Bioinformatics for Computer Scientists aungthurhahein.me@Atrhein

This is...

● Learning guideline for starters● Resources for starters● Thoughts from a computer technician who

does not have formal knowledge of bioinformatics

Bioinformaticist….

Bioinformaticist: Generalists, developers/advanced users of informatics tools that manipulate biological data.

Bioinformatics analyst: Biologists who conduct bioinformatics analyses full-time, but don’t develop software

Formal Knowledge

● Data Mining

● Data Analysis

● Machine Learning Algorithms

● Statistics

● Database Programming

Informal Knowledge

● Linux

● Bash scripting

● Bioinformatics Pipelining

● Biological data format

● Open source tools

● Bio-Linux

Python for bioinformatics

● Easy to learn

● Extensive libraries for statistics &

visualization

● Biopython (biopython.org)

● Python is awesome and beautiful!

Why Python?

● You can do ‘almost’ everything with python

● Options: Perl, R, Java, C, C#

● Choose it wisely

Python Libraries to learn

● Pandas

● Numpy

● Scipy

● Biopython

● scikit-bio

Books

Bioinformatics

● To understand & analyze biological data

● DNA & RNA sequence analysis

● Gene & protein differential expression

analysis

Data Types

● DNA, RNA

● EST, cDNA

● Protein Sequence

● Pathways

Sequence formats

● fasta

● fastq

● EMBL

● Genbank

● etc ...

Open source tools

● Evaluation of tools & softwares in essential

● Important to use right tool at right place

● Many open source projects (open source bioinformatics

software)

Books

Learning Resources

● List of free online bioinformatics courses

(wiki)

● Learn Bioinformatics

● Resources for learning Bioinformatics (reddit)

● An Online Bioinformatics Curriculum (NCBI)