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50 posts found.
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Gephi

January 20, 2017 by Laurie Parker
Categories: Design & Visualization

Availability: Labs | Download
Comparable: yEd Graph Editor

Gephi logoGephi is an open-source visualization and exploration software for graphs and networks. The software can be used for exploratory data analysis, link analysis, social network analysis, and biological network analysis. Users can interact with the representation and manipulate the structures, shapes, and colors to reveal patterns. View Gephi’s full features here.

Mendeley

February 08, 2016 by Laurie Parker
Categories: Productivity & Utility

Availability: Free Download
Comparable: Zotero, EndNote

Mendeley logoMendeley is a free reference manager and social network that helps users organize their research, collaborate with others, and discover new research. Search and sort references, documents and notes in one place. Users can read, annotate and add sticky notes to PDFs.

Mendeley generates citations and bibliographies in the desired style and is compatible with Microsoft Word, LibreOffice and BibTeX. Reading lists, references or full text articles can be shared either publicly or privately. Groups can be created to work on research assignments, share feedback, and write papers. Published research can be showcased with colleagues, peers, and classmates.

The program combines Mendeley Desktop, a PDF and reference management application with Mendeley Web, an online social network for researchers. Users can store all of their research in one place and access across devices. Mendeley requires the user to store all basic citation data on its servers and storing copies of documents is at the user’s discretion.

Mendeley is available for Mac, Windows, and Linux and provides 2GB of free online storage to automatically back up and synchronize the library across desktop, web and mobile.

SOFA Statistics

July 30, 2015 by Andy Voelker
Categories: Analysis & Modeling

big_brown_sofa

Availability: Free Download
Comparable: SAS, SPSS, Stata

SOFA Statistics is an open-source statistical package, with an emphasis on ease of use, learn as you go, and beautiful output. The name stands for Statistics Open For All. It has a graphical user interface and can connect directly to MySQL, PostgreSQL, SQLite, MS Access (mdb), Microsoft SQL Server, and CUBRID. Data can also be imported from CSV and Tab-Separated files or spreadsheets (Microsoft Excel, OpenOffice.org Calc, Gnumeric, Google Docs). The main statistical tests available are Independent and Paired t-tests, Wilcoxon signed ranks, Mann–Whitney U, Pearson’s chi squared, Kruskal Wallis H, one-way ANOVA, Spearman’s R, and Pearson’s R. Nested tables can be produced with row and column percentages, totals, sd, mean, median, lower and upper quartiles, and sum. Simple but dynamic bar charts (freq or means), clustered bar charts (freq or means), pie charts, single or multiple line charts (freq or means), area charts (freq or means), histograms, scatterplots, and box and whisker plots are available. It is also possible to create chart series.

Installation packages are available for several Operating Systems such as Microsoft Windows, Ubuntu,ArchLinux, Linux Mint, and Mac OS X (Leopard upwards).

SOFA Statistics is written in Python, and the widget toolkit used is wxPython. The statistical analyses are based on functions available through the Scipy stats module.  Analysis and reporting can be automated using Python scripts – either exported directly from SOFA Statistics or manually written.

Tags: satatistics

Zotero

July 30, 2015 by Andy Voelker
Categories: Productivity & Utility

zoteroAvailability: Free Download
Comparable:  EndNote

Zotero is free and open-source reference management software to manage bibliographic data and related research materials (such as PDF files). Notable features include web browser integration, online syncing, generation of in-text citations, footnotes and bibliographies, as well as integration with the word processors Microsoft Word,LibreOffice, OpenOffice.org Writer and NeoOffice. It is produced by the Center for History and New Media of George Mason University (GMU).

Zotero is the only research tool that automatically senses content in your web browser, allowing you to add it to your personal library with a single click. Whether you’re searching for a preprint on arXiv.org, a journal article from JSTOR, a news story from the New York Times, or a book from your university library catalog, Zotero has you covered with support for thousands of sites.

Zotero collects all your research in a single, searchable interface. You can add PDFs, images, audio and video files, snapshots of web pages, and really anything else. Zotero automatically indexes the full-text content of your library, enabling you to find exactly what you’re looking for with just a few keystrokes.

