Search Results for "interface"

Analyses and Interactive visualizations of the structures, functions and actions of biomolecules including molecular surface computation, and protein-ligand interface and protein-ligand docking where the ligand could a small compound, a nucleic acid, membrane and other proteins, written in C++/Qt/openGL/GLSL with more than 125,000 lines of codes. In addition to Qt, the only external library needed is GSL everything else is coded from the scratch.

This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. ...

HeatmapGenerator is a graphical user interface software program written in C++, R, and OpenGL to create customized gene expression heatmaps from RNA-seq and microarray data in medical research. HeatmapGenerator can also be used to make heatmaps in a variety of other non-medical fields. HeatmapGenerator is peer-reviewed published software (http://www.scfbm.org/content/9/1/30).

openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.

TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.

...The method is full automated and makes use of the generalized multihistogram (GMH) equations for estimation the density of states [1]. The package is implemented in C++ and has a convenient interface.

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Xmipp is a well-known package in the EM image processing. It is integrated into Scipion and contains the algorithms in the core libraries and command line programs.

Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.

GraFIX is a software and a method to detect fixations in low and high quality data, consisting of a two-step process in which eye-tracking data is initially parsed by using adaptive velocity-based algorithms, before it is hand-coded using the graphical interface, allowing accurate and rapid adjustments of the algorithms' outcome. GraFIX is released under the GPLv3 public license (http://www.gnu.org/licenses/). Please cite as: Saez de Urabain, I.R., Johnson, M.H., Smith, T.J., (2014) GraFIX: A semiautomatic approach for parsing low- and high-quality eye-tracking data. Behavior Research Methods. doi:10.3758/s13428-014-0456-0 Download the paper at: http://link.springer.com/article/10.3758/s13428-014-0456-0

GaloisExplorer provides a user-friendly interface for basic functionalities of Formal Concept Analysis (FCA) with different lattice generation algorithms and an interactive viewer to explore a 3-dimensionally laid out lattice.

...Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments.

This project is the implementation of The Virtual Collaborative Environment (VCE) which supports clinical applications of 3D modeling in medicine. The system is based on three layer client-server architecture.

LiverSegm has been developed with the processing of liver images in mind. This software implements a level set based variational approach that incorporates shape priors and appearance models. It uses ITK Snap as interface.

This is a wxWidgets-based, cross-platform graphical frontend for the maximum-likelihood phylogenetic inference program RAxML created by Alexis Stamatakis (A. Stamatakis, Bioinformatics 22(21):2688-2690, 2006)

gfit creates an interface between computational models and experimental data and provides tools for their analysis

IMAS is a Visual Analytics system for the discovery of knowledge in genomic information. IMAS enables genomic scientists to rapidly analyze and visualize a set of microbial genomic sequences using tools such as Glimmer, Blast, Clustal-W, Primer3.

BigBang/Horizon is a proteomics data analysis pipeline with focus on the shotgun LC/MSMS workflow.

The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!

DASS-GUI is a graphical user interface for pattern search in non-sequential data.

EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)

Web-based user interface for MAQ (Mapping and Assembly with Qualities), an Illumina / Solexa Deep Sequencing Reads (fastq format) mapping software. MAQGene classifies each found mutation based on its canonically predicted effect on the coding sequence.

An SQL handler to interface multiple databases data to the OpeNDAP Hyrax (BES) server. Written in C++, it uses unixODBC to query DB and can be dynamically extended to use proprietary ODBC API driver in many easy ways. It is bundled with scripts to ge

STR miner(or SSRdigger) is a SSR searching software which supports both perfect and imperfect SSR search with specified length, match percentage and repeat threshold. With a GUI interface, fasta and MS excel format output, STR miner is user-friendly.

this map system can synchronously record multi-sites electronic signals in a cardiac cycle, and then to demonstrate the activation's propagation path in a 3D cardiac model.

NGSView is a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.