Availability: Labs | Download
Comparable: yEd Graph Editor
Gephi 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.
Availability: Free Download
Comparable: Zotero, EndNote
Mendeley 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 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.