The aim of ADF MAGE-ML Tool is to provide a module for converting ADF files (a tab delimited file representing microarray design layout) into MAGE-ML format, and for generating an ADF from an array design described in MAGE-ML format. The module is build upon the ADF specifications and using MAGE-Stk APIs (Java). MIAME-compliance checking, a logging system, and integration of LifeScience Identifier (LSID) specifications are key components of the module. The module can be used via the command line or a graphical user interface.
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.
Arka provides a nice GUI for the gp package of command-line utilities for manipulation and display of DNA/RNA/protein sequences, the WU-BLAST and FASTA program families, and additional graphical tools for various aspects of sequence analysis (e.g., GC plots and 3D graphs). It provides editable and saveable windows for standard input, output and error, and a dialog for any command-line program with specifications in a configuration file.
Artemis is a DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. It can read and write complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK, or GFF format.
Babase is a baboon data management system. It is designed to facilitate the retrieval, storage, maintenance, and analysis of the following broad data categories: group membership, social status (dominance rank), life events, sexual cycle events (including progeny), sexual cycle day-to-day status, dyadic social interactions, focal animal samples, and multi-party social interactions. Integration of other data is supported. Babase is designed for Web access.