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.
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.
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 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.
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.
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.
Data fusion methods are powerful tools for evaluating experiments designed to discover measurable features of directly unobservable systems. We describe an interactive software platform, Visual Integration for Bayesia...
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Data fusion methods are powerful tools for evaluating experiments designed to discover measurable features of directly unobservable systems. We describe an interactive software platform, Visual Integration for Bayesian Evaluation, that ingests or creates Bayesian posterior probability matrices, performs data fusion and allows the user to interactively evaluate the classification power of fusing various combinations of data sources, such as transcriptomic, proteomics, metabolomics, biochemistry and function.
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.
Most software systems for oral implantology are based on a multiview approach and often accompanied with a 3-D rendered model. A more integrated and realistic 3-D approach for implant surgery-also guaranteeing correct...
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Most software systems for oral implantology are based on a multiview approach and often accompanied with a 3-D rendered model. A more integrated and realistic 3-D approach for implant surgery-also guaranteeing correctness in measures-is desirable to gain a deep and sure knowledge of the patient's anatomy before inserting the implants, thus reducing the risk of damaging surrounding structures. We present a 3-D software system where computer graphic techniques have been used to create a smooth and user-friendly 3-D environment to work upon for oral implant planning and simulation. Interpolation of the axial slices is used to produce a continuous radiographic volume and get an isotropic voxel to achieve a correct work context. Freedom of choosing, arbitrarily, during the planning phase, the best cross-sectional plane for achieving correct measurements is obtained through interpolation and texture generation. Correct orientation of the planned implants is also easily computed by exploiting a radiological mask with radio-opaque markers, which is worn by the patient during the computed tomography (CT) scan. Measurement precision was validated considering different scans of a dried human partially edentulous mandible, which was scanned several times, with different angular orientations. The achieved precision (from 0.14% to 0.84% of the absolute value of error) outperforms that using usual DentaScan multiview approaches, and it is even better than the precision previously obtained by the DentalVox tool.
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