BIOINFORMATICS & COMPUTATIONAL BIOLOGY (An
Description: BIOINFORMATICS COMPUTATIONAL BIOLOGY (An Introductory Course) Lecture 2: Introduction Contents What is Bioinformatics ? Bioinformatics and Data Mining What is Computational Biology ? Why Bioinformatics ? Types of Data Available
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slide1. BIOINFORMATICS & COMPUTATIONAL BIOLOGY (An Introductory Course) Lecture 2: Introduction<br>
slide2. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 2<br>
slide3. What is Bioinformatics? Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology.
Bioinformatics is the new science at the interface of molecular biology and computer science that seeks to develop better ways to explore, analyze, and understand this vast wealth of genomic data. January 19, 2024 Computational Biology & Bioinformatics 3<br>
slide4. What is Bioinformatics? Other Definitions
The National Centre for Biotechnology Information (NCBI 2001):
Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline.
The ultimate goal of the field is to enable the discovery of new biological insights and to create a global perspective from which unifying principles in biology can be discerned. January 19, 2024 Computational Biology & Bioinformatics 4 http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html<br>
slide5. What is Bioinformatics? Other Definitions
Wikipedia.org:
Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data,
in particular, when the data sets are large and complex.
As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics
and statistics to analyze and interpret the biological data. January 19, 2024 Computational Biology & Bioinformatics 5<br>
slide6. What is Bioinformatics? January 19, 2024 Computational Biology & Bioinformatics 6 Biology Computer Science Mathematics/
Statistics Medicine Bioinformatics<br>
slide7. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 7<br>
slide8. 8 Bioinformatics and Data Mining What Is Data Mining? Data mining (knowledge discovery from data)
Extraction of interesting (non-trivial, implicit, previously unknown and potentially useful) patterns or knowledge from huge amount of data
Data mining: a misnomer?
Alternative names
Knowledge discovery (mining) in databases (KDD), knowledge extraction, data/pattern analysis, data archeology, data dredging, information harvesting, business intelligence, etc.
Watch out: Is everything “data mining”?
Simple search and query processing
(Deductive) expert systems Slide from CS4435/5435: Data Mining<br>
slide9. Bioinformatics and Data Mining Bioinformatics involves:
the design of new algorithms and statistics for large molecular biology data sets analysis .
the design and construction of software that enable information extraction.
the analysis and interpretation of biological data including nucleotide and amino acid sequences, and protein structures using developed software tools.
We can imply that Bioinformatics is the mining of biological datasets January 19, 2024 Computational Biology & Bioinformatics 9<br>
slide10. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 10<br>
slide11. Computational Biology Computational biology is the application of mathematical methods and computer algorithms to biological problems.
Simply put, it is about studying biology using computational techniques, which further the understanding of the science.
Bioinformatics can be regarded as a branch of computational biology. January 19, 2024 Computational Biology & Bioinformatics 11<br>
slide12. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 12<br>
slide13. Why Bioinformatics? It provide an avenue for a better understanding of complex disorders such as PD, increasing our ability to work toward improved treatments or cures.
It solves existing biological questions using existing and newly developed algorithms and software tools.
Provides a better data management and visualization analysis for the growing amount of available datasets. January 19, 2024 Computational Biology & Bioinformatics 13<br>
slide14. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 14<br>
slide15. Types of Data available DNA/RNA Sequence Data
Protein Sequence Data
Protein structure Data
Protein function
Gene expression Data
Biomolecular interactions
Single Nucleotide Polymorphisms (SNPs)
Molecular pathways
Disease information
And many more … January 19, 2024 Computational Biology & Bioinformatics 15<br>
slide16. GenBank Data Growth January 19, 2024 Computational Biology & Bioinformatics 16 Clair, C. S., & Visick, J. E. (2013).<br>
slide17. Growth of PDB January 19, 2024 Computational Biology & Bioinformatics 17 https://www.rcsb.org/stats/growth/growth-released-structures<br>
slide18. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 18<br>
slide19. Popular Databases and Type of Data Stored January 19, 2024 Computational Biology & Bioinformatics 19<br>
slide20. Other Databases GSDB: Genome Structure Database
Store Three-Dimensional Chromosome and Genome Structure January 19, 2024 Computational Biology & Bioinformatics 20<br>
slide21. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 21<br>
slide22. Problems affecting Analysis Database Data Quality
Additional Noise stemming from
Incorrect interpretation of experiments and incorrect handling
Incorrect parameter entry in public databases
Spelling mistakes
Annotation errors
Frame shift errors January 19, 2024 Computational Biology & Bioinformatics 22<br>
slide23. Problems affecting Analysis Database Redundancy
Data from different experimental approach for same organism
Sequence discrepancies and variation
As a result of redundancy if data used for training and testing are closely related. Then the developed model will lack ability to generalize. January 19, 2024 Computational Biology & Bioinformatics 23<br>
slide24. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 24<br>
slide25. “The Million Dollar Question” What do we do with these huge amount of data?
