UPRM - ICOM 4036 - Programming Languages (Spring 2008)

Email: bvelez@acm.org
University of Puerto Rico - Mayagüez Campus
Department of Electrical and Computer Engineering

Home
Courses
Publications
Projects
My Favorite Links
My Favorite Search Engines

Essential Computing for Bioinformatics (Fall 2007)

This course provides a broad introductory discussion of essential computer science concepts that have wide applicability in the natural sciences. Particular emphasis will be placed on applications to Bioinformatics. The concepts will be motivated by practical problems arising from the use of bioinformatics research tools such as genetic sequence databases. Concepts will be discussed in a weekly lecture and will be practiced via simple programming exercises using Python, an easy to learn and widely available scripting language.

General Information

	Course Information Sheet A.K.A. Prontuario (PDF)
	Course Outline (PDF)

Lectures Tuesday & Thursday (4:10 - 5:25) @ Stefani 228

	Lecture 1 - Administrivia, Course Overview, Brief PL History, PL design criteria (PDF)
	Lecture 2 - The Nature of Computing (PDF)
	Lecture 3 - Programming Language Specification and Translation (PDF)
	Lecture 4 - Programming Language Paradigms I - Low-level programming (PDF,HandwrittenNotes, MITSlides)

	Lecture 5 - Programming Paradigms II - Imperative Programming (e.g. Fortran) (PDF)
	Lecture 6 - Programming Paradigms III - Functional Programming (e.g. Scheme) (PDF)
	Lecture 7 - Programming Paradigms IV - Logic Programming (e.g. Prolog) (PDF)
	Lecture 8 - Subroutines and Control Abstraction (PDF)

Exams

	Exam 1:TBA (Topics, Practice, Solution, Stats)
	Exam 2: TBA (Topics, Practice, Solution, Stats)
	Exam 3:TBA (Topics, Practice, Solution, Stats)
	Final Exam: (Topics, Practice, Solution, Stats)

Problem Sets

	Problem Set 1. TBA (PDF, Solution)
	Problem Set 2. TBA (PDF, Solution)
	Problem Set 3. TBA (PDF, Solution)
	Problem Set 4. TBA (Doc, Solution)

Programming Assignments

	Programming Assignment 1. TBA (Word, PDF, Solution)
	Programming Assignment 2. TBA (Word, PDF, Solution)
	Programming Assignment 3. TBA (RefCode, Doc, Solution)
	Programming Assignment 4. TBA (RefCode, Doc, Solution)

Email Lists

	icom4995-profs
	icom4995-students (Subscribe) (Archives)
	icom4995-forum (staff & students)(Archives)

Software Development Tools

	Emacs for Windows (download)
	.emacs File (download)
	SPIM Simulator (home site, windows version)
	UC Berkeley SPIM including SPIM for Mac OS (home site, macOS X)
	X Server for Windows (download)
	Check you linux account User id (section 156, section 166)

Supplementary Readings

"The Nature of Computing". Bienvenido Velez. COMPEL 2002 Plenary Talk. (PDF)

RFC 1855: Netiquette Guidelines. ABSTRACT: This document provides a minimum set of guidelines for Network Etiquette (Netiquette) which organizations may take and adapt for their own use. As such, it is deliberately written in a bulleted format to make adaptation easier and to make any particular item easy (or easier) to find. It also functions as a minimum set of guidelines for individuals, both users and administrators. This memo is the product of the Responsible Use of the Network (RUN) Working Group of the IETF.

"Lambda: The Ultimate Imperative". Guy Steel and Gerald Sussman. MIT AI Lab Memo 353. (PDF)

Computability and Turing Machines

CS 110 Notes University of Alberta

Turing Machines in Stanford's Encyclopedia of Philosophy

Language References and Documentation

MIPS Assembly Language and SPIM

	"Assemblers, Linkers and the SPIM Simulator". This is Appendix A of Hennessy & Patterson, Computer Organization and Design: The Hardware/Software Interface. Coutersy of Morgan Kaufmann Publishers.
	SPIM/MIPS Instruction Set Sheet (PlainText)
	Useful website with lots of MIPS/SPIM documentation (click)

Fortran 77

	Getting Started with G77 (Windows)
	Gilberto Urroz's Fortran 77 page
	Professional Programmer's Guide to Fortran77 (HTML)
	Fortran Language Reference @ Sun Product Documentation (Web)

Scheme

	Scheme home site @ MIT
	Revised Report on The Algorithmic Language Scheme" (HTML)

Prolog

Prolog Tutorial (HTML)

Perl

Picking up Perl Tutorial (Available here in several formats)

	Pagina del curso ICOM4036 del Profesor Wilson Rivera (click)
	Introduction to Programming Languages by Anthony A. Aaby (HTML)