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.
AGM Build is a molecular builder and conformational editor. It can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. It features geometry editing, lattice building, building of chain molecules (e.g. proteins), chains with predetermined conformations, and charges and atom types according to selected Force Field.
Analyze ECGs is a graphical data analysis tool for use on analog input DAQ data, such as that of RTLab. It is useful for opening the '.nds' file format produced by RTLab's data acquisition program, DAQSystem (it can also open regular ASCII files). Aside from being a general-purpose multichannel analog data editing tool, it also contains custom features useful for analyzing cardiac data. However, it can be used for editing/viewing general-purpose data as well. Additionally, this program can convert '.nds' files to ASCII format data.
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.
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.
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.