Zotero can be installed as a browser plugin for the popular Firefox browser or as a standalone program with browser extensions for Chrome, Safari, and Firefox.

Tags: endnote

Gramps

July 14, 2015 by Andy Voelker
Categories: Analysis & Modeling

Gramps_LogoTypeAvailability: Free Download
Comparable:  

 Gramps is an open source genealogical tool that is intuitive for hobbyists and feature rich for professional genealogists.  It is backed by an open community that supports research and is created and governed by professional genealogists.  Gramps will allow a user to track people, families, relationships, places, sources, citations, ancestry, media, history, and other information.  It also allows a user to generate reports on ancestors or descendants of an individual.  Translations exist for 31 different languages.  Gramps is available for Windows, Mac, Linux, and BSD.

GanttProject

April 10, 2015 by Andy Voelker
Categories: Productivity & UtilityProject Management

ganttproject

Availability: Free Download
Comparable: Project, Trello

GanttProject is open source Java based, project management software that runs under the Windows,Linux and Mac OS X operating systems.  It features most basic project management functions like a Gantt chart for project scheduling of tasks, and doing resource management using resource load charts. It does not have advanced features like cost accounting, message and document control. It has a number of reporting options (MS Project, HTML, PDF, spreadsheets).

Tags: ganttproject

Pixar Renderman

April 02, 2015 by Andy Voelker
Categories: Analysis & ModelingMultimedia
pixar-rendermanAvailability: Free Download
Comparable: After Effects, Blender

RenderMan is produced by Pixar and is used to render all of their in-house 3D animated movie productions. It is also available as a commercial product licensed to third parties. RenderMan has been used in creating digital visual effects for Hollywood blockbuster movies such as Titanic, the Star Wars prequels, and The Lord of the Rings.

On May 30, 2014, it was announced that Pixar would be offering a free non-commercial version of RenderMan that became available to download as of March 23, 2015.

VLC Media Player

March 18, 2015 by Andy Voelker
Categories: Multimedia

vlc-logo

Availability: Free Download
Comparable: Quicktime

VLC media player (commonly known as VLC) is a portable, free and open-source, cross-platform media player and streaming media server written by the VideoLAN project.

VLC media player supports many audio and video compression methods and file formats, including DVD-Video, video CD and streaming protocols. It is able to stream media over computer networks and to transcode multimedia files.

The default distribution of VLC includes a large number of free decoding and encoding libraries, avoiding the need for finding/calibrating proprietary plugins.  It also gained distinction as the first player to support playback of encrypted DVDs on Linux and OS X.

Tags: media player

Celestia

March 18, 2015 by Andy Voelker
Categories: Analysis & ModelingDesign & Visualization
Availability: Free Download
celestiaComparable: Google Earth, Starry Night Pro, Stellarium

Celestia is a free space simulation that lets you explore our universe in three dimensions. Celestia runs on Windows, Linux, and Mac OS X.

Unlike most planetarium software, Celestia doesn’t confine you to the surface of the Earth. You can travel throughout the solar system, to any of over 100,000 stars, or even beyond the galaxy.  All movement in Celestia is seamless; the exponential zoom feature lets you explore space across a huge range of scales, from galaxy clusters down to spacecraft only a few meters across. A ‘point-and-goto’ interface makes it simple to navigate through the universe to the object you want to visit.  Celestia is expandable. Celestia comes with a large catalog of stars, galaxies, planets, moons, asteroids, comets, and spacecraft. If that’s not enough, you can download dozens of easy to install add-ons with more objects.

Thunderbird

March 18, 2015 by Andy Voelker
Categories: Network & Communications

Mozilla_Thunderbird_logo

Availability: Free Download
Comparable: Outlook

Mozilla Thunderbird is a free, open source, extensible, cross-platform email, news, and chat client developed by the Mozilla Foundation.

Thunderbird is an email, newsgroup, news feed, and chat (XMPP, IRC, Twitter) client. It supports POP and IMAP methods of connecting to email servers. It also supports LDAP (directory) address completion. The built-in RSS/Atom reader can also be used as a simple news aggregator. Thunderbird supports the S/MIME standard, extensions such as Enigmail add support for the OpenPGP (security)standard. The vanilla version is not a personal information manager, although the Mozilla Lightning extension adds PIM functionality. Additional features, if needed, are often available via other extensions.

