introduction - university of pittsburghmscbio2025.csb.pitt.edu/notes/intro2019.pdf · department of...
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Introduction to Bioinformatics Programming in Python
IntroductionDavid Koes
8/27/19
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Bioinformatics”
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Bioinformatics”
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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
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Programming”
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Programming”
�3
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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.
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Python”
�4
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Python”
�4
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
“Python”
�4
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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
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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
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction �7
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Course Goals
�8
“Analyze the data”
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Course Goals
�8
“Analyze the data”
“Analyze the data”
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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”
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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”
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Course GoalsGain experience programming Learn Python Survey computational methods
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Improve skills to be a more productive and successful researcher
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Logistics
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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)
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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%
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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
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Department of Computational BiologyIntroduction to Bioinformatics
Programming in Python
Introduction
Website
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http://mscbio2025.csb.pitt.edu
Commandline Basics Laptop setup Change Account Password on ensemble.csb.pitt.edu