All resources described in this document are free and platform agnostic unless otherwise noted. This is not an exhaustive list by any means. It is meant to provide a jump start on resources available to graduate students who are conducting psychological research at Penn State.
Homepage: http://osdoc.cogsci.nl
GitHub: https://github.com/smathot/OpenSesame
OpenSesame is a python-based program for creating experiments. It has a number of capabilities built in, such as image and sound presentation, keyboard, mouse, and voice response, and questionnaire forms. OpenSesame also has the ability to be (essentially) endlessly extended with custom python scripts.
OpenSesame uses a graphical user interface (GUI) for experiment building, which means you can use point-and-click to build your experiments. Extending OpenSesame with python requires scripting code.
Homepage: http://www.psychopy.org
Github: https://github.com/psychopy/psychopy
PsychoPy is a python-based program for experiment building. It has both a GUI and a code editor. Unlike OpenSesame, PsychoPy uses specific python libraries built specifically for behavioral experimentation. Thus, it is more heavily based in programming, but also allows for greater manipulation, control, and extension. This program may be better if the experiment is abnormal or complex. PsychoPy does offer a GUI for building experiments, but fine-tuned control requires python coding knowledge using its “coding editor”.
The developers of PsychoPy are also attempting to make experiments built using this program deployable online. As of now, this is considered in-development and experimental.
Homepage: http://www.jspsych.org
GitHub: https://github.com/jspsych/jsPsych
A JavaScript library for creating experiments. It has no GUI, so all experiments are coded in HTML files. It has the ability to deploy experiment applications online (if you have a server). PsychoPy uses jsPsych as the backend for deploying experiments online.
A service that provides the ability to create simple online experiments and questionnaires. The maintainer of this service also provides free server use for data collection and storage. There is an academic paper describing the service.
https://pennstate.qualtrics.com/
As a Penn State graduate student you are entitled to a free Qualtrics account that allows for up to two active surveys at any time.
https://cran.r-project.org
https://www.rstudio.com
R is a programming language used for statistical analyses and graphics. R’s strength is its incredibly diverse number of packages that are available for download. Almost any type of analysis for any type of data in any format can be analyzed using a combination of R and one of its packages. You can browse R packages here to get a sense for the amount available.
RStudio is an Integrated Development Environment (IDE) for R. It enhances the standard R program by providing an easy and visually appealing way to organize R code, R files, projects, and R itself into a single space. You can run RStudio in your browser through a server operated by Penn State’s Institute for CyberScience.
https://rmarkdown.rstudio.com/
R Markdown documents are fully reproducible. Use a productive notebook interface to weave together narrative text and code to produce elegantly formatted output. Use multiple languages including R, Python, and SQL.
Shiny is an R package that makes it easy to build interactive web apps straight from R. You can host standalone apps on a webpage or embed them in R Markdown documents or build dashboards. You can also extend your Shiny apps with CSS themes, htmlwidgets, and JavaScript actions.
https://jasp-stats.org https://github.com/jasp-stats/jasp-desktop
A statistical program with a GUI (like SPSS) that allows for easily computing both frequentist and Bayesian analyses. It is built using R and some R packages as a backend.
https://www.gnu.org/software/octave/
Powerful mathematics-oriented syntax with built-in plotting and visualization tools. A free alternative to Matlab. Most Matlab scripts can be run using this software.
Plotly is a service for creating interactive data visualization. The service makes it easy to share these visualizations online with others. It also has an excellent R and python extension for transforming visualizations your create in these programs into interactive visualizations.
Another service for interactive data exploration and visualization. Offers an online component for sharing visualizations with collaborators.
An opensource text editor with many extensions. You can run code from a variety of languages, browse files on your system, and create a reproducible workflow using just ATOM and its extensions.
A text editor that is similar in scope to ATOM, provides lots of useful extensions, but is not as actively maintained or developed.
https://www.latex-project.org
http://www.texstudio.org
LaTex is a typesetting program language for technical and scientific documentation, manuscripts, articles, and books. It has many useful functions for providing high quality style, equations, and references for these types of documents.
TexStudio is one of many programs designed specifically for writing and creating LaTex documents.
Homepage: https://git-scm.com
Homepage: https://github.com
git is a program that tracks “versioning,” or how a document changes over time. This is an important part of good data science (check out why here). git is a command line program. GitHub is a service that provides a GUI for git, as well as a service for syncing your versioned projects across devices.
