Design and Implementation of Bioinformatics
Databases
BINF 8211/BINF 6211
UNCC
Spring 2008 |
|
Class Schedule:
(Note the following Schedule is subject to
change)
Each
week we plan to have a database design and implementation lecture and a
public
repository and access lecture.
|
Week
|
Dates
|
Topics
|
Readings/Homework
|
Lecture
Notes
|
| Week 1
|
Jan 9th
|
Course Business,
Introduction to Microarray Experiments, Overview of Data Modeling and
Technical Databases |
Read Book:
Introduction
Chapter 1
Chapter 2
|
Lecture 1
|
| Week 2 |
Jan 14th,
16th |
Database terminology,
management systems and architecture. Introduction to the software to be
used in class: MySQL, Visio. (PostgresSQL)
Sequence databases 1
|
Read Book:
Chapter 3
Chapter 4
Papers:
Reading #1
(Afieri)
Reading #2
(Kumar)
Reading#3
(Lichtenberg)
Reading
#4 (Rowicka)
|
Lecture 2
Lecture
3
|
Week
3
|
Jan 23rd
|
DBMS installation,
creation of a db instance, user, SQLscripts for forming a table, sql
statements for inserting and deleting data, columns other simple
commands.
Sequence databases 2
|
Reading#5(Brown)_Hmwk
#1
Homework
#1
|
Lecture 4
|
| Week 4 |
Jan 28th,
30th
|
Use cases, conceptual
modeling and normalization. Developing a use case.
Protein databases 1
|
Please have thought
about the conceptual model for Wednesdays class.
Visio ERM -
from lecture 6.
Note: this is an
example and not complete.
|
Lecture 5
(reposted
print fixed)
Lecture
6
|
| Week
5 |
Feb 4th,
6th |
Taking
a conceptual model to a logical model, ER diagrams, conversion to a
schema,
writing or extracting the SQL script to create the tables.
Protein
databases 2
|
Some Example Project
Questions
Visio
(Update) ~ Why Dr. Carr can't get Visio to work
|
Lecture 7
Lecture
8
|
| Week 6
|
Feb 11th,
13th |
Experiments and
scientific data: essential attributes, metadata and modeling of
biological data
Modeling an experiment
and producing a schema (example with Visio).
|
Reading
#6(Sarkans)
|
Lecture 9
Lecture10
|
| Week 7
|
Feb 18th,
20th |
Data access, export,
and QC methods, validation of results.
Microarray databases
|
Example Midterm
Reading#7(Istrail)
|
Lecture 11
Lecture 12
|
| Week 8
|
Feb 25th,
27th |
Project design presentations
(Archana, Barrett)
Midterm
|
|
|
| Spring Break |
Mar 3rd- 7th |
SPRING BREAK!
|
|
|
| Week 9
|
Mar 10th,
12th |
Project Design Presentations (Clary,
Khoshnevis, Keller)
SQL Continued: Querying and
joins continued (Chapter 7 and 8)
|
Homework#4
|
|
| Week 10
|
Mar 17th,
19th |
Advanced SQL: querying
and joins, indexing for performance (Chapter 8)
Populating tables:
scripts and tools for inserting data into databases
|
|
SQL Workshop
lectures 13 and 14
Python
and SQL lecture 15
|
| Week 11
|
Mar 24th,
26th |
Data interchange
standards and formats (XML)
Pathway databases:
KEGG, and the SOAP/WSDL protocols
|
Homework #5
|
XML Lecture 16
KEGG
and SOAP 17
|
| Week 12
|
Mar 31st,
Apr 2nd
|
The SRS databases:
BioCyc,MetaCyc
BioMOBY: locating data
|
Reading #8 BioMOBY
Consortium
Reading #9 Wilkinson
|
BioCyc, MetaCyc
and BioWarehouse 18
BioMOBY
and GBrowse MOBY 19
|
| Week 13 |
Apr 7th,
9th |
Distributed databases,
Data Warehouses, OLAP (Chapter 12, 13)
Protein databases
1:SwissProt and Structure databases (Federated Databases such as
PDBSum. Knowledge-added databases such as EzCATDB or CSA.
|
|
Distributed DB,
Data Warehouses, OLAP 20
|
| Week 14 |
Apr 14th,16th |
Protein databases 2:
SwissProt and Structure databases (Federated Databases such as PDBSum.
Knowledge-added databases such as EzCATDB or CSA.)
The Gene Ontology, OWL and Protege
|
Homework #6 (Homework 6 is due on Apr 30th by 5pm)
|
Protein
databases 21 and 22
Lecture
23 DataWarehouse and StarModel
|
| Week 15 |
Apr 21st, 23rd |
Genetics
databases: OMIM and SNPdb
April
23rd: no lecture: project work day
|
|
Lecture 24 OMIM and
dbSNP
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| Week 16 |
Apr 28th
|
ALL Project
Presentations
(Class
Extended)
Clary, Khoshnevis, Keller, Archana, Barrett
|
|
|
| Apr 30th |
Reading Day (No Class)
Homework 6 is due on Apr 30th by 5pm
|
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Week 17
NOTE:
|
May 5th
|
Final
In Class
PROJECT
DEADLINE:
May 5th at 5pm
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Home
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Course Syllabus
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Course Readings
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Software
Links |
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| This site was designed and maintained by
Dr. Andrew Carr. Jan 09, 2008 |
Dr. D. Andrew
Carr