Meep is a free finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems. It supports distributed-memory parallel simulations, nonlinear, anisotropic, and dispersive media, PML absorbing boundaries, and 1D/2D/3D and cylindrical problems. It is completely scriptable from either C++ or a Scheme (GNU Guile) interface.
Inlab-Scheme is an independent implementation of the algorithmic language Scheme and conforms to the R4RS and the IEEE Standard 1178. In addition to the language core, Inlab-Scheme has support for image processing which allows the implementation of OCR and image recognition applications. Inlab-Scheme comes with two built in graphic file format converters which convert the PATIMG patent file format and the ST.33 patent file format to multipage TIFF without decompressing.
GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position.
Esra is a scriptable, scalable, and highly hackable molecular mechanics library for Java. Its primary purpose is the statistical analysis of trajectory data generated with packages such as GROMOS, GROMACS, or AMBER, but it can also be used as a standalone package for performing simple molecular dynamics and Monte-Carlo simulations. It can be scripted with Jython, Mathematica, or Matlab.
CoaSim is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It efficiently constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on the states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.
FramerD is a semi-structured object database integrated with a Scheme-based scripting language which supports multi-lingual programming (with pervasive Unicode), a stable module system for programming in the large, distributed applications (via an extensible RPC protocol), non-deterministic (PROLOG-like) evaluation for search and set operations, multi-threaded program execution, extensive tools for text and language analysis, built-in HTML/XML/MIME parsers, and intuitive (CGI- and FastCGI-based) Web scripting. The built-in object database robustly supports millions of objects and indexed access to those objects, both through disk files and networked servers.
QuantLib is a cross-platform, quantitative finance C++ library for modeling, pricing, trading, and risk management in real-life. It is also wrapped as Python/Ruby/Scheme modules. Extensions for Excel, R, and Mathematica are available. Other such extensions are under consideration. QuantLib offers tools that are useful both for practical implementation and for advanced modeling. It features market conventions, yield curve models, solvers, PDEs, Monte Carlo (low-discrepancy included), exotic options, VAR, and so on.
A practical lambda-calculator is a normal-order evaluator for the untyped lambda-calculus, extended with convenient commands and shortcuts to make programming in it more productive. Shortcuts are distinguished constants that represent terms. Commands define new shortcuts, activate tracing of all reductions, compare terms modulo alpha-conversion, print all defined shortcuts and evaluation flags, etc. Terms to evaluate and commands are entered at a read-eval-print-loop (REPL) "prompt" or "included" from a file by a special command. A Haskell branch is an embedding of the lambda calculator (as a domain-specific language) into Haskell. The calculator can be used interactively within Hugs or GHCi.
MIT Photonic Bands (MPB) is a free program to compute the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures, and is applicable to photonic crystals (photonic band-gap materials), optical waveguides, and a wide range of other optical problems. Its features include: fully-vectorial 3D computations, a flexible user interface based upon the GNU Guile scripting language, output in HDF format, and iterative, targeted eigensolver methods to address very large problems by solving for only a few states near a specified frequency. It runs on both serial machines and parallel machines with MPI.