Tags: news

yEd Graph Editor

March 18, 2015 by Andy Voelker
Categories: Productivity & Utility

yworks logo

Availability: Free Download
Comparable: Dia, FreeMind, Inspiration, Visio

yEd is a free of charge general-purpose diagramming program with a multi-document interface.  It is a cross-platform application written in Java that runs on Windows, Linux, Mac OS, and other platforms that support the JVM.

yEd can be used to draw many different types of diagrams, including flowcharts, network diagrams, UML diagrams,BPMN diagrams, mind maps, organization charts, and Entity Relationship diagrams. yEd also allows the use of custom vector and raster graphics as diagram elements.

yEd loads and saves diagrams from/to GraphML, an XML-based format. The application can print diagrams including very large diagrams that span multiple pages.

FreeMind

March 18, 2015 by Andy Voelker
Categories: Productivity & Utility

128px-Free_Mind

Availability: Free Download
Comparable: Inspiration, yEd Graph Editor

FreeMind is a free, open source mind mapping application written in Java.  It provides extensive export capabilities. It runs on Microsoft Windows, Linux and Mac OS X via the Java Runtime Environment.

As with other mind mapping software packages, FreeMind allows the user to edit a hierarchical set of ideas around a central concept. The non-linear approach assists in brainstorming new outlines and projects as ideas are added around the mind map. As a Java application, FreeMind is portable across multiple platforms and retains the same user interface, causing some amount of variation from the common interface on each platform. Mac users may notice the most difference from their traditional user interface, but  the software’s features should still appeal to the segment of users who accept function over form.

Stellarium

March 10, 2015 by Andy Voelker
Categories: Analysis & Modeling
stellarium logoAvailability: Free Download
Comparable: Google Earth, Starry Night Pro

Stellarium is a free open source planetarium for your computer. It shows a realistic sky in 3D, just like what you see with the naked eye, binoculars or a telescope.

It is being used in planetarium projectors. Just set your coordinates and go.

Omeka

February 26, 2015 by Andy Voelker
Categories: Design & Visualization

omeka

Availability: Contact CLAS OAT
Comparable:  WordPress, Drupal

Omeka is a free, flexible, and open source web-publishing platform for the display of library, museum, archives, and scholarly collections and exhibitions. Its “five-minute setup” makes launching an online exhibition as easy as launching a blog.

Omeka is a Swahili word meaning to display or lay out wares; to speak out; to spread out; to unpack.

Omeka falls at a crossroads of Web Content Management, Collections Management, and Archival Digital Collections Systems: Tech Ecosystem

Omeka is designed with non-IT specialists in mind, allowing users to focus on content and interpretation rather than programming. It brings Web 2.0 technologies and approaches to academic and cultural websites to foster user interaction and participation. It makes top-shelf design easy with a simple and flexible templating system. Its robust open-source developer and user communities underwrite Omeka’s stability and sustainability.

Tags: web development

CentOS Linux

February 24, 2015 by Andy Voelker
Categories: Operating Systems

Availability: Free download
Comparable: Red Hat Enterprise Linux
CentOS (abbreviated from Community Enterprise Operating System) is a linux operating system that serves as the free, open source, functionally compatible mirror to Red Hat Enterprise Linux, its upstream source of code.  CentOS is often used by amateur developers or server administrators for testing purposes, or even in a live production environment.
Tags: linux

Handbrake

February 19, 2015 by Andy Voelker
Categories: Multimedia

handbrake

Availability: Free Download
Comparable: Quicktime

HandBrake is a tool for converting video from nearly any format to a selection of modern, widely supported codecs.  It is free and open source and available for Windows, Mac, and Linux.  Handbrake offers a variety of device presets to convert media to suit your device needs.  For instance, if you had a very large video file you wanted to scale down for viewing on a phone without taking up too much space, you could use an easy filter to convert the media for that specific situation.  Handbrake can also convert DVDs to video files, encode chapter markers, subtitles, and menus.

