Programming in a Nutshell

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

How do I construct a
valid sentence?
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!
[email protected]





abdrlrazik_eman
emanabdelrazik