The next generation of bioinformatics programs will have to (1) support the interoperation of rapidly evolving and sometimes brittle, computational software developed in a variety of scientific fields and programming languages; (2) support the integration of data across biological experiments and scales; (3) adapt to rapidly evolving hardware environments; and (4) empower users by allowing them to carry out operations unanticipated by the programmers such as trying new combinations (more…)

What is Computer Programming? How do People program Computers? Some mathematicians like to claim that “all programming languages are in principle equally powerful” (this is, essentially, the idea of ‘Turing Completeness’). However, this obscures the fact that there may be vast differences between different languages (Python, FORTRAN, C, Matlab, etc.) in terms of how easy it is for the programmer to get the job done using a particular tool. The key insight is: Programming is a Human Activity! (more…)

Created in 1989 and launched in 1991 by Guido Van Rossum ? Ideas from his work on ABC language, Modula-2+, and Modula-3 ? What is it? ? “Python is an interpreted, interactive, object-oriented programming language. It incorporates modules, exceptions, dynamic typing, very high level dynamic data types, and classes.”[1] ? Strongly Typed: ? A language does not allow (more…)

General rules for calling functions 9 • Positional arguments come before keyword arguments • The value of each argument must be given at most once >>> def f(a = 2):
… print a … >>> f(a = 30, 0) File ““, line 1 SyntaxError: non-keyword arg after keyword arg General rules for calling functions 10 • Positional arguments come before keyword arguments • The value of each argument must be given (more…)

This tutorial will teach you how to write MRG Messaging applications in C++, Python, or Java (using the JMS API). To run the programs in this tutorial, you will need to download and install MRG Messaging and be able to start the broker and run a sample application. These steps are described in Chapter 3, Installing MRG Messaging, and described in more depth in the MRG Messaging Installation Guide. MRG Messaging (more…)

This document contains some tutorials for the Python programming language. These tutorials accompany the free Python classes taught by the New Mexico Tech Computer Center. Another good tutorial is at the Python website 3 . 1.1. Starting Python in conversational mode This tutorial makes heavy use of Python’s conversational mode. When you start Python in this way, you will see an initial greeting (more…)

1.1 First things first So, you’ve never programmed before. As we go through this tutorial I will attempt to teach you how to program. There really is only one way to learn to program. You must read code and write code. I’m going to show you lots of code. You should type in code that I show you to see what happens. Play around with it and make changes. The worst that can happen is that it won’t work. (more…)

The TCP/IP network protocol suite is the standard method for intermachine communication. Though originally integral only to the UNIX operating system, its usage spread to all OS types, and it is the basis of the entire Internet. This document will briefly introduce the subject of TCP/IP programming using the Python language. See http://heather.cs.ucdavis.edu/˜matloff/Networks/Intro/ NetIntro. (more…)

1 Why Use Threads? Threads play a major role in applications programming today. For example, most Web servers are threaded, as are many Java GUI programs. Here are the major settings in which using threads has been founded convenient and/or efficient: • Programs with asynchronous events: Here the program must be ready for various events, but does not know the order in which they might occur. (more…)