Topics in Informatics

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Topics in Informatics

• Spring 2005, SJC

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About the Instructor

• Instructor Dr. Hong Zhou
• Office McDonough 317
• Office Hours MWF 1000 1100am
• Email hzhou_at_sjc.edu, Phone [phone]
• Syllabus
• You can all me either
• Hong
• Dr. Hong
• Dr. Zhou

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What is Informatics?

• Search for What is informatics at
  http//www.google.com, we got different
  definitions.
• Basically, the study and application of the
  knowledge and skills of data/information flow and
  manipulation (including storage, retrieval,
  analysis, and construction/deriving, etc).

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Informatics

• Data obtaining
• Data flow and control
• Data representation (records) and storage
• Data retrieval/mining
• Data analysis
• Data derivation (generating new data from
  existing data via analysis)

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What Will You Learn

• Obtaining reliable data.
• Data Management (Data Storage and Representation,
  Retrieval) ? database.
• Introduction to Bioinformatics.
• Introduction to Health Informatics.

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Part I Obtaining Reliable Data

• Complex and precise communication is something
  distinguishing us from non-human.
• The world development is somehow the development
  of our understanding, i.e. information of the
  universe including our social systems.
• Information and its uses are the center of such
  development.

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Information vs Data

• What is in your mind when we talk about
  INFORMATION?
• Is information touchable, visible?
• To my understanding, data is the description of
  information, and information is the
  interpretation of data.
• So, lets deal with the description ? data, in
  this class.

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What is Data?

• When we talk about data, the first image in our
  mind might be numbers such as 5, 87, 98.34, etc.
• However, are the numbers 5, 87, 98.34
  meaningful/informative?

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Data with Context

• Pure numbers are meaningless for us.
• Numbers with context are meaningful, however.
• For example, 5 pounds of sugar.
• So, in this class, we are talking about
  meaningful data and ignore all meaningless data.
  (Are we meaningful persons?)

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Quick Questions

• Are following data meaningful?
• 20
• 20 years
• A 20 years old girl
• A 20 years old girl named Amie
• A 20 years old girl named Amie who is a SJC
  student.

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Data Target

• Data is used to describe a subject.
• For example, age, height, weight, gender,
  profession, are description of a person.
• Medical record is a description of a patient

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Quick Question
What are the targets of the following two rows of
data?
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What is RELIABLE?

• When we talk about reliable data, what does that
  mean?
• Lets discuss this issue at two levels
• Individual level
• Group/population level (statistics)

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Individual Level

• Reliable data means that the data is closely
  related to the individual (or event) and
  precisely describes the individual (or event).
• A computer of 3.2 ghz CPU, 512 mb RAM, 512 kb
  cache, etc.

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Group/Population Level

• Reliable is more meaningful at the group level.
• Can a specific medical diagnose of a patient be
  representative of all patients with the same
  symptom?
• Probably not.

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Statistical Thinking

• One powerful approach to analyze data is
  statistics.
• We measure the reliability (significance) of data
  in the sense of statistics.
• Statistical thinking is to use data to build our
  understanding, gain insights, and draw
  conclusions or make inferences.
• Not drawing conclusion from an incident.

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Principles in Statistical Thinking

• Count on data instead of an incident
• Where the data is from matters.
• Lurking variables
• Variation is everywhere
• Conclusions are not absolutely certain

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Count on large amount of data instead of a few
incidents

• Famous fortune teller
• The thumb of a monk

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Where data is from

• Group data can be collected from surveys or
  observations, or obtained from experiments.
• When collecting data, where the data come from is
  important. For example, once there is a question
  If you had it to do over again, would you have
  children? 70 from the written responses are
  NO. Is this piece information reliable?

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Lurking Variables

• Is music practice improving test scores?
• What is behind?

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The Importance of RANDOM

• The key factor in data collection is the RANDOM
  concept, i.e. the data has to be randomly
  collected with no bias.
• Suppose that you are doing a survey of 2004
  election prediction from 10000 people in USA, how
  are you going to pick the 10000 persons? Only in
  schools? Only in New York? Only women? Avoid as
  much as bias as you can.

