BCB 712 Spring 2014
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. I do recommend several books (see list in Resources Books (XXX). All readings are available electronically, and linked from this page. Readings should be read before the class they are listed for. Assignments are due by the start of the class they are listed for.
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, wiki). Everyone should be connected to
wiki BEFORE the first class.
Thursday
Review Exercise 1 (Sports Exercise) work. (Put your work on the
wiki by Monday 12 noon). We will review with you in class.
Tuesday
SQL Lecture Notes
Thursday
Assignment: A1 is DUE.
Assignment 2 assigned.
Tuesday
XML
Thursday
Review A1. Continue discussion on XML related technologies.
Tuesday
Assignment 2 due.
Digital Libraries, Standards, Scholarly Publishing, Open
Access. In-class exercise.
Thursday
Assignment 3 due.
Assignment 4
is assigned.
Tuesday
SPRING BREAK
Thursday
SPRING BREAK
Tuesday
Information Seeking Lab: Guest Lecturer Barries Hayes of HSL.
Thursday
Assignment
4 is DUE 12 noon March 27th. 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.
2/11
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
wiki. Be sure you're enabled to edit the wiki.
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 at Tuesday's class to install it (but make sure you have already downloaded it).
2/12
A1 is assigned.
ER diagram to DDL Example
Review SQL querying
Practice connecting to MySQL server on SILS
Resources for MySQL:
Command Line MySQL Getting
Started (reference only, deprecated)
Example
MySQL Input Files
2/18
MySQL
Reference Card
Examples and exercise
Practice
SQL examples
Exercise 2
Instructions on connecting to the GO database.
The GO schema ER diagram
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
2/20
2/25
XSLT
XML Examples
PHP Example
Assignment
3 assigned
Bourret
Reading on Discussion about when to use XML versus RDMS.
2/27
3/4
Scholarly Communications in a changing world
Digital Scholarship
3/6
ILS Overview
Classification
Indexing
for Searching
3/11
3/13
3/18
Assignment 5
is assigned.
A5 is due Thursday March 27th by
12 noon. Put your work on Class Work Page
3/20
© 2004-present Bradley M. Hemminger