BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.
Cactus is a general, modular, parallel environment for solving systems of partial differential equations. The code has been developed over many years by a large international collaboration of numerical relativity and computational science research groups and can be used to provide a portable platform for solving any system of partial differential equations.
Genius is an arbitrary precision integer and multiple precision floating point calculator. It includes its own programming language similar in some aspects to C, bc, or Pascal. It can deal with rational numbers and complex numbers. It has matrix support as well. It uses the gmp library so it is very fast for calculations of large numbers. It has a command line and a GNOME interface. The GNOME interface supports plotting functions and 3D surfaces.
GNU TeXmacs is a free wysiwyw (what you see is what you want) editing platform with special features for scientists. The software aims to provide a unified and user friendly framework for editing structured documents with different types of content: text, mathematics, graphics, interactive content. TeXmacs can also be used as an interface to many external systems for computer algebra, numerical analysis, and statistics. New presentation styles can be written by the user and new features can be added to the editor using Scheme.
GtkMathView is a GTK widget for rendering MathML documents. It is meant to be a standalone, light-weight component and not a full browser. GTK applications can use the widget as a window for displaying mathematical formulas and doing simple interactions. Among other features, GtkMathView includes support for breaking long mathematical expressions, rendering of stretchy operators, and provides a customizable support for additional fonts.
The GNU Triangulated Surface Library (GTS) provides a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. It features metric operations (area, volume, curvature, etc.), 2D Delaunay and constrained Delaunay triangulations, robust geometric predicates and set operations on surfaces (union, intersection, etc.), surface refinement and coarsening (multiresolution models), and bounding-boxes trees for collision/intersection detection.
R is a language and environment for statistical computing and graphics. It is similar to S, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.). R is designed as a true computer language with control-flow constructions for iteration and alternation, and it allows users to add additional functionality by defining new functions. For computationally intensive tasks, Fortran and C code can be linked and called at run time.
MayaVi is a free, cross platform, easy-to-use scientific data visualizer. It provides a powerful GUI to ease the visualization process. It is written in Python and uses the Visualization Toolkit (VTK) for the graphics. MayaVi can be scripted from other Python programs and also from the interactive Python interpreter. MayaVi includes the VTK Pipeline browser. The VTK Pipeline browser is a Python module (vtkPipeline) that enables one to view and configure the objects in the VTK pipeline graphically with a Tkinter-based GUI. The browser should work for any Python script that uses VTK. MayaVi also provides classes to pickle a VTK object and a simple class documentation browser.