HapYDive – Excel Plugin for Y-STR Haplotype Diversity Calculation

HapYDive

:: DESCRIPTION

HapYDive is a software for Y-STR haplotype diversity calculation.This program allows fast and reliable determination of which Y-STRs are the most informative by evaluating all possible combinations.With the HapYDive it is possible to analyse any set of Y markers up to a maximum of 20, with a minimum number of 4 markers fixed for calculations. Results on the application of this program to different population samples and sizes and with a certain combination of Y-STR markers are presented and discussed, together with its usefulness mainly to the forensic community.

::DEVELOPER

Filipe Pereira

:: SCREENSHOTS

: REQUIREMENTS

  • Windows
  • Excel

:: DOWNLOAD

HapYDive

:: MORE INFORMATION

Citation

Alves C, Gusmão L, Meirinhos J, Amorim A (2006)
Making the most of Y-STR haplotypes. The HapYDive.
Forensic Genetics 11: 201-203.

PetriScape 1.0 – Plugin for discrete Petri net simulations in Cytoscape

PetriScape 1.0

:: DESCRIPTION

PetriScape is a tool for discrete Petri net simulation of biological networks in Cytoscape.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

PetriScape

:: MORE INFORMATION

Citation

J Integr Bioinform. 2016 Jun 4;13(1):284. doi: 10.2390/biecoll-jib-2016-284.
PetriScape – A plugin for discrete Petri net simulations in Cytoscape.
Almeida D, Azevedo V, Silva A, Baumbach J.

Species Delimitation 1.03 – Geneious plugin for the exploration of Species Boundaries

Species Delimitation 1.03

:: DESCRIPTION

The Species Delimitation plugin for the Geneious bioinformatics software is an exploratory tool that allows users to assess putative species in phylogenetic trees.

::DEVELOPER

Howard Ross

:: SCREENSHOTS

SpDelim

:: REQUIREMENTS

:: DOWNLOAD

 Species Delimitation

:: MORE INFORMATION

Citation:

Species Delimitation–a Geneious plugin for the exploration of species boundaries.
Masters BC, Fan V, Ross HA.
Mol Ecol Resour. 2011 Jan;11(1):154-7. doi: 10.1111/j.1755-0998.2010.02896.x.

ClueGO 2.0.5 – Cytoscape Plugin to Decipher Gene Ontology and Pathway Annotation Networks

ClueGO 2.0.5

:: DESCRIPTION

ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role.

::DEVELOPER

Integrative Cancer Immunology Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ClueGO

:: MORE INFORMATION

Citation

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J.
Bioinformatics. 2009 Apr 15;25(8):1091-3. Epub 2009 Feb 23.

CGAP – Contact Geometry Analysis Plugin for CMView

CGAP

:: DESCRIPTION

 CGAP (The Contact Geometry Analysis Plugin) is an experimental plugin for the CMView contact map analysis software. It provides rich, interactive tools for analysing the geometric environment of residue-residue contacts in protein structures.

::DEVELOPER

the Bioinformatics / Structural Proteomics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • CMView

:: DOWNLOAD

  CGAP

:: MORE INFORMATION

PathVisio-MIM 2.0.11 – Pathvisio Plugin which Adds the Ability to Draw MIM Glyph

PathVisio-MIM 2.0.11

:: DESCRIPTION

PathVisio-MIM is a software of MIM (Molecular Interaction Map) plugin for PathVisio allows users to produce diagrams of bioregulatory systems according to an implementation of notation first developed by Kurt Kohn in 1999. The plugin has two main features: 1) it provides users with the glyphs necessary to draw MIM diagrams and 2) it allows users to import and export to the MIM Markup Language (MIMML) format, a format developed to exchange MIM diagrams between MIM compatible tools and used to validate MIM diagrams. Diagrams produced using the MIM PathVisio plugin can be exported into several image formats including PDF, PNG, SVG, and TIFF.

::DEVELOPER

PathVisio-MIM Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PathVisio-MIM

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 1;27(15):2165-6. Epub 2011 Jun 2.
PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).
Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW.

ChemSpotlight 2.0 – Plugin of MacOsX Spotlight for Reading Chemical Files

ChemSpotlight 2.0

:: DESCRIPTION

ChemSpotlight is a Spotlight metadata importer plugin for Mac OS X, which reads common chemical file formats using the Open Babel chemistry library. Spotlight can then index and search chemical data: molecular weights, formulas, SMILES, InChI, fingerprints, etc.

::DEVELOPER

Geoff Hutchison

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

ChemSpotlight

:: MORE INFORMATION

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 2 of the License.

Reposition 0.02 – Cytoscape Plugin for reuse of layouts

Reposition 0.02

:: DESCRIPTION

Reposition is an open source Cytoscape Plugin for the reuse of existing Cytoscape network layouts in new Cytoscape projects.

::DEVELOPER

Andreas Hoppe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Reposition

:: MORE INFORMATION

N/A

 

Payao Uploader 1.0 – CellDesigner Plugin to Upload Model to Payao

Payao Uploader 1.0

:: DESCRIPTION

Payao Uploader is to allow the user to upload CellDesigner pathway models to Payao system – a web-based community curation platform

::DEVELOPER

Systems Biology Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Payao Uploader ; Manual

:: MORE INFORMATION

Compatibility: Built for CellDesigner 4.1.

Merge Models 1.03 – CellDesigner Plugin to Merge Models

Merge Models 1.03

:: DESCRIPTION

Merge Models is a CellDesigner plugin. The purpose of Merge Models is to allow the user to merge different biological pathway models and build new pathway maps. It also provides the ability to analysis two or more models for merging, to identify the duplicate species and highlight them on the merged model map.

::DEVELOPER

Systems Biology Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Merge Models ; Manual

:: MORE INFORMATION

Compatibility: Built for CellDesigner 4.1.