March 15, 2017 by Species Ecology
The Power of Linux and its Utilization- Free and Open Source Software (FOSS) Resources for Wildlife Ecologists & Conservation Biologists
I want to tell you a story. No, not the story of how, in 1991, a guy from Finland called Linus Torvalds wrote the first version of the Linux kernel. You can read that story in lots of Linux books. Nor am I going to tell you the story of how, some years earlier, Richard Stallman began the GNU (GNU is Not Unix hence it is recursive acronym) Project to create a free Unix-like operating system. That’s an important story too, but most other Linux books have that one, as well. No, I want to tell you the story of how you can take back control of your computer. When I began working with computers as a school student in the mid 1980s, there was a revolution going on. The invention of the microprocessor had made it possible for ordinary people like you and I to actually own a computer. It’s hard for many people today to imagine what the world was like when only big business (American Telegraph and Telephone-AT&T) and big government (Pentagon or FBI) ran all the computers. Let’s just say you couldn’t get much done. Today, the world is very different. Computers are everywhere, from iPhone to giant data centers to everything in between. In addition to ubiquitous computers, we also have a ubiquitous network connecting them together. This has created a wondrous new age of personal empowerment and creative freedom, but over the last couple of decades something else has been happening. A single giant corporation (guess who?) has been imposing its control over most of the world’s computers and deciding what you can and cannot do with them.
Fortunately, people from all over the world are doing something about it. They are fighting to maintain control of their computers by writing their own software. They are building Linux. Many people speak of “freedom” with regard to Linux, but I don’t think most people know what this freedom really means. Freedom is the power to decide what your computer does, and the only way to have this freedom is to know what your computer is doing. Freedom is a computer that is without secrets, one where everything can be known if you care enough to find out.
Why Use the Command Line?
Have you ever noticed in the movies when the “super hacker”—you know, the guy who can break into the ultra-secure military computer in under 30 seconds—sits down at the computer, he never touches a mouse? It’s because movie makers realize that we, as human beings, instinctively know the only way to really get anything done on a computer is by typing on a keyboard. Most computer users today are familiar with only the graphical user interface (GUI) and have been taught by vendors and pundits that the command line interface (CLI) is a terrifying thing of the past. This is unfortunate, because a good command line interface is a marvelously expressive way of communicating with a computer in much the same way the written word is for human beings. It’s been said that “graphical user interfaces make easy tasks easy, while command line interfaces make difficult tasks possible,” and this is still very true today. Since Linux is modeled after the Unix family of operating systems, it shares the same rich heritage of command line tools as Unix. Unix came into prominence during the early 1980s (although it was first developed a decade earlier), before the widespread adoption of the graphical user interface and, as a result, developed an extensive command line interface instead.
Linux on Conservation Science
If your work pivots around ecological science encompassing the broader rubric of conservation biology, you are bound to carry out research that is deeply grounded to mathematical modeling. The 21st century modern ecologists cannot escape the hard core mathematical programming in the direction of estimating the ecological parameters; be it demographic or niche model of endangered vertebrates or phylogenetic analysis of species that is literally extinct in the wild. Modern wildlife biologists require tools the broadly falls under the mathematical underpinnings of numerical modeling: the tasks that require strong command of computer programming language. For example, if you wish to conduct a ecological research to estimate the distribution parameter of tigers in the Sundarbans mangrove ecosystem in Bangladesh, you would need to require mandatory skills in environmental/ecological statistics, first and second derivative of calculus, matrix algebra, spatial, algebraic and statistical modeling and so forth. None of these areas are possible to explore or to understand without the power and freedom of computers that would allow you to perform advance mathematical programming tasks or to help you generate visually engrossing highly sophisticated graphs. If you are from tropical developing nations where biodiversity is most rich but economical resources are most poor, you face a dwindling situation to strike the right balance to manage meager fund that are at your disposal against the backdrop of prioritizing the tasks that you can do as a serious wildlife ecologist without compromising the quality and the breadth of the rigorous hard core science of ecology, wildlife biology, and mathematics. Unless you are backed up with ‘gigantic corporate based conservation research for lets say, transnational corporations protecting their vested interests, your work will largely dominate by the key issue of how good you are at managing your scarce funding hence to publish your invaluable research work into ‘high impact’ journals (e.g. Journal of Wildlife Management or Conservation Biology). Evidently you would require software that have the utilities, tools and the power to present you with robust mathematical algorithms which at times you can extrapolate, overlay in spatial and temporal scale, and generate stochastic models and scenarios under conceptually unified rigorous statistical framework. Linux has the power and the necessary tool to provide you with the mathematical packages and the programming power that would enable you to accomplish your research work without taxing your scarce research grant. Yes, Linux packages comes under GNU (a recursive acronym that means GNU is Not Unix)-GPL (General Public License) developed under Free and Open Source Software (FOSS) project that was founded by legendary computer scientist Richard Stallman back in 70s. Therefore you are not liable of ‘copyright infringe’ nor you are liable of getting harassed by ‘corporations as such Microsoft’ that takes up all your hard earn cash for their own vested profit. In Linux Operating System (OS), everything that comes with it is free and its all neatly packaged with most of the Linux distributions that are at your disposal. Below are the necessary GNU Linux Distribution based software packages that would help wildlife ecologist and conservation biologist alike to carry out solid hard core statistical, algebraic, spatial and temporal modeling with the power of geographic information system (GIS) based structured query language (SQL) without paying thousands of dollars under Windows based operating system. All these Linux Packages are free.
For ecological numeration of statistical modeling and spatial and temporal map production use R programming environment. For wildlife science, ecology, natural resource economics, and conservation biology that strongly integrate the tools, formula, principles and theorems of mathematical modeling including matrix algebra, calculus, trigonometry, analytic geometry, stochastic simulation, Monte Carlo simulation, Markov Chain models, Boolean algebra you can use both R and Python programming language. If you already use Java programing then Python would be very easy for you to pick up. For Species Distribution Model (SDM) that borrows tools from statistics and other branches of Mathematics: Python programming language, R programming and Octave programming environment is ideal along with QGIS for GIS based modeling and mapping in large ecological or hydrological landscape.
All these highly sophisticated mathematical software comes under GNU-GPL Linux free of cost and users are free to distribute, copy and manipulate the scripts indefinitely. I am providing top five Linux distributions (also known as Linux OS) that I would of benefit to serious wildlife ecologists and wildlife science students.
1. Debian Linux
3. Ubuntu Linux
5. Linux Mint