Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual...
Transcript of Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual...
![Page 1: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/1.jpg)
Introduction to Bioinformatics
APHL Annual MeetingBioinformatics Platform Options for Public Health LaboratoriansJune 3 2019Dr. Kelly F. Oakeson
![Page 2: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/2.jpg)
![Page 3: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/3.jpg)
![Page 4: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/4.jpg)
Bioinformatics
• Sequence analysis
• Gene & protein expression
• Analysis of cellular organization
• Structural bioinformatics
• Databases
• Algorithm Development
• Software & tools
• Others?
![Page 5: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/5.jpg)
Gene & protein expression
• Gene expression (RNA-Seq)
• Protein expression
• Analysis of regulation
![Page 6: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/6.jpg)
Databases
• Biological sequence analysis: Genbank, UniProt
• Structure analysis: Protein Data Bank (PDB)
• Finding Protein Families and Motif Finding: InterPro, Pfam
• Next Generation Sequencing: Sequence Read Archive
• Network Analysis: Metabolic Pathway Databases (KEGG, BioCyc), Interaction Analysis Databases, Functional Networks
• Antimicrobial Resistance: The Comprehensive Antibiotic Resistance Database (CARD), National Database of Antibiotic Resistant Organisms (NDARO)
• Virulence Factors: The virulence factor database (VFDB)
![Page 7: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/7.jpg)
Algorithm & Software Development
• Foundations in Discrete mathematics, control theory, system theory, information theory, and statistics
• Graph theory, artificial intelligence, soft computing, data mining, image processing, and computer simulation
• Open Source
• Commercial
![Page 8: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/8.jpg)
Sequence analysis
• DNA sequencing
• Sequence assembly
• Genome annotation
• Computational evolutionary biology
• Comparative genomics
![Page 9: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/9.jpg)
![Page 10: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/10.jpg)
Command Line (CLI) vs. Graphical User Interface (GUI)
Vs.
![Page 11: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/11.jpg)
Command Line (CLI) vs. Graphical User Interface (GUI)
Vs.
![Page 12: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/12.jpg)
Graphical User Interface (GUI)
![Page 13: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/13.jpg)
Graphical User Interface (GUI)
![Page 14: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/14.jpg)
Graphical User Interface (GUI)
![Page 15: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/15.jpg)
Graphical User Interface (GUI)
![Page 16: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/16.jpg)
Graphical User Interface (GUI)
![Page 17: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/17.jpg)
Command Line (CLI)
![Page 18: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/18.jpg)
Command Line (CLI)
![Page 19: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/19.jpg)
Command Line (CLI)
![Page 20: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/20.jpg)
Command Line (CLI)
![Page 21: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/21.jpg)
Command Line (CLI)
![Page 22: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/22.jpg)
Command Line (CLI)
![Page 23: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/23.jpg)
Command Line (CLI)
![Page 24: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/24.jpg)
Command Line (CLI)
![Page 25: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/25.jpg)
Command Line (CLI)
![Page 26: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/26.jpg)
Command Line (CLI)
![Page 27: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/27.jpg)
Command Line (CLI)
![Page 28: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/28.jpg)
Command Line (CLI)
![Page 29: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/29.jpg)
https://github.com/stephenturner/oneliners
![Page 30: Introduction to Bioinformatics Dr. Kelly F. Oakeson · Introduction to Bioinformatics APHL Annual Meeting Bioinformatics Platform Options for Public Health Laboratorians June 3 2019](https://reader036.fdocuments.us/reader036/viewer/2022070904/5f7289b32c454f58731478f1/html5/thumbnails/30.jpg)
Questions/Discussion