Dr Richard White

1
Dr Richard White
Basic Computing Concepts for Bioinformatics
2
Basic computing concepts

• Basic Computing concepts sounds a bit scary. I
  hope youll find it isnt really.
• Actually some of the Basic Computing Concepts
  youll be familiar with already.

3
What does the average biologist use computers for?

• Browsing the Web, searching with Google, etc.
• Email
• Word-processing for reports, etc. (e.g. MS Word)
• Data handling and simple statistics (e.g. Excel)
• Playing CDs, games, etc. (no, of course not,
  only joking)
• So youre probably quite experienced in computer
  use already
• Databases? The use of bioinformatics databases
  figures prominently in this course.

4
What should biologists use computers for?

• Access to biological databases, especially those
  containing bioinformatics information
• Visualisation ways to understand data better by
  visual exploration
• Analysing data, especially to test hypotheses (to
  understand biology better)

5
Computer use during this course

• Mostly well be concerned with access to
  biological databases
• Also some visualisation sessions and maybe some
  data analysis and hypothesis testing

6
Using predefined tools

• Youll be doing a lot of this work using tools
  available on the web.
• This makes life easy, because the hard work of
  setting these tools up for use has already been
  done by someone else.
• However, sometimes its useful to get your hands
  dirty and mess about with the data and ways to
  process it yourself,
• especially if you want to do something that
  zillions of other people havent already thought
  of.

7
Use of databases

• Ill be running a session on the use of databases
  in week 4, but at the moment I want to think
  about this in order to discover some Basic
  Computing Concepts.
• First, lets consider the characteristics of
  databases for a moment.

8
Simple database concepts

• Computers allow the analysis of large data sets.
  These are frequently arranged as two-dimensional
  data tables, based on the convention that
• each row holds information on a separate object
  (or abstract entity such as a species),
• each column holds information on a particular
  property or characteristic of the objects,
• in general there will be a single value in each
  cell of the table, representing the value of a
  specific characteristic for one particular
  object.

9
Spreadsheets

• Data in the form of two-dimensional tables is
  frequently analysed using computer spreadsheet
  programs such as Microsoft Excel, especially
  where the purpose is
• relatively simple data reorganisation,
• summarisation,
• statistical testing
• report generation.

10
Databases

• It is becoming harder to distinguish between
  spreadsheet and database programs.
• Most databases require more than one table for
  example, one table may store data about proteins
  and another table stores data about the species
  these proteins are found in.
• For more about database systems, see the
  PowerPoint presentation (DatabaseIntroduction.ppt)
  on my web site (see handout for details).

11
Methods for using databases

• What methods exist to use databases?
• Basically there are several approaches to the use
  of databases

12
Database use 1 direct access to database tables

• Run your own database on your own computer (e.g.
  MS Access)
• Use a program on your PC which gives you direct
  access to the tables in the remote database
  (client-server database access)
• In both cases, you need instructions as to what
  the tables are and what they contain, such as
  SQL.

13
SQL statements

• SQL (Structured Query Language) is a language
  for specifying the creation of databases and the
  updating and retrieval of information in them.
  It is general and portable so that it can be
  used with a variety of different database systems
  without having to learn a new language for each
  one.
• The language goes far beyond this scope of this
  course. Briefly, it can be used to
• Specify the tables in the database and the fields
  (columns) they contain
• Make additions and updates to the data in those
  tables
• Retrieve information from one or more of the
  tables

14
SQL for data retrieval

• A typical SQL statement for data retrieval would
  look something like this
• SELECT ltsome fieldsgt FROM lttablegt WHERE
  ltconditiongt
• The condition effectively selects certain rows
  from the table.
• Thus the result is often a smaller table than the
  one being queried.
• Tables can be joined together to combine
  information from more than one table, for example
  when extracting a molecular sequence from one
  table and the bibliographic details of the
  reference to where it was published from another
  table.

15
Database use 2 predefined operations

• Alternatively, you might have forms and queries
  already set up for you, which you can just run in
  order to perform predefined kinds of searches.
  These predefined operations can be made directly
  available to you by
• Browsing a web page, typically containing a form,
  which gives you access NPI to a database
  somewhere else. Youve done this if youve ever
  bought anything on the Internet.
• Using or even writing a small program (sometimes
  called a script to make it seem less scary) to
  fetch the data for you. This allows you to
  process the data in useful ways
• to search for features youre interested in,
• to summarise the data in the way you want, or
• to extract data for statistical analysis to test
  hypotheses.