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Experiments

• Some reliable data can only be produced by
  experiments, especially in science.
• For example, in biology, to pin down the function
  of a gene, you have to knock out the gene or
  depress it and check the phenotype changes. After
  that, you have to recover the gene and verify if
  the phenotype also recovers. Such experiments
  are very convincing, but expensive.

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Another Experiment

• It once was believed that women who take hormones
  after menopause reduce the risk of heart attack.
  The belief was resulted from the studies that
  simply compared women who were taking hormones
  with others who were not. Are such study results
  reliable?
• Such experiments lack proper Controls, which are
  the essential in all experiments.
• How are you going to design an experiment for
  this study?

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Reliable Data contd

• It is not a simple task to obtain reliable data,
  it requires extensive consideration and design.
• Some experiment results may look convincing at
  some time, but may lose their reliability over
  time or when the environment changes. For
  example, the third stop light of cars.

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Discussion

• Is absence of evidence the evidence of absence?

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Project 1

• Write a paragraph to discuss the claim Absence
  of evidence is evidence of absence. Please make
  your own judgment as the grading is based on your
  argument.
• Design a simple survey to collect opinions about
  terminating death penalty. Be aware of the
  importance of RANDOM. Write a short paragraph
  to argument that the data collected by your
  survey is reliable.
• Points 100.
• Due Date Feb 1st, 2005.
• Submit your work in the digital drop box in
  Blackboard.

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Part II Data Storage

• Can all information be recorded as data? Lets
  start the discussion.
• Feeling
• Knowledge
• Intelligence

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Personal Ideas

• My understanding Yes, just some of them are too
  complicated or too difficult to manifest
  precisely.
• And that is whey we have IQ test, MQ
  (motivational quotient), EQ, etc.

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Where to store

• Data is stored somewhere.
• Minds
• Books (paper documents)
• Computers
• Etc
• Lets compare the three storage methods, which
  one you think more lasting or appropriate?

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Passing Words

• In ancient time, knowledge is passed in words
  generation by generation.
• Here is a story about passing by words
• General called the captain telling tonight at
  700pm, the Halley comet will pass your camp in
  the sky. Organize your soldiers to watch.
• Captain informed his lieutenant Tonight at
  700pm, the Halley comet will pass our camp in
  the sky and the general is coming to watch with
  our soldiers.
• The lieutenant informed the sergeant Tonight at
  700pm, the general will accompany Halley comet
  passing over our camp, organize the soldiers
• The sergeant to soldiers Tonight at 700pm,
  general Halley will pass over our camp in sky and
  we are going to watch that.

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Data Storage

• Paper storage
• Size and cost
• Transportation
• Computer
• Signature ? legal effect
• Hacking
• What if computers are down?
• However, if data is not organized, it is
  difficult to make use of. So, data storage
  strategy is important.
• In this class, we talk about data storage by
  using computer technology.

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Ways to store

• Data storage is a big, and probably the largest
  issue related to computer data manipulation.
• Different database structures, different database
  managements, online storage, etc.

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Chapter 1. File structure

• Hierarchical structure
• Easy to deal with the hierarchical relationships.
• For example, the administration is a hierarchical
  structure.
• Let me use the DOD/NIMA VPF structure as an
  example

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VPF Structure

• DOD (Department of Defense) and NIMA (National
  Image and Mapping Agency) sponsored the VPF
  development (Vector Product Format) ? Nickname
  very poor format
• It is used to store the earth ground information
  and provide a digital map.

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VPF structure
Database

• Library

Library
Coverage
Coverage
Coverage
File1
File1
File1
File1
File1
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Navigation in Hierarchical Structure
What is the purpose of Index?
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Project 2

• Create a hierarchical file structure to store
  some your works in SJC.
• This is the way I prefer organize your works
  based on the classes you take.
• If you have other ways, that is ok as long as
  they are organized well.
• Show me in class what you have done.
• Points 100

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Chapter 2 XML

• Extensible Markup Language
• Purpose
• Data transportation
• Data representation
• Data storage
• Why we should talk about it here? Because the
  data inside a XML file is hierarchical

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What XML Promises?

