nut is nutrition software to record what you eat and analyze your meals for nutrient composition. The database included is the latest USDA Nutrient Database for Standard Reference. This database contains values for vitamins, minerals, fats, calories, protein, carbohydrates, fiber, etc., and includes the essential polyunsaturated fats, Omega-3 and Omega-6. Nutrient levels are expressed as a percentage of the Daily Value, the familiar standard of food labeling in the United States, but also can be fully customized. Foods can be added from recipes or food labels, and nutrient intake can be graphed. The program is completely menu-driven and there are no commands to learn.
Engauge Digitizer is digitizing software that converts an image showing a graph or map into numbers. The image file can come from a scanner, digital camera, or screenshot. The numbers can be read on the screen, and written or copied to a spreadsheet. Highlights for beginners include an intuitive interface and extensive context-sensitive documentation. Highlights for experts include compensation for image distortion, cartesian and polar coordinates, linear and logarithmic coordinates, automatic scanning, graphical previews, and browser help.
E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.
CGAL, the Computational Geometry Algorithms Library, is a large C++ library of geometric data structures and algorithms such as Delaunay triangulations, mesh generation, Boolean operations on polygons, and various geometry processing algorithms. CGAL is used in various areas: computer graphics, scientific visualization, computer aided design and modeling, geographic information systems, molecular biology, medical imaging, robotics and motion planning, and numerical methods.
The NCBI C++ Toolkit provides portable libraries and applications for assisting genetic science. These include libraries for networking, SQL and BerkeleyDB access, CGI and HTML handling, ASN.1 and XML handling, sequence alignment engines, sequence retrieval engines, BLAST database engines, FLTK and OpenGL graphics toolkits, and basic system utilities.
FreeDiams is a program for making prescriptions of pharmaceutical drugs and testing their interactions. It is the result of building the FreeMedForms prescriber plugins into a standalone application. It is developed by medical doctors and is intended for use by these same professionals. It can be used to prescribe drugs and test drug interactions within a prescription. It can be linked to any application by way of its command line parameters. FreeDiams can use several drug databases, including the FDA_USA drug database, the French AFSSAPS drug database, the Canadian drug databases, and the South African drug database (SAEPI).
ImLib3D is a C++ library and visualization system for 3D (volumetric) image processing. It contains most basic image processing algorithms, as well as some more sophisticated ones. Its images are STL-compliant templated containers. It inculdes a viewer that features multiplanar views, interactive image processing, animations, vector field views, and 3D (OpenGL) multiplanar. Its main application is medical image processing.
BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER, CHARMM, and MMFF94 force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, secondary structure calculation, molecular editing and docking. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code. In addition, it provides a Python interface with Integrated Development Environment features to allow interactive rapid prototyping.