BCB 712 Spring 2016
Instructor: Dr. Hemminger
This planned schedule lists the topics we'll cover with links to the presention materials, and readings and assignments due dates. Their are no required textbooks for this course, as part of my effort to educate using freely available materials. All readings are available electronically, and linked from this page. Readings should be read before the class they are listed for. Assignments are due two hours BEFORE the start of the class they are listed for. They should be posted on the class work page.
Tuesday
Before our first Class, please read through course web pages, add
yourself to the course listserv, and put your information in the
class roster by 9am of first day of class.
Introduction (course pages, class work webpages). Everyone should
be able to access the class work pages for the first class.
Thursday
Assignment
1 assigned
Tuesday
SQL Lecture Notes
Thursday
Assignment: A1 is DUE.
Assignment
2 assigned.
Tuesday
Assignment
3 assigned
Thursday
Review A1.
Tuesday
Assignment 2 due.
Thursday
Assignment 3 due.
Assignment 4
is assigned.
Tuesday
Assignment 5
is assigned. A5 is due Thursday March 15th by 12 noon. Put your
work on Class Work Page
Thursday
Assignment
4 is due. A5 is DUE 12 noon March 15th.
Digital Libraries, Standards, Scholarly Publishing, Open
Access. In-class exercise. This page was last modified on August 21, 2008, by
Bradley Hemminger. Address questions and comments about this page to him at
bmh@ils.unc.edu.
2/9
ER Model
Relational Model
Example ER Diagrams:
ER Diagram Example 1
ER Diagram Example 2
Things to do today:
1) Put your
Exercise 1 (Sports Exercise)
on class work
pages. Be sure you're enabled to edit the class work pages.
2) Download MySQL Workbench to your machine; best to do on campus with fast network connection. Takes up to 5 minutes.
Install this on your machine. You can get help from our TA at Tuesday's class to install it (but make sure you have already downloaded it).
2/11
Review Exercise 1 (Sports Exercise) work. (Be sure your work is
posted on the class work pages 2 hours before the start of class). We will review with you in class.
ER diagram to DDL Example
Review SQL querying
Practice connecting to MySQL server on SILS
Resources for MySQL:
DataBase
Input File for our SQL exercises
2/16
MySQL
Reference Card
Examples and exercise
Practice
SQL examples
Exercise 2
OPTIONAL MATERIAL: working with GO database.
Instructions on connecting to the GO database.
The GO database
The GO database guide
The GO schema autodoc
Exercise 3
1. Get all the genus with more than 10 species.
2. Get the counts of gene products grouped by database that belong to the genus from the question above
3. Find all the genes in goat (species.common_name) that are directly annotated to "nucleus"
Go
Database Setup Instructions
2/18
Review and work through Practice SQL queries.
Begin Exercise 2 queries.
2/23
XML
XSLT
XML Examples
PHP Example
Bourret
Reading on Discussion about when to use XML versus RDMS.
2/25
Continue discussion on XML related technologies.
3/1
3/3
Information Seeking Lab: Guest Lecturer Barries Hayes of HSL.
.
3/8
Indexing
for Searching
Classification
Ontologies
3/10
Scholarly Communications in a changing world
Digital Scholarship
CTSA/TraCS campus resoure
© 2004-present Bradley M. Hemminger