• Data portability
• Programming language Java promises the
  portability of programs.
• However, programs are working on data. Before
  XML, data is not portable, communication among
  systems, agencies are extremely difficult.
• XML allows systems to communicate using a
  standard means of data representation.

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HTML?

• HTML is the portable language for browsers.
• It is a standard.
• However, it governs how information is displayed
  in a browser with defined formats and defined
  tags.

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The Difficulties XML faces

• XML has some defined formats
• But doesnt have defined tags.
• User defined tags
• Unlimited types of data.

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Solution (Partially)

• Make the information self-explained.
• You have to invent your own tags!

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A Simple Example

• Fonship
• Michele
• female
• 9/1980
• 5/1985
• Badley school

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Tips about XML format

• A tag is case sensitive
• A starting tag must have a closing tag to match
• All XML elements must be properly nested.
• All XML documents must have a root element.
• Attribute values must always be quoted.

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Comments in XML

• Comments in XML
• The syntax for writing comments in XML is similar
  to that of HTML.
• A sample XML file.

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XML Element Naming

• Names can contain letters, numbers, and other
  characters
• Names must not start with a number or punctuation
  character
• Names must not start with the letters xml (or XML
  or Xml ..)
• Names cannot contain spaces.

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Is it valid or not?
nameRose Washingtonst name
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Element Content

• An XML element is everything from (including) the
  element's start tag to (including) the element's
  end tag.
• An element can have element content, mixed
  content, simple content, or empty content. An
  element can also have attributes.

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Is this valid?
appleit
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Child Elements vs. Attributes
Anna Smith
female Annastname Smith
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Disadvantages of Attributes

• attributes cannot contain multiple values (child
  elements can)
• attributes are not easily expandable (for future
  changes)
• attributes cannot describe structures (child
  elements can)
• attributes are more difficult to manipulate by
  program code
• attribute values are not easy to test against a
  Document Type Definition (DTD) - which is used to
  define the legal elements of an XML document

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Using Child Elements?

• So, it is a good idea to use Child Elements other
  than Attributes.
• Check this out. Tell which way you prefer.
• Can this file work? What is wrong?

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A case for Attribute

• What is metadata? Data about data. For example,
  your SJC student ID is a metadata about you since
  it does not describe you.

OReilly sssomewhere
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Is this valid?
Eng100 id5Math100 200-300pmfice Hour McDonough Hall 211

What are the errors?
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More about XML

• Now we have so called XML database whose basic
  element is XML document. It is not very
  successful yet.
• Remember that XML does not really do anything
  except describing data.
• We have to interpret whatever it is describing.
  In the sense of computer software, the user has
  to develop software to interpret.
• What are DTD and XML schema?
• What are the disadvantages of XML? Please
  discuss about it.

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Analyze the XML file

• Example XML file
• Lets discuss the weakness of this file.
• What do you suggest?
• How do you think about my solution?

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In class exercise

• Given the data shown in Access database, can we
  store the same data in XML format? Please try it
  in class. Thanks.

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Useful Sites about XML

• http//www.w3schools.com/xml/
• http//www.xml.org

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XML in Uses?

• BBC topic news are also available online via XML.
  Example.
• XML at work.
• XML in commerce?
• What is GML and SGML?

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Project 3

• Here are the requirements, which are also
  available in Blackboard.
• Discussion will XML really be the standard of
  data transportation or data storage?

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Part 3 Database

• Instead of listing it as Chapter 3, it is listed
  as Part 3, which shows that this is a big issue.

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Chapter 1 Database History

• Hierarchical database
• Network database
• Relational database
• Object-oriented database
• Object-oriented relational database
• XML database
• etc

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Relational Database

• The major database in use.
• Based on the relations between data items.
• Key element tables.
• Available relational databases Oracle, DB2,
  Sybase, MS SQL Server, Access, MySQL, etc.
• A site about evaluation.
• The instructors database work.