Students and teachers can get a free GitHub pro account. Pro accounts allow your repositories (repos) to be private.
Beginners can get to know git in this interactive tutorial. If you prefer to read, GitHub has provided an excellent introductory tutorial.
Penn State students have unlimited storage on Box with their PSU account. Box has partnered with Penn State and the Office of Research Protections to allow for research data to be stored on Box, even storage of Protected Health Information (i.e., sensitive data). You can read more about the rules and regulations for storing sensitive data on Box here.
GIMP is an image editor that can be considered a free alternative to PhotoShop. Because GIMP is opensource and community-driven, it has a lot of plugins that allow extending GIMP beyond just simple-to-moderate image editing.
Program for creating, editing, and manipulating vector graphics (e.g., .svg, .pdf). Vector graphics are images based on location, position, and attributes of points in an an image, rather than pixels. This allows for a vector graphic to be of much higher quality than a bitmap (e.g., .jpg,.png,.tiff). Thus, vector graphics maintain their resolution and graphical positions even when changing image size/dimensions (e.g., enlarging or shrinking an image to fit a presentation). Most journals require figures to be submitted either at very high resolution or as a vector graphic.
https://www.imagemagick.org/script/index.php
Program to create, edit, compose, or convert bitmap images. Typically this is done from the command line, but you can download extensions to integrate with other languages such as R, python, or C++.
http://www.xnview.com/en/xnconvert/
A program that allows for the batch manipulation of images. Useful if you have many bitmap photos that you need to grayscale, resize, or crop in a similar manner, for example.
Command line tools to record, convert and stream audio and video. This program has a learning curve, but is also very powerful. Useful for batch processing videos.
Comprehensive comparison of different softwares. Below are a few of the more popular programs and personal favorites.
A reference manager to organize, sort, and annotate all of your academic articles. Provides cloud storage to sync libraries across devices. It also integrates with Microsoft Word and LibreOffice via plugins so you can automatically insert and appropriate cite research as you write.
An alternative reference manager. Integrates well with your web browser to easily store references from the web. Syncs library across devices, and provides ability to insert citations into various documents (Word, emails, etc.).
A bibliography reference manager that is formatted in BibTex, the standard way LaTex documents cite bibliographies/references. Because of this, it works particularly well with TexStudio for an optimized workflow. It also has the ability to automatically search for the full text of an article and import it.
http://www.readcube.com/papers/
A non-free ($49.99 for students) PDF and reference manager. Recently were bought out and switched to a subscription model.
A non-free ($20 for students from PSU software store) reference manager. Works well cross platform, and has integration with MS Word.
PASS homepage: https://explorer.pass.psu.edu/
Personal homepage: http://personal.psu.edu/
Personal webspace provided by Penn State to host files. Must apply for webspace.
Your personal webspace has the ability to host files accessible either to just you (www_protected/) or the world (www/). If you upload HTML files, you can host dynamic web content. Theoretically, you can code experiments in HTML and host them on your personal webspace. For example, see a working example of the CyberBall task on my webspace.
Provides access to several popular applications (MS Office, MatLab, SAS) through your browser.
https://www.adobe.psu.edu/creative-cloud/
As a Penn State Student, you have access to download and install the Adobe Creative Cloud programs at no cost to you. This suit of programs include Adobe Acrobat Pro, Photoshop, and Dreamweaver.
http://software.psu.edu/news/microsoft-no-cost-software
As a full time Penn State student, you have the opportunity to receive Microsoft Office (for both Windows and Macs) and Microsoft Windows 10 for free. Instructions are provided at the link above.
https://ics.psu.edu/advanced-cyberinfrastructure/
Provides advanced computing needs for researchers that require specialized and/or high-performance computing. They maintain a variety of programs, and offer a tutorial for connecting to their system.
Some labs have recently switch to ICS server space with the closure of the CLA “R drive” space. If your lab has opted for ICS server space, you can access your lab drive space through the online ICS portal, which also allows students to access other interactive apps and servcies including MATLAB, SPM, and arcGIS.
If your lab does not have access to the ICS server, you can request a free ICS account on the the ICS webstite.
Highly discounted software for students, including (but not limited to):
SAS ($47)
minitab ($16)
Wolfram ($23)
ArcGIS (Free)
Matlab ($18)
NVivo ($50)
Endnote ($40)
The library offers a variety of free resources for students other than books, including free book scanning, and even free 3D printing for smaller projects, and affordable prices for larger ones.
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