Tags: multimedia

MPlus

November 24, 2014 by Andy Voelker
Categories: Analysis & Modeling

mplus

Availability: Labs  |  Download
Comparable: SPSS Amos
Training: Project Mosaic Workshops

Mplus is a latent variable modeling program with a wide variety of analysis capabilities:

  • Exploratory factor analysis
  • Structural equation modeling
  • Item response theory analysis
  • Growth modeling
  • Mixture modeling (latent class analysis)
  • Longitudinal mixture modeling (hidden Markov, latent transition analysis, latent class growth analysis, growth mixture analysis)
  • Survival analysis (continuous- and discrete-time)
  • Multilevel analysis
  • Complex survey data analysis
  • Bayesian analysis
  • Monte Carlo simulation

Read more…

Tags: statisticstrm

TexMaker

November 24, 2014 by Andy Voelker
Categories: Math & Programming
Availability: Labs  |  Free Download
Comparable: 

Texmaker is a cross-platform open source LaTeX editor with an integrated PDF viewer. Texmaker is entirely a Qt app.

The editor includes full unicode support, inline spell checking, auto-completion, code folding and rectangular block selection. Regular expressions are also supported for the find-and-replace actions.  Texmaker includes wizards for the following tasks:

  • Generate a new document or a letter or a tabular environment.
  • Create tables, tabulars, figure environments, and so forth.
  • Export a LaTeX document via TeX4ht (HTML or ODT format).

Some of the LaTeX tags and mathematical symbols can be inserted in just one click and users can define an unlimited number of snippets with keyboard triggers.  Texmaker automatically locates errors and warnings detected in the log file after a compilation.  The integrated PDF viewer supports continuous, rotation and presentation mode. Direct and reverse synchronization between source TeX files and the resulting PDF file is supported via the SyncTeX support.  The Asymptote graphics language is also fully supported by Texmaker (for both editing and compilation).

TexMaker has replaced Kile in CLAS computer labs.

Tags: LaTeX

Orca

November 21, 2014 by Andy Voelker
Categories: Accessibility

orca2-sm

Availability: Free Download
Comparable:  JAWS

Orca is a free and open source, flexible, extensible screen reader from the GNOME project for individuals who are blind or visually impaired. Using various combinations of speech synthesis and braille, Orca helps provide access to applications and toolkits that support the AT-SPI (e.g., the GNOME desktop, Mozilla Firefox/Thunderbird, OpenOffice.org/LibreOffice and GTK+, Qt and Java Swing/SWT applications).

 

Tags: accessibilityscreen reader

Spartan

November 21, 2014 by Andy Voelker
Categories: Analysis & Modeling

logo_SpartanStudentV6

Availability: Labs  |  Download
Comparable: ChemDraw

Spartan is a molecular modeling and computational chemistry application from Wavefunction. It contains code for molecular mechanics, semi-empirical methods, ab initio models, density functional models, post-Hartree–Fock models, and thermochemical recipes including G3(MP2) and T1.

Primary functions are to supply information about structures, relative stabilities and other properties of isolated molecules. Molecular mechanics calculations on complex molecules are common in the chemical community. Quantum chemical calculations, including Hartree–Fock molecular orbital calculations, but especially calculations that include electron correlation, are more time consuming in comparison.

Quantum chemical calculations are also called upon to furnish information about mechanisms and product distributions of chemical reactions, either directly by calculations on transition states, or based on the Hammond Postulate, by modeling the steric and electronic demands of the reactants. Quantitative calculations, leading directly to information about the geometries of transition states, and about reaction mechanisms in general, are increasingly common, while qualitative models are still needed for systems that are too large to be subjected to more rigorous treatments. Quantum chemical calculations can supply information to complement existing experimental data or replace it altogether, for example, atomic charges for QSAR analyses, and intermolecular potentials for molecular mechanics and molecular dynamics calculations.

Spartan applies computational chemistry methods (theoretical models) to a number of a standard tasks that provide calculated data applicable to the determination of molecular shape (conformation), structure (equilibrium and transition state geometry), NMR, IR, Raman, and UV/visible spectra, molecular (and atomic) properties, reactivity and selectivity.

Lab Availability
Tags: trm
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