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Open access software for scientists

Good software is necessary for the modern scientist. Here, we review free software supported on multiple platforms. Not only is this all the software one needs for obtaining a graduate degree, but open software leads to open science that benefits everyone.

The glorified ecologist would be that patient naturalist carefully taking notes in the field, perhaps tracking muskoxen in Greenland or exploring the life history parameters affecting the invasiveness of thistles throughout the Americas. But, what happens after leaving the field? Modern ecologists will spend a significant amount of time using a personal computer. Data entry, statistics, writing, literature review, graphic design, communication, and planning are commonly done using specialized software. Both new and experienced ecologists will benefit from being aware of software available to them for free. Free is not something to be afraid of; all the software presented here is of the highest quality and comparable to software costing hundreds of dollars. In this age of open access and free knowledge for all, even the most fundamental tools of science are becoming increasingly available to anybody with a computer and internet connection. This article will provide a short survey of some tools available to us.

Software

Use

Replaces

Platforms

Ubuntu

Operating system

Windows and OS X

 

LibreOffice

Word processor, spreadsheets, presentations

Microsoft Office

Linux, OS X, Windows

R and RStudio

Statistics and graphics

SAS, SPSS, etc.

Linux, OS X, Windows

Mendeley Desktop

Reference manager

Endnote

Linux, OS X, Windows

GIMP

Bitmap image manipulation

Photoshop

Linux, OS X, Windows

Inkscape

Vector graphics creation and manipulation

Illustrator

Linux, OS X, Windows

ImageJ

Image measurements

 

Linux, OS X, Windows

QGIS

Geographic information systems

ArcGIS

Linux, OS X, Windows

 

The operating system (OS) is the basic environment that connects human to machine and provides much of the experience of using a computer. Most of us are familiar with Windows and Mac OS X, and while we may bicker about which is better, in fact you can do pretty much anything on either. Linux is open source, meaning its code is readily available to anybody. Over time, a vast number of people have given their time and intellect to craft a very capable, efficient, and secure operating system. However, Linux has a reputation as an operating system only for geeks and of being too hard to learn or use for normal computer users. With the advent of the Ubuntu version of Linux this is no longer true. Ubuntu is truly an OS for the masses.  You can try Ubuntu by running it from a USB drive without affecting your primary OS, and if you want to commit a little more you can easily set up a dual boot where you may choose between Ubuntu or your other OS when turning on your computer. To try it is completely risk free, and you may be pleasantly surprised.

LibreOffice is the extant branch of the discontinued OpenOffice that some of you may be familiar with. It has almost all the features of Microsoft Office, including a word processor, a spreadsheet program, and a program for making presentations. It does not, however, have a replacement of OneNote (see Tech Corner in Notes from the Field Volume 10 Issue 1). The only drawback to using LibreOffice is that most people are using the Microsoft products so you may run into formatting issues, and the use of tracking changes and adding comments can conflict between the two products. Convincing your colleagues to also use LibreOffice is one way around that issue.

Most new ecologists are probably acquainted with the R statistical package, though SAS and its companions remain popular. R can be used in conjunction with a vast library of additional packages to perform most statistical tests, as well as other computationally intensive procedures, such as genome wide association studies (GWAS) and simulation modeling. R is also fabulous for data manipulation by indexing and the creation of custom functions, and R benefits from a vast user community. You can rest assured that if you have a question, you are probably not the first person to ask it, and a simple web search will yield an answer. R can make fantastic graphics, from bar graphs to networks to 3D landscapes.

R itself is a simple command line interface, so it is augmented greatly by RStudio that acts as a sort of wrapper on top of R. RStudio allows the creation of projects within which your code and files (workspace) are automatically saved. RStudio also offers point and click abilities for opening data files and loading packages. Install RStudio after installing R and you will save yourself a lot of pain and frustration. RStudio has been quickly adopted by many ecologists because it makes our lives easier by putting everything we need to do our stats in one place.

Mendeley is a reference manager and PDF organizer. You can save PDFs for journal articles in a watched folder and Mendeley will automatically try to take information like authors and journal name from information embedded in the PDF itself. It will store this information in your library and you can even open and read PDFs within Mendeley. Mendeley has plugins for both Microsoft Office and LibreOffice that allow you to insert citations from Mendeley, which can then be used to automatically generate the works cited list. Formatting is available for a variety of journals. Mendeley also offers cloud storage of your PDF library which provides a convenient backup. Mendeley has iOS and Android apps that can sync your library to provide on-the-go reading on tablets.

GIMP is an image manipulation program. Basic uses include accurately scaling and cropping photographs. This can be done in batch mode. Images can be manipulated with regards to brightness, contrast, and colors, as well as through the use of many plugins that may give a desired effect. GIMP can be used to add text to photographs for making diagrams. Use GIMP to make publication ready images for presentations or manuscripts.

Inkscape is used for making vector graphics. Vector graphics are recommended to use when creating a figure or diagram from scratch because vectors can be scaled to any size without loss of quality. Inkscape can generate diagrams like flow charts with ease, or make more advanced graphics depicting experimental setups or results. Visit the online version of this article for some examples.

ImageJ is an image manipulation program with a twist: it was designed by the NIH to be used for taking measurements from images. It can be extended using Java and there are already many plugins available. For example, I use a plugin called ObjectJ to measure angles and diameters from images taken of maize roots. Others use it for measuring bacterial or fungal colonies, or even for measuring canopy cover in crop stands. The possibilities are endless, so it’s worth asking yourself if some routine measurement you do could be done from images.

For those of you using geographic information systems, you might find QGIS to be a reasonable alternative to ArcGIS for making maps and extracting information from geographic data.

This article has outlined the use of several popular programs that are freely available. For most students, this software would be enough to complete a PhD. Free software embodies the spirit of an equitable sharing of knowledge. Open software leads to open science that can benefit the lives of us all.