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.

Slicing Scientific Data

I've covered scientific software in previous articles that either analyzes image information or actually generates image data for further analysis. In this article, I introduce a tool that you can use to analyze images generated as part of medical diagnostic work.

Image Processing on Linux

I've covered several scientific packages in this space that generate nice graphical representations of your data and work, but I've not gone in the other direction much. So in this article, I cover a popular image processing package called ImageJ.

Solving Physics Problems on Linux

Several years ago, I wrote an article on using Elmer to solve complicated physics problems. Elmer has progressed quite a bit since then, so I thought it would be worth taking a fresh look at this simulation software.

Jmol: Viewing Molecules with Java

Let's dig back into some chemistry software to see what kind of work you can do on your Linux machine. Specifically, let's look at Jmol, a Java application that is available as both a desktop application and a web-based applet.