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.
EAsea Specification of Evolutionary Algorithms (EASEA), is a high-level language dedicated to the specification of evolutionary algorithms. The language and compiler are quite mature. EASEA compiles .ez specification files into C++ or Java object files, using existing evolutionary libraries. Supported C++ libraries currently are GALib or EO.
EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX, and inhomogeneous clusters of UNIX workstations under PVM or MPI. EGO also runs sequentially on any decent UNIX workstation, even Windows95/NT PC's (with a GNU-C compiler) can be used.
EMBOSS (European Molecular biology Open Software Suite) is a software analysis package that was developed for the molecular biology user community. It automatically copes with data in a variety of formats and allows the transparent retrieval of sequence data from the Web. As it includes extensive libraries, it can be used by other scientists for developing software. It seamlessly integrates a range of packages and tools for sequence analysis.
EPoS is a modular software framework for phylogenetic analysis and visualization. EPoS combines a powerful graphical user interface with a plugin system that allows simple integration of new algorithms, visualizations, and data structures. EPoS currently supports distance based tree construction from multiple sequence alignments and distance matrices as well as different algorithms to create consensus trees and supertrees. EPoS also integrates a tree visualization module that can be used to compare two trees and export visualizations.
ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. It is not a gene prediction program, nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity.
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.
Emergent is a neural network simulator with a built-in scripting language which allows for the creation and analysis of complex, sophisticated models of the brain in the world. Networks and all of their state variables are visually inspected in 3D, allowing quick "visual regression" of network dynamics and robot behavior. Emergent is a direct descendant of the PDP and PDP++ neural network packages.