my talk at first Egyptian Bioinformatics Competition ^^

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