Science

Antennas in Linux

For this article, I want to introduce a piece of software I've actually used recently in my own work. My new day job involves studying the ionosphere using an instrument called an ionosonde. This device is basically a giant radio transmitter that bounces radio waves off the ionosphere to see its structure and composition. Obviously, an important part of this is knowing the radiation pattern of the various transmitters and receivers.

Weekend Reading: Science

Mathematics and science tools often depend on cluster and high performance computing, both undeniably Linux strengths. Couple that with the maturity of the science tools available for Linux and you get a lot of computational bang for your buck. Join us this weekend as we review physics, chemistry, biology, astronomy, and other science programs for Linux. Open Science Means Open Source--Or, at Least, It Should Why open source was actually invented in 1665.

Astronomy Software by Any Other Name

In this article, I introduce another option available for the astronomers out there—specifically, Cartes du Ciel, also known as SkyChart. Similar to other larger astronomy programs, you can use SkyChart from the desktop to the observatory.

Modeling the Entire Universe

For this article, I want to look at the largest thing possible, the whole universe. At least, that's the claim made by Celestia, the software package I'm introducing here. In all seriousness though, Celestia is a very well done astronomical simulator, similar to other software packages like Stellarium. Celestia is completely open source and is licensed under the GPL.

Using Linux for Logic

I've covered tons of different scientific applications you can run on your computer to do rather complex calculations, but so far, I've not really given much thought to the hardware on which this software runs. So in this article, I take a look at a software package that lets you dive deep down to the level of the logic gates used to build up computational units.

Weekend Reading: Python

Python is easy to use, powerful, versatile and a Linux Journal reader favorite. We've round up some of the most popular recent Python-related articles for your weekend reading. Introducing PyInstaller by Reuven M. Lerner: Want to distribute Python programs to your Python-less clients? PyInstaller is the answer. Bytes, Characters and Python 2 by Reuven M. Lerner: Moving from Python 2 to 3? Here's what you need to know about strings and their role in in your upgrade. Introducing Python 3.7's Dataclasses by Reuven M. Lerner: Python 3.7's dataclasses reduce repetition in your class definitions. Examining Data Using Pandas by Reuven M. Lerner: You don't need to be a data scientist to use Pandas for some basic analysis. Multiprocessing in Python by Reuven M. Lerner: Python's "multiprocessing" module feels like threads, but actually launches processes.

A Look at KDE's KAlgebra

Many of the programs I've covered in the past have have been desktop-environment-agnostic—all they required was some sort of graphical display running. This article looks at one of the programs available in the KDE desktop environment, KAlgebra. You can use your distribution's package management system to install it, or you can use Discover, KDE's package manager. After it's installed, you can start it from the command line or the launch menu. When you first start KAlgebra, you get a blank slate to start doing calculations.

Astronomy on KDE

I recently switched to KDE and Plasma as my main desktop environment, so I thought I'd start digging into some of the scientific software available on KDE. First up is KStars, the desktop astronomy program. KStars probably won't be installed with the standard KDE desktop, so you may need to install it. If you're using a Debian-based distribution, you can install KStars with the following command:

Atomic Modeling with GAMGI

For this article, I'm moving back into the realm of chemistry software—specifically, the General Atomistic Modelling Graphic Interface, or GAMGI. GAMGI provides a very complete set of tools that allows you to design and visualize fairly complex molecules. GAMGI has the special ability to make creating repeating structures much easier, which is handy when you're trying to create crystalline structures.

Drawing Feynman Diagrams for Fun and Profit with JaxoDraw

I've been covering chemistry software in my last few articles, so this time, I decided to move to physics and introduce a package called JaxoDraw. In physics, there's a powerful technique for visualizing particle interactions at the quantum level. This technique uses something called Feynman diagrams, invented by physicist Richard Feynman. These diagrams help visualize what happens when one or more particles have some kind of interaction.

A Good Front End for R

R is the de facto statistical package in the Open Source world. It's also quickly becoming the default data-analysis tool in many scientific disciplines. R's core design includes a central processing engine that runs your code, with a very simple interface to the outside world. This basic interface means it's been easy to build graphical interfaces that wrap the core portion of R, so lots of options exist that you can use as a GUI.

Evolving Your Own Life: Introducing Biogenesis

Much of the software I've covered in the past has focused on engineering, chemistry or physics. However, a growing number of software packages are being written to apply computational resources to problems in biology. So in this article, I want to look at one particular package for biology named Biogenesis.

Using Python for Science

Introducing Anaconda, a Python distribution for scientific research. I've looked at several ways you could use Python to do scientific calculations in the past, but I've never actually covered how to set up and use Python itself in a way that makes scientific work easier. Anaconda does just that.

Visualizing Molecules with Python

Introducing PyMOL, a Python package for studying chemical structures. I've looked at several open-source packages for computational chemistry in the past, but in this article, I cover a package written in Python called PyMOL.

Emacs for Science

I typically cover software packages that do actual calculations to advance scientific knowledge, but here I'm exploring a slightly stranger tool in the arsenal of scientific computation.