Alternatively, should our question be, What can we get from these huge and growing amount of data? January 19, 2024 Computational Biology & Bioinformatics 25<br>
slide26. What do we do with these huge amount of data? Store
Search
Analyze, Annotate, visualize and Recognize patterns
Build biological models and make Predictions January 19, 2024 Computational Biology & Bioinformatics 26<br>
slide27. What do we do with these huge amount of data? Need to have some biological knowledge to know the questions to ask.
Need to have knowledge of the data to know what possible questions it could answer.
What are the research areas/topics in bioinformatics? January 19, 2024 Computational Biology & Bioinformatics 27<br>
slide28. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 28<br>
slide29. Common Tools used for Analysis BLAST(Basic Local Alignment Search Tool)
Sequence similarity(“Homology”) searching
Clustal Omega(Protein)/ MUSCLE (DNA Alignment)
Sequence Alignment
GenScan
To identify complete gene structures in genomic DNA.
UniFold
RNA Structure
JPred
Protein Structure Prediction
PHYLIP
Phylogenetics: Inferring evolutionary relationships among biological entities. January 19, 2024 Computational Biology & Bioinformatics 29<br>
slide30. Methodology for Tool development in Bioinformatics January 19, 2024 Computational Biology & Bioinformatics 30<br>
slide31. Summary Bioinformatics is the application of tools of computation and analysis to the capture and interpretation of biological data
Bioinformatics is essential for management of data in modern biology and medicine
The bioinformatics toolbox includes computer software programs such as BLAST and Ensembl, which depend on the availability of the internet
Many tools have been developed to ensure knowledge can be extracted from biological datasets
Errors due to data handing and redundancy is common in bioinformatics. Hence, an efficient data preprocessing or normalization method is needed. January 19, 2024 Computational Biology & Bioinformatics 31<br>
slide32. Computer Scientist vs Biologist (Serafim Batzoglou, Stanford) January 19, 2024 Computational Biology & Bioinformatics 32<br>
slide33. Computer Scientist vs Biologist (almost) Everything is true or false in computer science
(almost) Nothing is ever true or false in Biology January 19, 2024 Computational Biology & Bioinformatics 33<br>
slide34. Computer Scientist vs Biologist Biologists seek to understand the complicated, messy natural world
Computer scientists strive to build their own clean and organized virtual world January 19, 2024 Computational Biology & Bioinformatics 34<br>
slide35. Computer Scientist vs Biologist Computer scientists are obsessed with being the first to invent or prove something
Biologists are obsessed with being the first to discover something January 19, 2024 Computational Biology & Bioinformatics 35<br>
slide36. References Clair, C. S., & Visick, J. E. (2013). Exploring bioinformatics. Jones & Bartlett Publishers
Bayat, A. (2002). Bioinformatics. Bmj, 324(7344), 1018-1022.
http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html
https://www.nature.com/subjects/systems-biology
Bioinformatics: The Machine Learning Approach, Pierre Baldi and Soren Brunak, 2001, MIT press.
