1. Computer Applications for Biological
Introduction

2. Count every " F" in the following text:
FINISHED FILES ARE THE RE SULT OF YEARS OF SCIENTI FIC STUDY COMBINED WITH THE EXPERIENCE OF YEARS...

3. “Discovery is to see what everyone else has seen, but think what no one else has thought.”
Albert Szent-Györgyi (The Nobel Prize in Physiology or Medicine, 1937 )
“By inventing elegant software tools, we can help biologists see and think.”
“Invention  Discovery”
Kun-Mao Chao

4. What is Bioinformatics?

5. The field of science in which biology, computer science and information technology merge into a single discipline
Biologists
collect molecular data:
DNA & Protein sequences,
gene expression, etc.
Bioinformaticians
Study biological questions by analyzing molecular data
Computer scientists
(+Mathematicians, Statisticians, etc.)
Develop tools, softwares, algorithms to store and analyze the data.

6. What can we do with sequences of information?

7. What is a Database?
A structured collection of data held in computer storage; esp. one that incorporates software to make it accessible in a variety of ways; transf., any large collection of information.
database management: the organization and manipulation of data in a database.
database management system (DBMS): a software package that provides all the functions required for database management.
database system: a database together with a database management system.
Oxford Dictionary

8. What is a database? A collection of data
structured
searchable (index) -> table of contents
updated periodically (release) -> new edition
cross-referenced (hyperlinks) -> links with other db
Includes also associated tools (software) necessary for access, updating, information insertion, information deletion….
Data storage management: flat files, relational databases…

9. Database: a « relational » example
Relational database (« table file »):
Teacher
Accession number
Education
Amos 1
Biochemistry
Dan 2
Genetics
John 3
Scientology
Course
Year
Involved teachers
Advanced Pottery
2000; 2001
1; 2
Ballet for Fat People
2001; 2002
2; 3

10. Why biological databases?
Exponential growth in biological data.
Data (genomic sequences, 3D structures, 2D gel analysis, MS analysis, Microarrays….) are no longer published in a conventional manner, but directly submitted to databases.
Essential tools for biological research. The only way to publish massive amounts of data without using all the paper in the world.

11. Distribution of sequences
Books, articles > 1985
Computer tapes > 1992
Floppy disks > 1990
CD-ROM >
FTP >
On-line services > 1994
WWW >
DVD >

12. Some statistics More than 1000 different ‘biological’ databases
Variable size: <100Kb to >20Gb
DNA: > 20 Gb
Protein: 1 Gb
3D structure: 5 Gb
Other: smaller
Update frequency: daily to annually to seldom to forget about it.
Usually accessible through the web (some free, some not)

13. Google Scholar

14. What is Google Scholar?
Enables you to search specifically for scholarly literature, including peer-reviewed papers, theses, books, preprints, abstracts and technical reports from all broad areas of research.

15. Google Scholar orders your search results by how relevant they are to your query, so the most useful references should appear at the top of the page
This relevance ranking takes into account the: full text of each article. the article's author, the publication in which the article appeared and how often it has been cited in scholarly literature.

16. Web of science

19. Bits and Bytes A bit is a binary digit.
A bit is like a light switch. It has two positions, off = 0 and on = 1.

20. Bits and Bytes
A byte is like a row of 8 switches.

21. Bits and Bytes
Because it has only two digits, 0 and 1, the binary number system is base 2.
We are accustomed to using base 10 which has 10 digits which are as follows:
0, 1, 2, 3, 4, 5, 6, 7, 8, 9
Computers work in base 2 while we work in base 10.

22. Review of Base 10 Consider the number 3178.
3 is the thousands place = 3000 = 3 x 103
1 is the hundreds place = 100 = 1 x 102
7 is the tens place = 70 = 7 x 101
8 is the units place = 8 = 8 x 100

23. Review of Base 10
Each numeral is multiplied by 10 raised to the appropriate power for its position.

24. Review of Base 2
A byte is 8 bits which are like 8 switches.

25. Properties of Base 2
Each numeral is multiplied by 2 raised to the appropriate power for its position.
So, a byte can hold a number between 0 and 255.

26. Converting Base 2 Numbers to Base 10
What is the value of in base 10?
The answer is 73.

27. To solve this type of question, remember the sequence of positions.
The values are in the following sequence:
1, 2, 4, 8, 16, 32, 64, 128
Find which switches are on and add the values together.

28. Octal is Base 8
If we take the bits by threes, we get octal, which is base 8.
The base 8 numerals are:
0, 1, 2, 3, 4, 5, 6, 7
The positions for the octal digits are:
000 = = 4
001 = = 5
010 = = 6
011 = = 7

29. Use of Octal
Some computers actually use octal for calculations but it is a big problem because the 8-bit byte is not evenly divisible by 3.
Octal us used for setting the UNIX access rights to directories on server computers.
You will use this for sure if you are putting things into a directory on a server for use on the Internet.

30. Setting UNIX Access Rights
UNIX access rights are assigned to every file and directory on the server.
Rights have the form: drwxrwxrwx
d means if it is a directory or not
r means read
w means write
x means execute
There are three sets of rwx rights. These are for you, for those in your group and for everyone else. Each letter is one bit.

31. Setting UNIX Access Rights
On the Kean turbo server, a faculty member may have an account.
All other faculty are in the same group.
Anyone from the outside, such as on the World Wide Web, can have access if the rights are set correctly.

32. Setting UNIX Access Rights
drwxrwxrwx - The first set of bits is for yourself. You want to be able to read, write, create, delete or alter your file without any problems. Use octal 7 = 111 to set this part.
drwxrwxrwx - This is for your group--the other users at your place. Unless you want someone monkeying with your files, let them have read-only (100 = 4) which makes it r--. If you do not want them to know it is there, set it to 000 = 0, which makes it ---.

33. Setting UNIX Access Rights
drwxrwxrwx - The last set of bits is for everybody else.
For your Internet pages, make a directory called www and set the access rights to 100 which makes it read-only. The server will let anyone on the Internet read the contents, but they will not be able to delete or change anything.
So, your www directory is set as 447 which corresponds to dr--r--rwx.

34. Hexadecimal is Base 16
If we take the bits by fours, we get hexadecimal, which is base 16.
The base 16 numerals are:
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F
As base 10 does not have single numerals for the numbers from we use A-F.

35. Table of Binary and Hex Equivalents

36. Properties of Hexadecimal
A hexadecimal number is exactly one-half of a byte.
Since a byte can be from in decimal, it also can be from #00 to #FF in hexadecimal.
Use the pound sign (#) as a prefix for hexadecimal numbers.
Binary and hexadecimal numbers carry to the other half of the same byte at the same time.

37. Uses of Hexadecimal
On the Internet, documents are written in HTML, the hypertext markup language.
All colors on computers are a combination of three colors; red, blue and green; known as RGB.
In HTML, you set the values of RGB using hexadecimal numbers.
The form for a color is: #RRGGBB

38. Some Hexadecimal HTML Color Codes

39. More about Hexadecimal Color Codes
With #RRGGBB, each can have a value from 0 to This gives:
256 x 256 x 256 = 16, 777, 216 different possible colors.
The most commonly used hex values are:
#00, #33, #66, #99, #CC, and #FF. These give a total of 216 colors.
Find Dave Taylor's list at the following url:

40. ASCII Codes
ASCII stands for American Standard Code for Information Interchange.
ASCII values range from 0 to 255.
Values 0 through 31 - control characters
32 through 47 are special keyboard characters
48 through 64 are numerals and characters
65 through 96 capital letters and characters
97 through 127 lower case letters and characters
128 through 255 special characters

41. The End