This document provides an overview of programming and its applications in bioinformatics. It discusses why programming is important for data analysis, integration and visualization. It also outlines the basic concepts of algorithm and program design, programming languages, compilers, interpreters and debugging. Common programming language structures like syntax, semantics, variables and data types are explained. Finally, the document introduces Bioconductor, an open source software for bioinformatics that uses the R programming language for high-throughput genomic data analysis.

1. Programming in
a Nutshell
Eman Abdelrazik
B.Sc. in Biotechnology
Post-Grade Student at Nile University
Data Analyst at Omicsense

2. A Computer
Just
Solved
100-Year-Old
Biology Problem!

3. • 3
Road Map
❏ Part I : Why Programming?
❏ Part II: Programming at a glance!
❏ Part III: Programming for Bioinformatics (Bioconductor)

4. Part I
Why Programming?

5. • 5
Why ?

6. • 6
Data Analysis
Data management
curation & retrieval
& maintatince
Data analysis Data integration
& visualization

7. • 7
Data Management
Server User

8. • 8
Data Integration

9. • 9
Applications
D Data/statistical Analysis
M Modeling
S Software Developing

10. • 10
Define yourself!
User Analyst Developer

11. Part II
Programming at a glance!

12. • 12
How to design a program?
Release
❏ Release
program
❏ Iterate steps
for next
version
Problem
❏ Understand
problem
❏ Design
solution
❏ Write a
pseudocode
❖
Code
❏ Write
code
❏ Test
❏ Test with
real-world
users

13. Systematic Program Design

14. Programs = Algorithms + Data Structures

15. • 15
Algorithms
❏ Step by step list of instructions that if
followed exactly will solve the problem
under consideration
❏ General solution
❏ Computer automate execution

16. • 16
Algorithms Representation
Could be represented
by:
❏ Pseudocode
❏ Flowcharts
● Best code is the shortest code

17. • 17
Pseudocode
❏ Not a real code but it code be written in
English to divide a big problem into smaller
ones (outline the logic of the problem).
#Problem: sending man to the moon
● Launch
● Navigate to the moon
● Land on the moon

18. • 18
Programming Language
❏ Formal language communicates instructions of
a program to the computer.

19. • 19
Programming Language Types

20. • 20
Programming Language Types

21. • 21
Compiler
Source
code
Compiler
Machine
code
Program
Run
“.exe”
Input Output
The file that contains the
instructions written in
the high level language
Ex: Subtitles in movie

22. • 22
Interpreter
Source
code
Input
Interpreter
Output
Ex: Translation in conference

23. • 23
❏ An Integrated Development Environment (IDE) is a
software suite that consolidates basic tools required
to write and test software.
Ex: Visual Studio Code, R studio, PyCharm, Jupyter
IDE

24. • 24
IDE

25. • 25
Where do I begin?
Bash
PythonR
Executing Scripts
Statistical Analysis
& Visualization
Coding
Algorithms

26. • 26

27. • 27
Programming Language Structure
HowdoIconstructa
validsentence?
Syntax
Commands
➔ Punctuation
➔ Indentation= spacing
➔ Ordering
➔ Comments
➔ Sentence
➔ Variables &
values
➔ Keywords

28. • 28
Programming Language Structure
What does the sentence mean?
Code LogicSemantics
Syntax is different among programming
languages but logic is the same!

29. • 29
Programming Language Structure
Variable value
keywordStatement

30. • 30
Punctuation

31. • 31
Ordering: in procedures

32. • 32
Ordering: in mathematical operations
P
E
M
D
A
S

33. • 33
Comments

34. • 34
Debugging
❏ Syntax error
❏ Semantic error

35. • 35
Data Types
❏ Boolean
❏ String “str” ❏ Integer “int”
❏ Float
DNA, RNA, protein
sequence
Gene Expression
Level
3.051
(Decimal)

36. • 36
Data Structures

37. Part III
Programming for Bioinformatics
(Bioconductor )

38. • 38
Bioconductor
Bioconductor Release 3.9. 1741
Software Packages!

39. • 39
Bioconductor
High- throughput Data:
❏ DNA sequencing
❏ RNA sequencing
❏ Microarray
❏ Proteomics
❏ Imaging
Statistical Analysis &
Comprehension:
❏ Large data volume
❏ Designed experiments
❏ Technological artifacts
❏ Complex data
integration

40. • 40
Conclusion
Bioconductor
Data
Information
Knowledge
Wisdom
Understanding
Connectedness
● understand
relations
● understand
patterns
● understand
principles

41. ● Top IDE: http://pypl.github.io/IDE.html
interactive programming:
● https://www.datacamp.com/home
● http://pythontutor.com/
● https://www.w3schools.com/
● https://www.sololearn.com/
● https://runestone.academy/runestone/books/published/thinkcspy/index.
html
● https://scratch.mit.edu/
Ask someone!
● https://askubuntu.com/
● https://stackoverflow.com/
● https://stackexchange.com/
● https://www.biostars.org/
What is unique about each programming language?
https://dafoster.net/articles/2013/01/29/unique-features-of-various-progr
amming-languages/
R
E
S
O
U
R
C
E
S

42. THANK YOU!
e.abdelrazik@nu.edu.eg
abdrlrazik_eman
emanabdelrazik