Welcome!

Welcome to Python programming workshop for bioinformatics: AnkaPy. AnkaPy is a sequel of the OstraPy workshop (http://ostrapy.pythonanywhere.com/) situated in the capital of Turkey, Ankara. The main goal of this project is to spread knowledge and teach people how to use Python efficiently in their scientific projects. Students will learn basic programming concepts, essentials of Biopython package (working with fasta files, blast, Entrez database) and some key packages for data science in Python (numpy, pandas, matplotlib).

General info

📅 25-29 November 2019

🏫 Hacettepe University, Ankara

💰 Free

📋 registration form

📧 ezgialtinisik@gmail.com, zihaladavid@gmail.com, eren26285@gmail.com

Instructors

• David Žihala, Department of Biology and Ecology, University of Ostrava, Czech Republic
• N. Ezgi Altınışık, Department of Anthropology, Hacettepe University, Turkey
• Eren Yüncü, Department of Biology and Ecology, University of Ostrava, Czech Republic
• Yasin Kaya, Department of Biology, Hacettepe University, Turkey
• Dilek Koptekin, Department of Biology, Middle East Technical University, Turkey

Organized by: RSG-Turkey, Hacettepe University, University of Ostrava, SOVA

Preliminary Program

Day 1:

9:00 – 9:30 Introduction
9:30 – 11:00 Basic data types
11:00 – 11:15 Coffee break ☕
11:15 – 12:30 Control statements(1), Exception handling
12:30 – 13:30 Lunch break 🍴
13:30 – 15:00 Control statements(2), working with files
15:00 – 15:15 Coffee break ☕
15:15 – 17:00 Functions

Day 2:

9:00 – 11:00 Working with files, string formatting
11:00 – 11:15 Coffee break ☕
11:15 – 12:30 Classes
12:30 – 13:30 Lunch break 🍴
13:30 – 15:00 Modules, Packages, Introduction to standard library
15:00 – 15:15 Coffee break ☕
15:15 – 17:00 Generators, Iterators

Day 3:

9:00 – 11:00 Regular expressions
11:00 – 11:15 Coffee break ☕
11:15 – 12:30 Classes(2)
12:30 – 13:30 Lunch break 🍴
13:30 – 15:00 Biopython – SeqIO

Day 4:

9:00 – 11:00 Biopython - AlignIO
11:00 – 11:15 Coffee break ☕
11:15 – 12:30 Biopython – Blast.NCBIWWW
12:30 – 13:30 Lunch break 🍴
13:30 – 15:00 Biopython – Blast.NCBIXML
15:00 – 15:15 Coffee break ☕
15:15 – 17:00 Biopython - Entrez

Day 5:

9:00 – 11:00 Introduction to scientific Python
11:00 – 11:15 Coffee break ☕
11:15 – 12:30 pandas
12:30 – 13:30 Lunch break 🍴
13:30 – 15:00 Matplotlib
15:00 – 15:15 Coffee break ☕
15:15 – 17:00 More pandas and Matplolib

literature 📚

mice book
python for biologist

——

for Ecology and Genomic cases —> https://datacarpentry.org

for Bayesian Inferences —> https://seeing-theory.brown.edu for pandas —> https://pandas.pydata.org/pandas-docs/stable/getting_started/10min.html

for Linux, Python and R https://software-carpentry.org/lessons/

Hands-on Python Course ->> https://www.codecademy.com && datacamp.com

edX exercism Coderbyte Lynda PluralSight Rosalind Coursera

for more and detail: http://rsgturkey.com/en/resources/