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Records and Attributes

• A table has multiple records, each has multiple
  values.
• For example.
• The attributes define the data types. All data
  in that column must conform to the given data
  types.

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Primary Key

• The primary key of a relational table uniquely
  identifies each record in the table. It can
  either be a normal attribute that is guaranteed
  to be unique (such as Social Security Number in a
  table with no more than one record per person) or
  it can be generated by the DBMS (such as a
  globally unique identifier, or GUID, in Microsoft
  SQL Server). Primary keys may consist of a single
  attribute or multiple attributes in combination
• For example, in the table example, the primary
  key is Student.
• Every table must have Primary Key defined.

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Primary Key (2)

• Guess what would be the Primary Key in the SJC
  database for students?
• Will it be ok to use your name (last name and
  first name) as the primary key?

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Create a table for

• Smith, Jack, male, 8/15/1989, 421865241, Forrest,
  Shoplifting, Linda Luke, [phone], 105.
• Marsa, Rose, female, 7/1/1988, 3245691877, Jones,
  Dog fighting, Nancy Charles, [phone], 106.
• Lese, Sam, male, 3/21/1986, 425423785, Hartford,
  Dwell breaking, Linda Luke, [phone], 105.
• Haly, Rachel, female, 3/25/1989, 423671841,
  Hartford, misconduct, Linda Luke, [phone],
  105.
• Horse, James, male, 11/2/1987, 765213456, Lama,
  misconduct, Nancy Charles, [phone], 106.
• Lincoln, George, male, 10/5/1988, 324342342,
  Jones, fighting, Linda Luke, [phone], 105.
• Doom, Jade, female, 9/9/1988, 423213495,
  Hartford, misconduct, Nancy Charles,
  [phone], 106.

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TableS

• Surely we will deal with multiple database tables
  concerning any complete datasets.
• When dealing with complicate datasets, first
  thing is to categorize the data into groups with
  each group represented by a table.
• The second thing is to find and build the
  relationships between the tables.

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Analyze the data

• How many categories we have?
• Lets use UML to clear the data relationship!
• UML is Unified Modeling Language which arises in
  1990s. It derived from the three greatest minds
  of system modeling.
• It is the standard language used to analyze
  system design.

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Practice

• The UML diagram
• What tables you would construct for the data in
  the XML file?
• Do this exercise in class.

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Relationship

• Now lets talk about the relationship types
• One-to-One
• One-to-many vs many-to-one
• Many-to-many

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One-One

• SSN Person

SSN
Person
1
1
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One-Many

• Bank accounts ? ? person (one person can have
  multiple accounts, but one account belongs to one
  person/family).

Bank account
person

1
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Many-Many

• Course-Student. A student may take multiple
  courses, and a course may be taken by multiple
  students.

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Foreign Key

• A foreign key is a relationship or link between
  two tables which ensures that the data stored in
  a database is consistent.
• The foreign key link is set up by matching
  columns in one table (the child) to the primary
  key columns in another table (the parent).
• Referential Integrity

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Foreign Key Example 1
Table Students
PK
Basket Ball players
studentID First name Last name Major SSN Gender DO
B
playerID First name Last name Position number
PK
One-to-one
parent
child
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Foreign Key Example 2

• Given a table about instructors whose columns are
  ID, first name and last name.
• Suppose the basic information of a offered course
  is the instructor and the course name.

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Contd

1
Course name Instructor
ID First name Last name
One-Many
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Contd

• Look at this example.

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Exercise in Depth

• UML diagram of the exercise.
• Now, how to define the tables that can properly
  represent the UML diagram?

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Common Rules

• One object (entity) one table
• One attribute one column
• Additional PK optional in some cases.

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How to define Relations between Tables?

• First of all, we have to know that Parents come
  before children. Tables that can be built
  without referencing other tables/data could be
  used as parent table.
• For example, student table vs basket ball player
  table.

