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Tool is being activelty miantained. This tool is considered complete. Bugs will be fixed, but no new features will be added 

Miru (formerly known as BioLayout Express3D)

Miru (formerly known as BioLayout Express3D) is a powerful tool for the visualization and analysis of network graphs. Network-based approaches are becoming increasingly popular for the analysis of complex systems of interaction and high dimensional data. Networks can be produced from a wide variety of relationships between entities. In biology this includes the interactions between individuals, disease transmission, sequence similarity, metabolic pathways, protein interactions, pathways, regulatory cascades, gene expression, etc. BioLayout Express3D has been specifically designed for visualization, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space derived primarily, but not exclusively, from biological data.

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Institution: The Roslin Institute, University of Edinburgh; European Informatics Institute (EMBL-EBI)

Assemble2

Assemble 2 allows you to construct your RNA 3D model interactively, starting from a solved tertiary structure and the orthologous sequence to model. But you can also use Assemble2 for more simple tasks: the prediction and manipulation of a secondary structure, the annotation and exploration of a solved tertiary structure.

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Institution: University of Strasbourg, France

UCSC Genome Browser

The UCSC Genome Browser integrates information from a wide variety of genomic resources, including gene predictions; disease associations, including HGMD, OMIM and locus-specific databases; gene-expression data; copy-number variation; comparative genomics; SNPs; HapMap data; gene-chip mappings; and histone- and DNA- modification data.

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Institution: University of California, Santa Cruz

NetBioV

NetBioV (network biology visualization) is an R package that provides many easy to use functions, layout styles and color schemes to visualize biological networks

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Institution: Computational Biology and Machine Learning

ParaView

ParaView is an application framework and turnkey application. Users can quickly build visualizations to analyze their data using qualitative and quantitative techniques, with data exploration done interactively in 3D or programmatically using ParaView's batch processing capabilities. Furthermore, the ParaView code base is designed in such a way that all of its components can be reused to quickly develop vertical applications. This flexibility allows ParaView developers to quickly develop applications that have specific functionality for a specific problem domain.

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Institution: Kitware

Gitools

Gitools is a desktop application for analysis and visualization of multidimensional data using interactive heat-maps.

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Institution: University Pompeu Fabra, Barcelona

MembraneEditor

The CELLmicrocosmos 2.2 MembraneEditor can be used to model membranes based on lipid and protein files in PDB format. It is possible to interactively generate structural and compositional heterogeneous membrane patches as well as vesicles. The created structures can be used for visualization purposes, structural analysis or as a base for molecular simulations. Windows, Mac OS X as well as Linux are supported. Requirement: Java 7+ has to be installed beforehand. For semi-automatic placement of proteins, the OPM and PDB_TM database are used. A direct connection to the PDB database for downloading PDB files is also integrated. The PDB export module provides many options, enabling compatibility to all PDB viewers to the best of our knowledge.

Introduction videos you will find here: http://www.cellmicrocosmos.org/index.php/videos

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Institution: University of Konstanz

Paver

Paver is a software product for the analysis and visualization of large OMICs data sets, including data from transcriptome, proteome and / or metabolome analyses. A newly developed integrated visualization technique aggregates complete sets of expression data with available biological knowledge from a variety of gene functional classification systems on a minimum of screen space. This makes it possible to visualize expression sets as a whole without any kind of pre-filtering.e from a variety of gene functional classification systems on a minimum of screen space. 

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Institution: Ernst Moritz Arndt University of Greifswald

Amira

Amira® is a powerful, multifaceted 3D software platform for visualizing, manipulating, and understanding biomedical data coming from all types of sources and modalities. Initially known and widely used as the 3D visualization tool of choice in microscopy and biomedical research, Amira has become a more and more sophisticated product, delivering powerful visualization and analysis capabilities in all visualization and simulation fields in life sciences.

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Institution: The University of Dundee

UCSF Chimera

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use.

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Institution: University of California, San Francisco

Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics, funded by the National Institutes of Health (NIGMS P41-GM103311).

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