Dr. Jianhua Ruan, Department of Computer Science, UTSA
Dr. Jianlin Cheng, Deparmtment of Electrical Engineering and Computer Science, University of Missouri, Columbia January 19, 2024 Computational Biology & Bioinformatics 36<br>
slide2. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 2<br>
slide3. What is Bioinformatics? Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology.
Bioinformatics is the new science at the interface of molecular biology and computer science that seeks to develop better ways to explore, analyze, and understand this vast wealth of genomic data. January 19, 2024 Computational Biology & Bioinformatics 3<br>
slide4. What is Bioinformatics? Other Definitions
The National Centre for Biotechnology Information (NCBI 2001):
Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline.
The ultimate goal of the field is to enable the discovery of new biological insights and to create a global perspective from which unifying principles in biology can be discerned. January 19, 2024 Computational Biology & Bioinformatics 4 http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html<br>
slide5. What is Bioinformatics? Other Definitions
Wikipedia.org:
Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data,
in particular, when the data sets are large and complex.
As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics
and statistics to analyze and interpret the biological data. January 19, 2024 Computational Biology & Bioinformatics 5<br>
slide6. What is Bioinformatics? January 19, 2024 Computational Biology & Bioinformatics 6 Biology Computer Science Mathematics/
Statistics Medicine Bioinformatics<br>
slide7. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 7<br>
slide8. 8 Bioinformatics and Data Mining What Is Data Mining? Data mining (knowledge discovery from data)
Extraction of interesting (non-trivial, implicit, previously unknown and potentially useful) patterns or knowledge from huge amount of data
Data mining: a misnomer?
Alternative names
Knowledge discovery (mining) in databases (KDD), knowledge extraction, data/pattern analysis, data archeology, data dredging, information harvesting, business intelligence, etc.
Watch out: Is everything “data mining”?
Simple search and query processing
(Deductive) expert systems Slide from CS4435/5435: Data Mining<br>
slide9. Bioinformatics and Data Mining Bioinformatics involves:
the design of new algorithms and statistics for large molecular biology data sets analysis .
the design and construction of software that enable information extraction.
the analysis and interpretation of biological data including nucleotide and amino acid sequences, and protein structures using developed software tools.
We can imply that Bioinformatics is the mining of biological datasets January 19, 2024 Computational Biology & Bioinformatics 9<br>
slide10. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 10<br>
slide11. Computational Biology Computational biology is the application of mathematical methods and computer algorithms to biological problems.
Simply put, it is about studying biology using computational techniques, which further the understanding of the science.
Bioinformatics can be regarded as a branch of computational biology. January 19, 2024 Computational Biology & Bioinformatics 11<br>
slide12. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 12<br>
slide13. Why Bioinformatics? It provide an avenue for a better understanding of complex disorders such as PD, increasing our ability to work toward improved treatments or cures.
It solves existing biological questions using existing and newly developed algorithms and software tools.
Provides a better data management and visualization analysis for the growing amount of available datasets. January 19, 2024 Computational Biology & Bioinformatics 13<br>
slide14. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 14<br>
slide15. Types of Data available DNA/RNA Sequence Data
Protein Sequence Data
Protein structure Data
Protein function
Gene expression Data
Biomolecular interactions
Single Nucleotide Polymorphisms (SNPs)
Molecular pathways
Disease information
And many more … January 19, 2024 Computational Biology & Bioinformatics 15<br>
slide16. GenBank Data Growth January 19, 2024 Computational Biology & Bioinformatics 16 Clair, C. S., & Visick, J. E. (2013).<br>
slide17. Growth of PDB January 19, 2024 Computational Biology & Bioinformatics 17 https://www.rcsb.org/stats/growth/growth-released-structures<br>
slide18. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 18<br>
slide19. Popular Databases and Type of Data Stored January 19, 2024 Computational Biology & Bioinformatics 19<br>
slide20. Other Databases GSDB: Genome Structure Database
Store Three-Dimensional Chromosome and Genome Structure January 19, 2024 Computational Biology & Bioinformatics 20<br>
slide21. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 21<br>
slide22. Problems affecting Analysis Database Data Quality
Additional Noise stemming from
Incorrect interpretation of experiments and incorrect handling
Incorrect parameter entry in public databases
Spelling mistakes
Annotation errors
Frame shift errors January 19, 2024 Computational Biology & Bioinformatics 22<br>
slide23. Problems affecting Analysis Database Redundancy
Data from different experimental approach for same organism
Sequence discrepancies and variation
As a result of redundancy if data used for training and testing are closely related. Then the developed model will lack ability to generalize. January 19, 2024 Computational Biology & Bioinformatics 23<br>
slide24. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 24<br>
slide25. “The Million Dollar Question” What do we do with these huge amount of data?
