developing bioinformatics computer skills - cynthia gibas, per jambeck

[...]... software and peripheral devices for Linux is improving as the popularity of the operating system increases However, it can't (yet) go head-to-head with the consumer operating systems in these areas Linux is no more difficult to maintain than a normal PC operating system, once you know how, but the skills needed and the problems you'll encounter will be new at first As of this writing, my desktop computer. .. time and resources 1.7 How Can I Configure a PC to Do Bioinformatics Research? Up to now you've probably gotten by using word-processing software and other canned programs that run under user-friendly operating systems such as Windows or MacOs In order to make the most of bioinformatics, you need to learn Unix, the classic operating system of powerful computers known as servers and workstations Most scientific... Chapter 12 contains examples of how to use Perl as a driver to make your favorite program process large volumes of data using your own computer 1.9 Can I Learn a Programming Language Without Classes? Anyone who has experience with designing and carrying out an experiment to answer a question has the basic skills needed to program a computer A laboratory experiment begins with a question, which evolves... molecular modeling The experience of learning one of these packages makes it much easier to learn to use other software quickly You should be comfortable working in a command-line computing environment Working in Linux or Unix will provide this experience You should have experience with programming in a computer language such as C/C++, as well as in a scripting language such as Perl or Python There are... that can be tested for truth based on the results of an experiment or experiments The processes developed to test the hypotheses are analogous to computer programs The essence of an experiment is: if you take system X, and do something to it, what happens? The experiment that is done must be designed to have results that can be clearly interpreted Computer programs must also be carefully designed so that... years by the development of the Perl language Perl, referred to by its creator as "the duct tape of the Internet, and of everything else," began its evolution as a scripting language optimized for data processing It continues to evolve into a full-featured programming language, and it's practical to use Perl to develop prototypes for virtually any kind of computer program Perl is a very flexible language;... community at the gene level isn't being tackled by developing a nomenclature It's being attacked directly with computers and databases from the start The evolution of computers over the last half-century has fortuitously paralleled the developments in the physical sciences that allow us to see biological systems in increasingly fine detail Figure 1-4 illustrates the astonishing rate at which biological... to get the computer to do what you want 1.7.1 Why Use Unix or Linux? Setting up your computer with a Linux operating system allows you to take advantage of cutting-edge scientific-research tools developed for Unix systems As it has grown popular in the mass market, Linux has retained the power of Unix systems for developing, compiling, and running programs, networking, and managing jobs started by... instructions to the computer and must think through, in advance, what different types of results mean and what the computer should do with them A large part of practical computer programming is the ability to think critically, to design a process to answer a question, and to understand what is required to answer the question unambiguously Even if you have these skills, learning a computer language isn't... physics, computer science, and engineering Figure 1-2 shows how quantitative science intersects with biology at every level, from analysis of sequence data and protein structure, to metabolic modeling, to quantitative analysis of populations and ecology Figure 1-2 How technology intersects with biology Bioinformatics is first and foremost a component of the biological sciences The main goal of bioinformatics . Analysis with Perl 305 12.1 Why Perl? 305 12.2 Perl Basics 306 12.3 Pattern Matching and Regular Expressions 312 12.4 Parsing BLAST Output Using Perl 313 12.5 Applying Perl to Bioinformatics. hypotheses. In the last two decades, both personal computers and supercomputers have become accessible to scientists across all disciplines. Personal computers have developed from expensive novelties. using computers productively in your research. Audience for This Book Most biological science students and researchers are starting to use computers as more than word-processing or data-collection