MorphoLibJ 1.2.2 – Collection of Mathematical Morphology Methods and Plugins for ImageJ

MorphoLibJ 1.2.2

:: 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

  • Linux / Windows/ MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 MorphoLibJ

:: 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.

ActiveICM 1.2-4 – PowerPoint & Web Browsers Plugin to Display 3D Modules

ActiveICM 1.2-4

:: 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

Molsoft LLC.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/Mac OS X
  • PowerPoint
  • IE / Firefox / Chrome / Safari

:: DOWNLOAD

ActiveICM

:: MORE INFORMATION

Autodock/Vina plugin for PyMOL

Autodock/Vina plugin for PyMOL

:: 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

Daniel Seeliger

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Autodock/Vina plugin for PyMOL

:: 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)

NeMo 1.4 – Network Module Identification Plugin for Cytoscape

NeMo 1.4

:: DESCRIPTION

NeMo is a network community-finding plugin for cytoscape. This plugin has the unique ability to find both densely connected networks and densely connected bipartite structures in a unified approach.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows / MacOsX
  • JRE
  • Cytoscape

:: DOWNLOAD

  NeMo

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S61. doi: 10.1186/1471-2105-11-S1-S61.
NeMo: Network Module identification in Cytoscape.
Rivera CG, Vakil R, Bader JS.

CySBML 1.4.0 – Cytoscape Plugin for SBML

CySBML 1.4.0

:: 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

Matthias König

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CySBML

:: 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.

ThunderSTORM 1.3 – ImageJ plugin for PALM and STORM data analysis and super-resolution imaging

ThunderSTORM 1.3

:: 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

Institute of Cellular Biology and PathologyFirst Faculty of MedicineCharles University in Prague, Czech Republic.

:: SCREENSHOTS

ThunderSTORM

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 ThunderSTORM

:: 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.

FunMod 2.8.3 – Cytoscape plugin for Identifying Functional Modules in undirected Protein-protein Networks

FunMod 2.8.3

:: 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

FunMod team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java
  • Cytoscape

:: DOWNLOAD

 FunMod

:: 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.

chemViz2 1.0.3 – Cheminformatics Plugin for Cytoscape

chemViz2 1.0.3

:: 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

chemViz

:: REQUIREMENTS

:: DOWNLOAD

  chemViz

:: MORE INFORMATION

FoldX/Yasara 4.4.23 – FoldX plugin for Yasara

FoldX/Yasara 4.4.23

:: DESCRIPTION

The FoldX/Yasara ( FoldX plugin for YASARA) is a software package to access and run FoldX commands in YASARA.

::DEVELOPER

Joost Van Durme

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Yasara
  • Python

:: DOWNLOAD

 FoldX/Yasar

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1711-2. Epub 2011 Apr 19.
A graphical interface for the FoldX forcefield.
Van Durme J, Delgado J, Stricher F, Serrano L, Schymkowitz J, Rousseau F.

GLay – Cytoscape Plugin of Community Analysis

GLay

:: DESCRIPTION

GLay is a cytoscape plugin that offers an assorted collection of community analysis algorithms and layout functions, dynamically linked from igraph.

::DEVELOPER

Microarray Lab, Department of Psychiatry / Molecular and Behavioral Neuroscience Institute, University of Michigan

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  GLay

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Dec 15;26(24):3135-7. doi: 10.1093/bioinformatics/btq596.
GLay: community structure analysis of biological networks.
Su G1, Kuchinsky A, Morris JH, States DJ, Meng F.