Week 1 : Introduction to the course
Introduction to Bioinformatics (LF:DSIB01)


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Introductions
2
Introduce ourselves
Name
Project
Motivation for the course
Lessons on How to Introduce People | Southern Living

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Bioinformatics
3
What is bioinformatics?
Bioinformatics- Introduction and Applications - Bioinformatics - Microbe Notes

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What is Bioinformatics?
Computer
Science
Statistics
Biology
Biostatistics
Computational
Biology
Data
Science
Bioinformatics
A science that uses Computational and Statistical tools in order to address Biological questions.
Key Skills
Scientific Rigor
Engineering Mentality
Collaborative Spirit
Interdisciplinary Understanding
Simplification and Presentation
Key Pitfalls
Hacker Mentality
Bad Code > Reproducibility
Uninterpretable Models
Jargon and Gatekeeping
Losing track of goal: Biology

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Goals of this course
•Someone finishing this course should:
•
a)Have a basic understanding of the theory and practice of Bioinformatic Research
b)
b)Be able to practically function in a Bioinformatics research group setting or other collaborative
setting
c)
c)Be able to produce and present analysis results
•
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Syllabus / week
6
Week
Date
Material
Week 1
17-Sep-21
Introduction to the course
Week 2
24-Sep-21
Intro to Molecular Biology / Genomics
Organizing data, Git
Week 3
1-Oct-21
Exploring the human genome
Sequence Databases, Preprocessing NGS data
Week 4
8-Oct-21
Sequence Alignment
NGS data Alignment, Peak Calling
Week 5
15-Oct-21
Sequence (over)Representation
Motif Finding Tools
-
22-Oct-21
Week Off
-
29-Oct-21
Week Off
Week 6
5-Nov-21
Evaluation Metrics and Data Visualization
Week 7
12-Nov-21
ML techniques I (log regresion, SVM)
Week 8
19-Nov-21
ML techniques II (decision trees, random forest)
Week 9
16-Nov-21
ML techniques III (ANN, perceptrons)
Week 10
3-Dec-21
ML techniques IV (CNN) + Advances
-
10-Dec-21
Wrap up
 -
17-Dec-21 (?)
Colloquium

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Resources / Tools
•Tools
•Python
•Github
•Google Colaboratory
•Jupyter Notebook
•
•Resources
•https://www.kaggle.com/learn/overview
•https://wiki.python.org/moin/BeginnersGuide/NonProgrammers
•https://wiki.python.org/moin/BeginnersGuide/Programmers
•https://guides.github.com/activities/hello-world/
•https://research.google.com/colaboratory/faq.html
•https://www.dataquest.io/blog/jupyter-notebook-tutorial/
•http://www.biostathandbook.com/index.html
•
•
7
File:NewTux.svg - Wikimedia Commons
Linux

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Evaluation
8
Ongoing project through the semester
Small task after each practical – can be finished at home
Colloquium: discussion of questions, results etc

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www.ceitec.eu
CEITEC
@CEITEC_Brno
For any questions, comments etc
panagiotis.alexiou@ceitec.muni.cz

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