:: DESCRIPTION
QuickLookPDB is the QuickLook plugin for displaying PDB files and provides two visualisation options. plugin can use pymol to quickly render thumbnail images, while the heart of the plugin lies with the integration of a HTML-5 PDB viewer, Jolecule.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MOSAIC (MOdels, Simulations, and Algorithms for Interdisciplinary Computing) , the image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy , are available as plugins for the popular free image processing software ImageJ.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
I. F. Sbalzarini and P. Koumoutsakos.
Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology,
Journal of Structural Biology 151(2):182-195, 2005.
:: DESCRIPTION
DomainGraph is the successor tool of DomainNetworkBuilder and works as Java plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin decomposes protein networks into domain-domain interactions and generates a new network of interacting domains. It also allows the integration of exon expression data measured using Affymetrix GeneChip microarrays, which supports the analysis of alternative splicing events and the characterization of their effects on protein and domain interaction networks.
::DEVELOPER
Max-Planck-Institut Informatik
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Emig, D., Salomonis, N., Baumbach, J., Lengauer, T., Conklin, BR., Albrecht, M. (2010)
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data.
Nucleic Acids Res. 2010 July 1; 38
:: DESCRIPTION
UCSF chemViz is a Cytoscape plugin that extends the capabilities of Cytoscape into the domain of cheminformatics. chemViz displays 2D diagrams of compounds specified by InCHI or SMILES strings. chemViz can also calculate Tanimoto similarities of compounds and use the values to create chemical similarity networks. Part of such a network is shown above. The 2D diagrams can be presented as scalable independent windows or as part of a table also showing Cytoscape attributes and calculated compound descriptors, including number of hydrogen bond donors, number of hydrogen bond acceptors, molecular weight, ALogP, molecular refractivity, number of Rule of Five violations, and several more. Any of the calculated descriptors can be mapped onto Cytsocape attributes where they can be used by the VizMapper and saved with the session.
::DEVELOPER
the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
FunMod is an innovative Cytoscape version 2.8 plugin that is able to mine undirected protein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways.
::DEVELOPER
the Systems Biology Research Group at the Department of Control and Computer Engineering of Politecnico di Torino.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FunMod: a Cytoscape plugin for identifying functional modules in undirected protein-protein networks.
Natale M, Benso A, Di Carlo S, Ficarra E.
Genomics Proteomics Bioinformatics. 2014 Aug;12(4):178-86. doi: 10.1016/j.gpb.2014.05.002.
:: DESCRIPTION
ThunderSTORM is an open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Apr 25. pii: btu202. [Epub ahead of print]
ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging.
Ovesný M, Křížek P, Borkovec J, Svindrych Z, Hagen GM.
:: DESCRIPTION
CySBML is a Cytoscape plugin for the import and work with SBML files in Cytoscape providing the visualisation of SBML network annotations within the network context. SBML models can be imported from BioModels.net or via file or urls. One click access to the annotation resources is provided. SBML validation information about the imported files is available.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Sep 15;28(18):2402-3. doi: 10.1093/bioinformatics/bts432. Epub 2012 Jul 5.
CySBML: a Cytoscape plugin for SBML.
König M, Dräger A, Holzhütter HG.
:: DESCRIPTION
Autodock/Vina plugin for PyMOL can be used to set up docking and virtual screening with AutoDock Vina and to view the results.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Daniel Seeliger and Bert L. de Groot.
Ligand docking and binding site analysis with PyMOL and Autodock/Vina.
J. Comput.-Aided Mol. Des. 24:417-422 (2010)
:: DESCRIPTION
ActiveICM create 3D molecular documents for the web and PowerPoint. ActiveICM enables you to view and display 3D ICM graphical slides and animations interactively inside Microsoft PowerPoint and web browsers such as Internet Exporler and Mozilla Firefox. The files can be prepared and saved in ICM Browser Pro or ICM Pro.
Inside a single file you can save and display many different data types such as sequences, alignments, plots, tables, protein and DNA/RNA structures. Each data element can be linked to one another and annotated and then shared via the web, MS Office tools or in the free ICM-Browser. Pharmaceutical and biotech companies use ActiveICM to share data between scientists in different disciplines. Academic laboratories such as the SGC publish their data to the world using ActiveICM in a web browser.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The MorphoLibJ library proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins.
::DEVELOPER
IJPB Modeling and digital imaging lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ.
Legland D, Arganda-Carreras I, Andrey P.
Bioinformatics. 2016 Jul 13. pii: btw413.