16
Database use 3 using predefined operations

• The predefined operations may be packaged as CGI
  programs or Web Services or in a variety of other
  ways, but basically you just send a request to
  the service, optionally with some parameters to
  specify what you want, and wait for the reply.
• The reply may come back, usually,
• in HTML (as a web page containing the data
  requested) or
• as some other sort of file to be downloaded (i.e.
  stored on your PC), either
• in one of a number of formats invented by the
  data providers,
• in XML, a standard but flexible (and verbose) way
  to structure a data file, so that other programs
  (rather than humans) can process it easily.

17
Overview of NCBI Entrez

• In a later session, youll be introduced to a
  number of bioinformatics databases, but its
  worth spending a moment looking at a popular way
  to make use of some of them, because you will
  explore this in Practical 2 in week 4 of this
  course.
• NCBI web site
• Entrez utilities

18
Brief introduction to Perl programming

• (What? In ten minutes??)
• This will help you prepare for Practical 2 (the
  practical part of the 4th week of the course), in
  which we shall use simple Perl programs to
  request data from a bioinformatics information
  provider such as NCBI, by connecting with their
  Entrez utilities. (Additional Perl tutorial
  material may be made available.)
• What is a Perl program? (or script)
• How to run one
• How to write one
• What do you need? See the handout

19
A computer program

• A program is a set of instructions to the
  computer, such as
• Get input from user
• Perform calculation
• Display window
• React to mouse click
• These are instructions at a very high level.
  They need to be broken down into smaller details.
  A program consists of combinations of
• Sequences of instructions (statements)
• Repetitions (to execute statements repeatedly)
• Selections (to choose which statements to
  execute)
• Functions (subroutines or methods groups of
  instructions)

20
A simple program

• Here is a simple Perl program.
• !/usr/local/bin/perl
• Program to do the obvious
• print 'Hello world.'
• The first line every Perl program starts off
  with this as its very first line, although it may
  vary from system to system, or not be used at
  all. It tells the machine what to do with the
  file when it is executed (it tells it to run the
  file through the Perl software to execute it).
• Everything which is not a comment is a Perl
  statement which must end with a semicolon, like
  the last line above.
• So the next thing to do is to run it.

21
Running the program

• Type in the example program using a text editor,
  and save it in a file called something.pl.
• Now to run the program just type the following at
  the Command Prompt.
• perl something.pl
• If something goes wrong then you may get error
  messages, or you may get nothing at all.

22
Perl programming concepts variables

• Variables can hold both strings and numbers. For
  example, the statement
• priority 9
• sets the scalar variable priority to 9, but you
  can also assign a string to exactly the same
  variable
• priority 'high'
• In general variable names consists of numbers,
  letters and underscores, but they should not
  start with a number. Perl is case sensitive, so
  a and A are different variables.

23
Operations and Assignment

• Perl uses all the usual arithmetic operators
• a 1 2 Add 1 and 2 and store in a
• a 3 - 4 Subtract 4 from 3 and store in a
• a 5 6 Multiply 5 and 6
• a 7 / 8 Divide 7 by 8 to give 0.875
• etc.
• and for strings Perl has the following among
  others
• a b . c Concatenate b and c

24
Array variables

• A slightly more interesting kind of variable is
  the array variable which is a list of scalars
  (single values, i.e. numbers and strings). Array
  variables have the same format as scalar
  variables except that they are prefixed by an _at_
  symbol. The statement
• _at_food ("apples", "pears", "eels")
• assigns a three element list to the array
  variable _at_food.
• The array is accessed by using indices starting
  from 0, and square brackets are used to specify
  the index. The expression
• food2
• returns eels. Notice that the _at_ has changed to a
  because food2 and eels are scalars, not
  arrays.

25
File handling

• Here is a basic Perl program which does the same
  as the UNIX cat or Dos/Windows type command on a
  certain file.
• !/usr/local/bin/perl
• Program to open the password file, read it in,
• print it, and close it again.
• file '/etc/passwd' Name the file
• open(INFO, file) Open the file
• _at_lines ltINFOgt Read it into an array
• close(INFO) Close the file
• print _at_lines Print the array

26
Control structures

• Perl supports lots of different kinds of control
  structures. Have a look at the Perl resources
  listed on the handout. Most Perl programs use
  these features.
• Programs can make choose between alternative
  branches
• Programs can repeat statements until something
  happens
• Frequently used statements to carry out some
  common task can be made into a subroutine or
  function and called from others part of the
  program

27
End