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Relations contd

• In case of One-One relation, the parent table is
  the table that can be built without referencing
  any data in the child table. The child table
  must be the table that references data in the
  parent table.

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Example
studentID First name Last name Major SSN Gender DO
B
playerID First name Last name Position number
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Relation contd

• In case of One-Many, the One must be the parent
  table, and the Many must be the child table

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Example
child
parent
BookID Title Author Publish year Publisher ID
PublisherID Name Address
Many-One
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Many-Many

• It is pretty hard to express the Many-Many
  relations between two tables.
• For example, students ? ? Courses relationship.
• How are we going to do it?

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Solution

• Make use of another table! In this case, we have
  three tables. One for students only, one for
  courses only, and one to link students with
  courses.

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Solution Example
studentID lastname firstname DOB gender
Course Title Location
StudentID Course
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The full table construction

• Lets work on this data to build the whole
  tables!
• Now, lets do this project 4!

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Sword, a real application

• Publicly information about Sword.
• A success story of data representation, storage
  and management in Mississippi.
• Please form 2 or 3 groups for the coming projects
  since they are kind of complicated. Inform me of
  the group members in the next class. Thanks.

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Discussion of Sword in Class

• The sword data scenario

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Chapter 2 Access Basics I

• Please form 2 or 3 groups to for the coming
  projects since they are kind of complicated.
  Inform me of the group members in the next class.
  Thanks.
• Every student is supposed to collect at least 2
  restaurant menus of the Hartford area. Keep them
  for later use.

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Basics (1)

• Open and save an Access database.
• Create a table in Design View.
• To create good tables, we need to understand our
  data first. Lets have a look at the existing
  data in next slide.

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Try

• Create a table to hold the information below?
• Smith, Jack, male, 8/15/1989, 421865241, Forrest,
  Shoplifting, Linda Luke, [phone], 105.
• Marsa, Rose, female, 7/1/1988, 3245691877, Jones,
  Dog fighting, Nancy Charles, [phone], 106.
• Lese, Sam, male, 3/21/1986, 425423785, Hartford,
  Dwell breaking, Linda Luke, [phone], 105.
• Haly, Rachel, female, 3/25/1989, 423671841,
  Hartford, misconduct, Linda Luke, [phone],
  105.
• Horse, James, male, 11/2/1987, 765213456, Lama,
  misconduct, Nancy Charles, [phone], 106.
• Lincoln, George, male, 10/5/1988, 324342342,
  Jones, fighting, Linda Luke, [phone], 105.
• Doom, Jade, female, 9/9/1988, 423213495,
  Hartford, misconduct, Nancy Charles,
  [phone], 106.

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Try contd

• First, primary key!
• Continue the building of one table for all the
  data.
• After done, save the work and give the table a
  sensible name.

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Create Table wizard

• Lets explore the table creation function of
  Access we can create table by Wizard, i.e. with
  templates.

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Create Multiple Tables

• Based on the UML diagram of the data, lets
  create multiple tables.

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Normalization

• Normalization in database means to remove the
  redundant data to improve data storage
  efficiency, data integrity and scalability.
• It is essential
• Good online explanation

100
3 Level Normalization

• The first level of normalization removes
  redundant data horizontally, i.e. no repeated
  columns.
• The second level of normalization removes
  redundant data vertically, i.e. no repeated data
  in rows.
• The third level of normalization organize data
  that does not depend on the primary key into
  another table.

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Normalization

• Totally there are 5 levels of normalization.
• It is absolutely necessary to apply the 1st and
  2nd levels of normalization.
• The 3rd level is applied sometimes.
• Dont bother with the 4th or 5th levels of
  normalization

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Exercise

• What is the normalization level of the database
  constructed?

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Basics (2) Simple Query

• Based on the constructed table, lets have some
  fun with Query.
• Query is a programming language called SQL
  (structured query language).
• SQL is a standard interactive and programming
  language for getting information from and
  updating a database.
• Click here to learn more?

