BCB 712 Schedule Spring 2013

BCB 712 Spring 2013
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.

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Tuesday 2/12	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. 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).
Thursday 2/14		Review Exercise 1 (Sports Exercise) work. (Put your work on the wiki by Monday 12 noon). We will review with you in class. A1 is assigned. ER diagram to DDL Example Review SQL querying Practice connecting to MySQL server on SILS Resources for MySQL: MySQL Getting Started Example MySQL Input Files

YYY

Tuesday 2/19		SQL Lecture Notes MySQL Reference Card Examples and exercise Practice SQL examples Exercise 2 Exercise 3 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
Thursday 2/21	Assignment: A1 is DUE.	Assignment 2 assigned.

Tuesday 2/26		XML XSLT XML Examples PHP Example Assignment 3 assigned Bourret Reading on Discussion about when to use XML versus RDMS.
Thursday 2/28		Review A1. Continue discussion on XML related technologies.

Tuesday 3/5	Assignment 2 due.	Digital Libraries, Standards, Scholarly Publishing, Open Access. In-class exercise. Scholarly Communications in a changing world Digital Scholarship
Thursday 3/7	Assignment 3 due.	Information Seeking Lab: Guest Lecturer Barries Hayes of HSL. Assignment 4 is assigned.
Tuesday 3/12	SPRING BREAK
Thursday 3/14	SPRING BREAK
Tuesday 3/19		ILS Overview Classification Indexing for Searching Final Project Assigned. Final Project is due Thursday March 28th by 12 noon. Put your work on Wiki
Thursday 3/21	Assignment 4 is DUE.	Metadata Vocabularies Ontologies CTSA/TraCS campus resoure

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