APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.
AntFlow builds upon Apache Ant to provide a new approach to simplifying system automation that uses pipelines of hot folders chained together to perform a given task. Using XML, it associates an automated task such as data transfer, encryption, or XML processing with a directory on the local system. Whenever a file is copied or written into the hot folder, the associated task is executed and the file is moved to the next hot folder in the pipeline for further processing.
The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.
Berkeley DB XML is a native XML database engine for use within your product. Made available as a C++ library with language bindings for Java, Perl, Python, PHP, and Tcl, it integrates directly into your application (it is not a standalone database server). It provides XQuery access into a database of document containers. XML documents are stored and indexed in their native format using Berkeley DB as the transactional database engine.
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.
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.
ESP is a secure, automated system that analyzes electronic medical record (EMR) data to identify and report patients with notifiable diseases to the Massachusetts Department of Public Health. The growing use of electronic medical record systems (EMRs) permits efficient re-use of data already being collected by clinicians during routine private practice, offering an unparalleled opportunity to improve public health practice. Information held in EMR systems includes diagnoses, procedures, laboratory test, and treatment information, as well as patient demographic data. This software permits secure, simple, and robust messaging from electronic medical record systems to public health authorities.
GRIDportal is a Web-based application portal that acts as a frontend to GRID computing. Its aim is to make common GRID applications like Abaqus, Matlab, or BLAST more accessible to the user. Use of GRIDportal does not require any knowledge of Unix nor GRID computing whatsoever. All the user needs to know is how to use the given application, so the step from desktop computing to GRID computing should thus become a much smaller one than it otherwise would be.