104
(No Transcript)
105
Create Query

• Create Query in design view
• Create Query by using wizard
• View the result sheet.

106
Query Syntax

• Though we now know how to create simple queries
  graphically, we still need to understand the
  syntax.
• SELECT sth FROM somethere.

Select from classes Select ID from
classes Select classes.ID, lastname from classes
107
Set Conditions

• SELECT something FROM somewhere WHERE
  conditions-are-met
• Select from students where gender0
• Select from students where lastnameSmith
• Select from students where DOB between
  1/1/1988 and 1/1/1990

108
Set Conditions

• Select from students where lastname like
  Smi
• Select from students where lastname like
  smi
• SELECT FROM students WHERE gender0 AND
  lastname like smi
• Be aware in standard SQL, LIKE smi

109
JOIN

• In many cases, we need to fetch data from
  multiple tables. Thus, we need to bind together
  the data from the tables. The binding is based
  on some keys, usually the primary key or some
  other unique data items.
• Good online material (but be aware that this is
  for standard SQL, not for Access!)
• FOR Microsoft inquiry, please go to
  http//msdn.microsoft.com/

110
Join in Access

• Select sth1, sth2 from table1 INNER JOIN table2
  ON table1.key1 table2.key2.
• For example
• Select students. from (students INNER JOIN
  studentscourses ON students.ID
  studentscourses.studentID) where
  studentscourses.courseNumComp200

111
Other JOINS

• There are two different types of JOIN
• INNER JOIN
• OUTER JOIN
• LEFT JOIN
• RIGHT JOIN
• Lets not deal with OUTER JOIN in this class
  to make it simple.

112
INNER JOIN

• INNER JOIN only join the records that both tables
  have the corresponding key!.
• See the MSDN explanation

113
Sort the Results

• You can order the results in ascending or
  descending order.
• Select from students order by studentID desc
• Select from students order by lastname (if it
  is ascending order, you dont need to specify it)

114
Subquery

• Inside a query, we can have another query to
  provide some information for a condition, i.e. we
  have subquery(s) inside a query.
• Select from students where studentID in (select
  studentID from studentscourses where
  coursenumberComp200)

115
Functions

• Access query could use built-in functions. For
  example, MAX, MIN, COUNT, etc. Lets experience
  COUNT.
• Question how to find the number of students who
  are taking courses currently in the school?

116
Others

• SO far, we have been dealing with SELECT queries.
  There are other types
• CREATE create tables
• INSERT insert rows
• DROP drop tables
• DELETE delete rows
• ALTER - change the table structures
• Etc.

117
Sample Database

• Here is a sample database with some queries
  constructed. Might be useful as references.
• Remember that this class is not only for
  database, so we cannot go very deep into database
  issues. If you have more interests in database,
  I may be able to offer a class specifically on
  database.

118
Project 5

• Project 5 requests you to construct a database
  for a group of restaurant. Please use UML
  diagram to analyze the data first, then construct
  your database. Also, please provide some
  queries. -- Imaging that you are provide a
  hotline services for customer inquiries about
  food services in Hartford area.

119
Part 4 Bioinformatics

• What is bioinformatics?
• The study of the application of computer and
  statistical techniques to the management of
  biological information
• The science of creating and managing biological
  databases to keep track of, and eventually
  simulate, the complexity of living organisms.
• There exist different definitions, though.

120
The Possible Role of Bioinformatics?

• Look over the history of biology, different
  approaches are used over the time.
• Initially Guessing ? Observation ? Dissection.
• Mendal started genetic experiments.
• Biochemists used organics to clear out the
  metabolic pathways.
• Molecular biology is another approach now used to
  decode the life secrets.
• Is it the time for bioinformatics as another
  approach?

