Course Introduction

Tom Ferrin

April 3, 2017

Why are we offering this course?

• Scientific Software Development Is Not an Oxymoron S.M. Baxter, S.W. Day, J.S. Fetrow, and S.J. Reisinger, PLoS Computational Biology 2(9):975-978, September 2006.
• How Do Scientists Really Use Computers? G. Wilson, American Scientist 97:8-10, September 2009.
• Where's the Real Bottleneck in Scientific Computing? G. Wilson, American Scientist 94(1):5, October 2006.

This course is about learning how to...

• Use proven software development methodologies and development tools
• Design and implement relational databases and SQL queries/updates
• Write web applications using HTML, Javascript and AJAX
• Use Python for connecting a web application to a relational database
• Work with Linux
• Work as a member of a development team
• Demonstrate that sophiscated software applications can be built pretty quickly

Course Schedule

• Week 1:
  • Mon – Lecture: Course introduction, software development tools, the development process
  • Tue – Lecture: Linux and the Linux Shell; Lab: software development tools
  • Wed – Lecture: Data modeling
  • Thu – Lecture: Relational database technology
  • Fri – Lab: Database programming
• Week 2:
  • Mon – Lecture: Web client data model (XML/XHTML/CSS/DOM)
  • Tue – Lecture: Web client programming (HTTP/Forms/JavaScript)
  • Wed – Lab: Web client software development
  • Thu – Lecture: Web applications (CGI/JavaScript/Intro to AJAX)
  • Fri – Lab: AJAX; Lecture: Regular Expressions
• Week 3:
  • Mon – Lecture: Testing, debugging, optimization
  • Tue – Lecture: Web security; Lab: Web application development
  • Wed – Lab: Team project development
  • Thu – Lab: Team project development
  • Fri – Team project presentations

Instructors

Tom Ferrin, Ph.D.
Professor, Pharmaceutical Chemistry
Director, Resource for Biocomputing, Visualization, and Informatics

Conrad Huang, Ph.D.
Adjunct Professor, Pharmaceutical Chemistry
Lead Software Architect for UCSF Chimera and ChimeraX

Scooter Morris, Ph.D.
Adjunct Professor, Pharmaceutical Chemistry
Roving Engineer, Cytoscape Development Team

Students

Course Web Site