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Introduction to Bioinformatics Programming in Python
IntroductionDavid Koes
8/27/19
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Bioinformatics”
�2
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Bioinformatics”
�2
Sequence Analysis
Molecular Dynamics
Protein Structure
Data Analysis
Protein Dynamics
Systems Modeling
Genomics
Proteomics
Cheminformatics
Drug Discovery
Bioimaging
Biomedical Informatics
Bioinformatics, Computational, and Systems Biology
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Programming”
�3
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Programming”
�3
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Programming”
�3
There is an on-going debate on the extent to which the writing of programs is an art form, a craft, or an engineering discipline.
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Python”
�4
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Python”
�4
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Python”
�4
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
PythonDesigned to be easy to learn Full featured, powerful language Free - Costs nothing and open-source Ideal for scripting Popular
�5
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction �6
http://pypl.github.io/PYPL.html
https://spectrum.ieee.org/at-work/innovation/the-2018-top-programming-languages
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction �7
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Course Goals
�8
“Analyze the data”
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Course Goals
�8
“Analyze the data”
“Analyze the data”
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Course Goals
�8
“Analyze the data”
“Analyze the data”
“Do it again”
“Do it again”
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Course Goals
�8
“Analyze the data”
“Analyze the data”
“Do it again”
“Do it again”
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Course GoalsGain experience programming Learn Python Survey computational methods
�9
Improve skills to be a more productive and successful researcher
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Logistics
�10
12 Programming AssignmentsDue midnight on TuesdayAutograded - submit until it worksMost can be submitted for partial credit1 day late - 90% credit2 days late - 50% credit>3 days late - 0% creditLate penalty only applied to additional pointsEach assignment worth ~7%
Final Project (create an assignment)
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Logistics
�11
Communication over Piazzahttp://piazza.com/pitt/fall2019/mscbio2025
Building access• email Kelly Gentille ([email protected]) pictures of
the front and back of your userid • you may need to get a new id from Panther central
Final Grades• A: >93%• B: >85%
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Academic Honesty
�12
Do your own work
Do not share or look at other students’ code
Do discuss concepts and problem solving strategies
Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Website
�13
http://mscbio2025.csb.pitt.edu
Commandline Basics Laptop setup Change Account Password on ensemble.csb.pitt.edu