121
Several Foundations of Bioinformatics

• Lives are from the same ancestors, either
  evolved or created. That means that knowledge
  obtained on one form of life may be applied to
  other forms. In fact, molecular biology started
  from bacteria, then yeast, then mammal. ?
  database
• Publicly available data resources.
• Human Genome Project

122
Publicly Resources

• I am not sure how many biological research
  laboratories we have in the world, it must be
  MANY MANY.
• No other science has equal or even close amount
  of research laboratories.
• The largest amount of research funds from
  government, states, private corporations, etc.

123
Most famous Agencies

• NIH (National Institute of Health)
• WHO (World Health Organization)
• Others

124
Huge Amount of Information

• All the scientists in the world generated large
  amount of scientific information, and it is
  likely much of them is repeated.
• Communication among scientists become extremely
  important.
• That is why there are so many publicly available
  biological resources.
• Internet plays a critical role in the information
  sharing.

125
Internets Information

• Access to information for anyone with an Internet
  browser.
• The data stored in centralized database us
  redundant by a factor of about 2.5, which
  provides a quality control.
• Information from yeast (for example) could be
  helpful in finding/understanding homologous
  genes/pathways in humans (comparative genomics).

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Human Genome Project

• HGP.
• Without HGP, there is no real Bioinformatics.
• Bioinformatics boosted up after large amount of
  Human Genome are decoded ? how to use these DNA
  information? ? Computer technologies!

127
Bioinformatics and Evolution
Mutations
128
Mutations

• Mutations that occur in germ cells will be passed
  on to the next generation, like any other DNA
  sequences.
• So, as time and generations go by, a DNA sequence
  will acquire more and more mutations and resemble
  less and less the original DNA sequence.

129
Need to know where from

• From an evolutionary perspective, we cannot know
  where we are going unless we know where we have
  been. Before, the study of human evolution was
  largely the province of paleoanthropologists who
  studied the fossil record.
• However, gene comparisons now become the major
  and more accurate techniques ? using computer
  technologies/bioinformatics

130
Do you know

• We all started from Africa?
• Using the Mitochondrial DNA analysis among women
  from different nations, it is found that African
  people have larger variations in DNA sequence ?
  oldest group has the greatest genetic diversity ?
  African is the oldest population ? the ancestor.

131
Bioinformatics with AIDS

• Analysis of the human genome guides AIDS
  research. Some persons long-infected with HIV
  have not shown any symptoms of the disease.
  Studies found that these people possess a variant
  of a receptor CCR5 ? Rarely in Asian and African
  ? guess it may come to European in 14th century.

132
Tools of Bioinformatics

• Gene Predication Software
• Sequence Alignment Software
• Molecular Phylogenetics
• Molecular Modeling and 3-D Visualization.

133
NCBI

• National Center for Biotechnology Information.
• PubMed (Medline)
• Entrez
• BLAST
• OMIM
• Books
• TaxBrowser
• Structure

134
PubMed

• Access to the Medline database ? largest
  biomedical literature source.
• Medline database contains citations and abstracts
  from more than 4600 biomedical journals published
  in USA and other countries.
• Searches are commonly conducted using a
  keyword(s), author names, publication date,
  and/or journal titles.

135
Entrez

• A search and retrieval system that integrates all
  of the databases available at NCBI. These
  databases include nucleotide sequences, protein
  sequences, genomes, molecular structure and
  PubMed.
• GenBank, DNA DataBank of Japan, European
  Molecular Biology Laboratory make up the
  International Nucleotide Sequence Database
  Collaboration. These organizations exchange data
  every day.
• Search for Bcl2 as an example.

136
BLAST

• Basic Local Alignment Search Tool.

Sequence 1 AGTTCGATAGCTAAGGTCGG Sequence
2 AGTTCGATAGCTATGGTCGG
137
BLAST
Sequence 3 AGTTCGATAGCTAAGGTCGG Sequence
4 AGTTCGATAGCTAGGTCGGG
138
BLAST Another Look
Sequence 3 AGTTCGATAGCTAAGGTCGG Sequence
4 AGTTCGATAGCTAGGTCGG
139
Use BLAST

• Click here.
• Lets choose blastn.
• Now, lets practice its uses.

