontology.org/page/lead- database-guide#mirrors http://geneontology.org/page/lead- database-guide#mirrors

24. Human Genome  Genome Browser Database  http://users.soe.ucsc.edu/~kent/gbd.html http://users.soe.ucsc.edu/~kent/gbd.html  UCSC’s Genome Browser  http://hgdownload.cse.ucsc.edu/downloa ds.html http://hgdownload.cse.ucsc.edu/downloa ds.html

25. Drosophila Database  ftp://ftp.flybase.net/releases/FB2014_06/p sql/README ftp://ftp.flybase.net/releases/FB2014_06/p sql/README  Who knows what Drosophila are?  High school biology…

26. Public Data Sources  Try to find other SQL files out there!  Amazon Public Datasets  https://aws.amazon.com/datasets https://aws.amazon.com/datasets  Images of the Night Sky  http://classic.sdss.org/dr1/access/index.html http://classic.sdss.org/dr1/access/index.html  Influenza Database  http://www.ncbi.nlm.nih.gov/genomes/FLU/FL U.html http://www.ncbi.nlm.nih.gov/genomes/FLU/FL U.html  Don’t always have to be completely scientific…

27. Marvel Teamup Database  http://bioinfo.uib.es/~joemiro/marvel.html http://bioinfo.uib.es/~joemiro/marvel.html  Used to study social characteristics of the Marvel Universe  Example of a “Social Collaboration Network”  Mirrors real-world collaboration  More of a directed graph  You will study later  Vertices and branches

28. Baseball Reference  http://www.baseball-reference.com/ http://www.baseball-reference.com/  All statistics from Baseball History  They are hiring!  http://www.sports- reference.com/jobs_2014_fall.shtml http://www.sports- reference.com/jobs_2014_fall.shtml

29. Fashion Database  https://www.myfdb.com/ https://www.myfdb.com/

30. Many Other Databases  Many other databases out there  Look on Google  Many use PostgreSQL  Another type of Free, Open source Database  Practice this  Code a little different, logic always same

31. Query Languages  SQL not the only query language  Many are proprietary  FQL  Facebook Query Language  YQL  Yahoo Query Language  Freebase  Google Product

32. Facebook Query Language (FQL)  https://developers.facebook.com/docs/t echnical-guides/fql https://developers.facebook.com/docs/t echnical-guides/fql  Used to search Facebook information like a database  Information organized in tables  Like a relational database  We covered this earlier…

34. Facebook Query Language (3)  Deprecated (no longer used), but interesting  Look at query guidelines:  https://developers.facebook.com/docs/techni cal-guides/fql https://developers.facebook.com/docs/techni cal-guides/fql  What technique can’t you use for queries?  Notice a pattern?  What programming language does this use?

35. Yahoo Query Language (YQL)  https://developer.yahoo.com/yql/ https://developer.yahoo.com/yql/  Different than FQL  Designed to manipulate data across the internet  Including other sites and treating their info like databases  Flickr, Yelp, etc.  Queries web services (you will learn later)  Let’s look at the tutorial:  https://developer.yahoo.com/yql/guide/two- minute-tutorial.html https://developer.yahoo.com/yql/guide/two- minute-tutorial.html

36. Yahoo Query Language (2)  Two minute tutorial:  https://developer.yahoo.com/yql/guide/two- minute-tutorial.html https://developer.yahoo.com/yql/guide/two- minute-tutorial.html  Let’s get the Weather Forecast for Los Angeles:  First get LA weather id.  select woeid from geo.places where text="los angeles, ca“  Then get forecast... (Subquery)  Lots of things to query here… results in XML…

37. Google Freebase  https://developers.google.com/freebase/ https://developers.google.com/freebase/  An “open, shared database of the world’s knowledge”  User collected, “curated” content  Uses Metaweb Query Language (MQL)  Returns XML or JSON info (objects)  Just organized data (like generalized HTML)

38. Database Jobs  Everyone needs a database  SQL DBA / SQL Database Administrator - View similar jobs Job type: Full-Time | Pay: $85k - $95k/year Database Administrator and the salary is in the $85K-$95K range plus benefits. Only candidates authorized... SQL DBA / SQL Database Administrator View similar jobs

39. Food For Thought…  For your own information…  15 Coveted Programming Skills  http://readwrite.com/2013/04/09/15-programming-skills- most-coveted-by-employers http://readwrite.com/2013/04/09/15-programming-skills- most-coveted-by-employers  Why technology will always change:  http://readwrite.com/2013/05/01/10-technology-skills-no- longer-in-demand http://readwrite.com/2013/05/01/10-technology-skills-no- longer-in-demand  Remember, code changes, but logic always stays the same!!!

40. Go See “The Imitation Game!” Alan Turing The type of crazy that produced modern Computer Science!!!