Alternatively, should our question be, What can we get from these huge and growing amount of data? January 19, 2024 Computational Biology & Bioinformatics 25<br>
slide26. What do we do with these huge amount of data? Store
Search
Analyze, Annotate, visualize and Recognize patterns
Build biological models and make Predictions January 19, 2024 Computational Biology & Bioinformatics 26<br>
slide27. What do we do with these huge amount of data? Need to have some biological knowledge to know the questions to ask.
Need to have knowledge of the data to know what possible questions it could answer.
What are the research areas/topics in bioinformatics? January 19, 2024 Computational Biology & Bioinformatics 27<br>
slide28. Contents What is Bioinformatics ?
Bioinformatics and Data Mining
What is Computational Biology ?
Why Bioinformatics ?
Types of Data Available
Bioinformatics Databases
Problems in Bioinformatics
The Question
Some common analysis tools
Summary January 19, 2024 Computational Biology & Bioinformatics 28<br>
slide29. Common Tools used for Analysis BLAST(Basic Local Alignment Search Tool)
Sequence similarity(“Homology”) searching
Clustal Omega(Protein)/ MUSCLE (DNA Alignment)
Sequence Alignment
GenScan
To identify complete gene structures in genomic DNA.
UniFold
RNA Structure
JPred
Protein Structure Prediction
PHYLIP
Phylogenetics: Inferring evolutionary relationships among biological entities. January 19, 2024 Computational Biology & Bioinformatics 29<br>
slide30. Methodology for Tool development in Bioinformatics January 19, 2024 Computational Biology & Bioinformatics 30<br>
slide31. Summary Bioinformatics is the application of tools of computation and analysis to the capture and interpretation of biological data
Bioinformatics is essential for management of data in modern biology and medicine
The bioinformatics toolbox includes computer software programs such as BLAST and Ensembl, which depend on the availability of the internet
Many tools have been developed to ensure knowledge can be extracted from biological datasets
Errors due to data handing and redundancy is common in bioinformatics. Hence, an efficient data preprocessing or normalization method is needed. January 19, 2024 Computational Biology & Bioinformatics 31<br>
slide32. Computer Scientist vs Biologist (Serafim Batzoglou, Stanford) January 19, 2024 Computational Biology & Bioinformatics 32<br>
slide33. Computer Scientist vs Biologist (almost) Everything is true or false in computer science
(almost) Nothing is ever true or false in Biology January 19, 2024 Computational Biology & Bioinformatics 33<br>
slide34. Computer Scientist vs Biologist Biologists seek to understand the complicated, messy natural world
Computer scientists strive to build their own clean and organized virtual world January 19, 2024 Computational Biology & Bioinformatics 34<br>
slide35. Computer Scientist vs Biologist Computer scientists are obsessed with being the first to invent or prove something
Biologists are obsessed with being the first to discover something January 19, 2024 Computational Biology & Bioinformatics 35<br>
slide36. References Clair, C. S., & Visick, J. E. (2013). Exploring bioinformatics. Jones & Bartlett Publishers
Bayat, A. (2002). Bioinformatics. Bmj, 324(7344), 1018-1022.
http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html
https://www.nature.com/subjects/systems-biology
Bioinformatics: The Machine Learning Approach, Pierre Baldi and Soren Brunak, 2001, MIT press.
Dr. Jianhua Ruan, Department of Computer Science, UTSA
Dr. Jianlin Cheng, Deparmtment of Electrical Engineering and Computer Science, University of Missouri, Columbia January 19, 2024 Computational Biology & Bioinformatics 36<br>