140
OMIM

• Online Mendelian Inheritance in Man
• It is a database containing information about
  human genes and genetic disease. This resources
  is often used by physicians and researchers
  interested in genetic diseases.

141
Books

• NCBI collaborates with authors and publishers to
  create a virtual bookshelf.

142
TaxBrowser

• The taxonomy site contains a classification of
  all the organisms that are represented by
  sequences in the public databases, including
  model organisms commonly used in molecular
  biology.

143
Structure

• The structure site features the Molecular
  Modeling Database (MMDB), which contains
  macromolecular 3-D structures as well as tools to
  analyze them. Included in the MMDB are
  experimentally determined structures obtained
  from the protein data bank.

144
Cn3D4.1

• You can download it.
• It reads MMDB instead of PDB file. This is
  because MMDB will ensures the correctness of the
  read PDB file.
• The Link

145
Applications of Bioinformatics

• Forensic Science
• Agriculture
• Medicine
• Pharma/Biotechnology
• Environmental Science
• Ethical Legal, and Social ISsues

146
Forensic Science

• Minisatellites consists of short DNA sequences
  that repeat in tandem. The number of repeats
  the sequence within each repeat can exhibit wide
  variation in a population. Techniques based on
  this were developed to identify individuals.
  E.g. FBI established Combined DNA Index System
  (CODIS) that contains profiles of convicted
  offenders.

147
Forensic Science

• DNA testing is now the standard technique for
  confirm paternity.
• Is also a technique to identify criminals and
  victims.
• Computer technology is essential to search
  through the database for the identification.

148
Agriculture

• Genome projects for major crop plants are well
  underway
• Pest control
• Seed quality
• Plant micronutrients (golden rice)
• Etc.

149
Medicine

• The ability to correlate genetic data with
  medical records promises to improve our
  understanding of disease and improve treatments.
• Microarray ? cancer classification
• Associating SNPs with disease helps scientists to
  identify genes that play roles in disease
  progression.

150
Pharma/Biotechnology

• Bioinformatics is providing a complete list of
  candidate genes for drug discovery. The tools of
  functional genomics are being used to establish
  the metabolic roles played by the candidate gene
  products.
• Pharmaceutical companies are using bioinformatics
  to search for new antibiotics.

151
Contd

• Advances in genomics are expanding the range of
  drug targets and are shifting the discovery
  effort from direct screening programs to rational
  target-based drug designs.

152
Environmental Sciences

• Global biodiversity.
• Global Biodiversity Information Facility (GBIF)
• How to analyze these diversity and make use of
  them.
• Computer software to monitor environmental
  changes, via birds and other animals behaviors.

153
Ethical, Legal and Social Issues

• Anonymous databases ? include nonidentifiable
  genetic data.
• Non-anonymous databases ? its data could be
  linked to individuals.
• An ethical concern most relevant to non-anonymous
  databases is Informed Consent.

154
Informed Consent

• Informed consent is the ethical practice of
  respecting individual autonomy and protecting an
  individual from harm. It refers to a process
  whereby an individual freely and knowingly weighs
  the risks and benefits of donating a tissue or
  DNA sample for research purposes.

155
Privacy Confidentiality

• Personal privacy is an important aspect of
  informed consent. Privacy is the right to
  control access to information about oneself.
• Confidentiality is the obligation for those who
  obtain information about individuals to protect
  the privacy of that information.

156
More

• If society is to gain the most from genomic
  biology, then the public must be able to
  rationally consider scientific issues. They
  should not place a blind trust in scientists, nor
  should they dismiss new technologies out of hand.

157
In-Class Exercise

• Human Genome is sequenced via the shortgun
  approach in which human chromosomes were randomly
  cut into pieces.
• Each DNA pieces are sequenced separately.
• Computer technology is then used to find the
  overlap and construct the contiguous sequence.

158
In-Class Exerices

• Group 1
• Group 2
• Group 3
• Each group will constitute two fragments and all
  groups work together for the final sequences.
• For simplicity, we are dealing with only one
  strand for simplicity.