CIS 115
Lecture 26: Databases, Bioinformatics & Genomics
kst8r
K-State's new social network!
- What features should it have?
- What data do we need?
- How should it be stored?
- How can we retrieve it?
Relational Database
| userID | Name | Birthday | Major |
| russfeld | Russell | May 10th | Comp. Sci |
| johnsmith | John | June 1 | Info. Sci |
| smiller | Sheila | Sept. 26 | Soft. Engg. |
| gameguy | Jayson | Dec 26 | computersci |
| sharpie | Reily | Dec. 18th | IS |
Database Normalization
- Avoid modification anomalies
- Minimize errors when redesigning
- Mirror real-world concepts
- Avoid problems with different types of queries
Relational Database
| userID | Name | Birthday | Major |
| russfeld | Russell | May 10th | Comp. Sci |
| johnsmith | John | June 1 | Info. Sci |
| smiller | Sheila | Sept. 26 | Soft. Engg. |
| gameguy | Jayson | Dec 26 | computersci |
| sharpie | Reily | Dec. 18th | IS |
Related Tables
| userID | Name | Birthday | Major |
| russfeld | Russell | May 10th | 1 |
| johnsmith | John | June 1 | 3 |
| smiller | Sheila | Sept. 26 | 2 |
| gameguy | Jayson | Dec 26 | 1 |
| sharpie | Reily | Dec. 18th | 3 |
| majorID | Major | Abbreviation |
| 1 | Computer Science | CS |
| 2 | Software Engineering | SE |
| 3 | Information Systems | IS |
Storing Phone Numbers
| userID | Name | Phone1 | Phone2 |
| johnsmith | John | 555-1234 | |
| smiller | Sheila | 555-5134 | |
| gameguy | Jayson | 555-1235 | 555-5134 |
| sharpie | Reily | 555-5134 |
Many-to-One?
| userID | Name |
| johnsmith | John |
| smiller | Sheila |
| gameguy | Jayson |
| sharpie | Reily |
| Phone | user1 | user2 | |
| 555-1234 | johnsmith | ||
| 555-5134 | smiller | gameguy | ?sharpie? |
| 555-1235 | gameguy |
One-to-Many
| userID | Name |
| johnsmith | John |
| smiller | Sheila |
| gameguy | Jayson |
| sharpie | Reily |
| userID | phone |
| johnsmith | 555-1234 |
| smiller | 555-5134 |
| gameguy | 555-1235 |
| gameguy | 555-5134 |
| sharpie | 555-5134 |
Bioinformatics
Interdisciplinary field that focuses on developing and improving methods for storing, retrieving, organizing and analyzing biological data
Genomics
Discipline that applies methods to sequence, assemble and analyze the function and structure of genomes, a complete set of DNA within a single cell of an organism
Image Source: Wikipedia
Image Source: Wikipedia
Image Source: Wikipedia
Image Source: Wikipedia
Image Source: BLDG BLOG
Image Source: scragz on Flickr
Death Tolls
Finding Virus DNA
- Compare DNA samples of people infected with the virus to samples of people without the virus
- If you find discrepancies, it could be
- Genetic differences between people
- The Virus!!
We need your help!
- We have samples from infected individuals and genomes taken before the outbreak
- Compare the infected samples with the good ones and find suspect DNA mutations. They could be the virus!
Process
- Choose a pattern from the virus genome
- Calculate its complement
- See if that complement exists in the human genome
- If not, then it may be part of the virus
Assignments
- Textbook Rough Draft - Due Friday 11/22 10:00 PM via KSOL or email
- Blog 12: Textbook Review: Making Meaning - Due 12/1 10:00 PM
Blog 12: Textbook Review - Making Meaning
Now that we’ve (almost) finished reading the textbooks, it is time to step back and think about what we read. Choose one of the three textbooks for this course and write about your reactions to it and what you learned from it. I’d recommend almost treating this like an in-depth book review for others who are interested in reading the book, but don’t mind some spoilers. Some questions I’d like you to answer:
- How did you feel reading this book? Engaged? Bored? Interested?
- What was the most interesting thing you learned?
- Were there any parts of the book you didn’t like?
- Were there any terms or concepts that you looked up (Googled) to find more information about? What were they? What did you find?
- Did this book help explain things you didn’t know about computers?
- Would you recommend this book to a friend that wanted to know more about computers?