RSS 221 projects tagged "Bioinformatics"

Download Website Updated 23 Aug 2005 ADF MAGE-ML Tool

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Pop 13.71
Vit 1.42

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.

Download Website Updated 26 Jul 2007 AGM Build

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Pop 23.32
Vit 49.59

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.

No download Website Updated 24 Feb 2007 APBS

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Pop 23.75
Vit 51.11

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.

Download Website Updated 22 Jan 2008 Adun

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Pop 26.36
Vit 2.91

Adun is an extensible biomolecular simulation program that includes data management and analysis capabilities.

Download No website Updated 22 Dec 2003 Analyze ECGs

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Pop 33.62
Vit 1.75

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.

Download Website Updated 06 Jun 2001 Arka

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Pop 14.11
Vit 3.20

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.

Download Website Updated 17 Oct 2004 Artemis

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Pop 19.36
Vit 2.00

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.

No download Website Updated 22 Mar 2010 Ascalaph

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Pop 22.11
Vit 38.62

Ascalaph is a general purpose 3D graphical molecular modeling suite that performs molecular mechanics and molecular dynamics simulations as well as quantum mechanics calculations.

No download Website Updated 16 Apr 2004 Asymptopia Flashcard System

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Pop 49.19
Vit 3.26

Asymptopia Flashcard System uses Motif and LaTeX to produce, manage, and use attractively formatted flashcards. You load some or all of your "collections" and set the timer for pop-up frequency. The GUI interface and "Collection Manager" make creating and modifying flashcards as simple as pushing a single button. A knowledge of LaTeX is only required when entering special symbols.

No download Website Updated 07 Dec 2010 BALL

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Pop 43.27
Vit 3.56

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.

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Firejail

A Linux namespaces sandbox program.

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CoreTML framework

A tool allowing the developer to create user-configurable source code templates.