People exert large amounts of problem-solving effort playing computer games. Simple image-and text-recognition tasks have been successfully 'crowd-sourced' through games(1-3), but it is not clear if more compl...
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People exert large amounts of problem-solving effort playing computer games. Simple image-and text-recognition tasks have been successfully 'crowd-sourced' through games(1-3), but it is not clear if more complex scientific problems can be solved with human-directed computing. Protein structure prediction is one such problem: locating the biologically relevant native conformation of a protein is a formidable computational challenge given the very large size of the search space. Here we describe Foldit, a multiplayer online game that engages non-scientists in solving hard prediction problems. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology(4), while they compete and collaborate to optimize the computed energy. We show that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms;unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems.
Motivation: The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate commu...
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Motivation: The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate communication of biological knowledge between different research communities in the life sciences. However, to increase the use of SBGN, tools for editing, validating and translating SBGN maps are desirable. Results: We present SBGN-ED, a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from the KEGG and MetaCrop databases into SBGN and the export of SBGN maps into several file and image formats. Availability: SBGN-ED is freely available from http://***/addons/sbgn-ed. The web site contains also tutorials and example files. Contact: schreibe@ipk-gatersleben.
EBImage provides general purpose functionality for reading, writing, processing and analysis of images. Furthermore, in the context of microscopy- based cellular assays, EBImage offers tools to segment cells and extra...
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EBImage provides general purpose functionality for reading, writing, processing and analysis of images. Furthermore, in the context of microscopy- based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and use of existing tools in the R environment for signal processing, statistical modeling, machine learning and data visualization.
Enumeration of the dense sub-graphs of a graph is of interest in community discovery and membership problems, including dense sub-graphs that overlap each other. Described herein is ODES (Overlapping DEnse Sub-graphs)...
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Enumeration of the dense sub-graphs of a graph is of interest in community discovery and membership problems, including dense sub-graphs that overlap each other. Described herein is ODES (Overlapping DEnse Sub-graphs), pthreads parallelized software to extract all overlapping maximal sub-graphs whose densities are greater than or equal to a specified cutoff density of at least 1/2.
We present a suite of UNIX shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as s...
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We present a suite of UNIX shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes.
Motivation: DataPfex is aMATLAB-based application that facilitates the manipulation and visualization of multidimensional datasets. The strength of DataPflex lies in the intuitive graphical user interface for the effi...
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Motivation: DataPfex is aMATLAB-based application that facilitates the manipulation and visualization of multidimensional datasets. The strength of DataPflex lies in the intuitive graphical user interface for the efficient incorporation, manipulation and visualization of high-dimensional data that can be generated by multiplexed protein measurement platforms including, but not limited to Luminex or Meso-Scale Discovery. Such data can generally be represented in the form of multidimensional datasets [for example ( time x stimulation x inhibitor x inhibitor concentration x cell type x measurement)]. For cases where measurements are made in a combinational fashion across multiple dimensions, there is a need for a tool to efficiently manipulate and reorganize such data for visualization. DataPflex accepts data consisting of up to five arbitrary dimensions in addition to a measurement dimension. Data are imported from a simple. xls format and can be exported to MATLAB or. xls. Data dimensions can be reordered, subdivided, merged, normalized and visualized in the form of collections of line graphs, bar graphs, surface plots, heatmaps, IC50's and other custom plots. Open source implementation in MATLAB enables easy extension for custom plotting routines and integration with more sophisticated analysis tools.
SimiCon is a web server designed for an automated identification of equivalent protein-ligand atomic contacts in different conformational models of a complex. The contacts are computed with internal coordinate mechani...
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SimiCon is a web server designed for an automated identification of equivalent protein-ligand atomic contacts in different conformational models of a complex. The contacts are computed with internal coordinate mechanics (ICM) software with respect to molecular symmetry and the results are shown in the browser as text, tables and interactive 3D graphics. The web server can be executed remotely without a browser to allow users to automate multiple calculations.
We present an open source, platform independent tool, called CisGenome Browser, which can work together with any other data analysis program to serve as a flexible component for genomic data visualization. It can also...
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We present an open source, platform independent tool, called CisGenome Browser, which can work together with any other data analysis program to serve as a flexible component for genomic data visualization. It can also work by itself as a standalone genome browser. By working as a light-weight web server, CisGenome Browser is a convenient tool for data sharing between labs. It has features that are specifically designed for ultra high-throughput sequencing data visualization.
Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process th...
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Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process that can be performed by homology and ab initio with or without electron density maps. Those include the interactive editing of a secondary structure and a searchable, embedded library of annotated tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA research.
ExpressionView is an R package that provides an interactive graphical environment to explore transcription modules identified in gene expression data. A sophisticated ordering algorithm is used to present the modules ...
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ExpressionView is an R package that provides an interactive graphical environment to explore transcription modules identified in gene expression data. A sophisticated ordering algorithm is used to present the modules with the expression in a visually appealing layout that provides an intuitive summary of the results. From this overview, the user can select individual modules and access biologically relevant metadata associated with them.
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