PaVESy 20060803 – Pathway Visualization Editing System

PaVESy 20060803

:: DESCRIPTION

 PaVESy allows user-driven, interactive creation and visualization of pathway maps.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 PaVESy

:: MORE INFORMATION

Citation

A. Luedemann, D. Weicht, J. Selbig, J. Kopka (2004)
PaVESy: Pathway Visualization and Editing System.
Bioinformatics 2004 20(16): 2841-2844

SNPsea 1.0.3 – Identify Cell Types and Pathways Affected by Risk Loci

SNPsea 1.0.3

:: DESCRIPTION

SNPsea is an algorithm to identify cell types and pathways likely to be affected by risk loci. It requires a list of SNP identifiers and a matrix of genes and conditions.

::DEVELOPER

The Raychaudhuri Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 SNPsea

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 May 10. [Epub ahead of print]
SNPsea: an algorithm to identify cell types, tissues, and pathways affected by risk loci.
Slowikowski K1, Hu X, Raychaudhuri S.

BitPhylogeny 0.99 – Reconstruct Intra-tumor Evolutionary Pathways

BitPhylogeny 0.99

:: DESCRIPTION

BitPhylogeny is a probabilistic framework to reconstruct intra-tumor evolutionary pathways.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • R

:: DOWNLOAD

 BitPhylogeny

:: MORE INFORMATION

Citation

Genome Biol. 2015 Feb 13;16:36. doi: 10.1186/s13059-015-0592-6.
BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.
Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N.

Pathway – Heritable Clustering Algorithms

Pathway

:: DESCRIPTION

Pathway uses methylation profiles and clinical variables to group tumor samples into clusters and then organize them into a tree to represent tumor progression pathways that conform to strict heritability.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • MATLAB

:: DOWNLOAD

  Pathway

:: MORE INFORMATION

Citation

Wang, Z., Yan, P., Potter, D., Eng, C., Huang, T.H., Lin, S. (2005)
Heritable Clustering Algorithms – Recapitulation of Breast Tumor Progression Pathways Using DNA Methylation Data.

KGML-ED 1.0 – Edit, Process, and Visualize KGML pathway files

KGML-ED 1.0

:: DESCRIPTION

KGML-ED supports the dynamic exploration and editing of KEGG Pathway diagrams. It is a graphical network editor, that provides read- and write-support for the KGML (KEGG Markup Language) file format. Pathway files are loaded and transformed into a graph network which may be modified to fulfill user-specific needs (e.g. it is possible, to delete or add network elements, change labels and colors). Novel network exploration approaches are supported by the system as well.

::DEVELOPER

KGML-ED team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 KGML-ED

:: MORE INFORMATION

Citation

Christian Klukas and Falk Schreiber
Dynamic exploration and editing of KEGG pathway diagrams.
Bioinformatics 2007 23: 344-350.

Hi-Jack – Pathway-based Inference of Host-pathogen Interactions

Hi-Jack

:: DESCRIPTION

Hi-Jack, a novel computational framework, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking.

::DEVELOPER

InfoCloud Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C++ Compiler

:: DOWNLOAD

Hi-Jack

:: MORE INFORMATION

Citation:

Hi-Jack: A novel computational framework for pathway-based inference of host-pathogen interactions.
Kleftogiannis D, Wong L, Archer JA, Kalnis P.
Bioinformatics. 2015 Mar 9. pii: btv138

MITHrIL 1.0 – Mirna enrIched paTHway Impact anaLysis

MITHrIL 1.0

:: DESCRIPTION

MITHrIL (Mirna enrIched paTHway Impact anaLysis) is an algorithm developed for the analysis of signaling pathways. It extends pathways by adding missing regulatory elements, such as microRNAs, and their interactions with genes.

::DEVELOPER

MITHrIL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

MITHrIL

:: MORE INFORMATION

Citation:

Oncotarget. 2016 Aug 23;7(34):54572-54582. doi: 10.18632/oncotarget.9788.
Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification.
Alaimo S, Giugno R, Acunzo M, Veneziano D, Ferro A, Pulvirenti A.

FNV 1.0 – Light-weight Flash-based Network and Pathway Viewer

FNV 1.0

:: DESCRIPTION

FNV (Flashed-based Network Viewer) is for the visualization of small to moderately sized biological networks and pathways. FVN can also be used to embed pathways inside PDF files for the communication of pathways in soft publication materials

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

FNV

:: REQUIREMENTS

  • Windows/Linux
  • Flash Player 

:: DOWNLOAD

 FNV

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1181-2. doi: 10.1093/bioinformatics/btr098. Epub 2011 Feb 23.
FNV: light-weight flash-based network and pathway viewer.
Dannenfelser R, Lachmann A, Szenk M, Ma’ayan A.

DIRAC – Studying Gene Expression within Pathways

DIRAC

:: DESCRIPTION

DIRAC (Differential Rank Conservation) is a software which permits one to assess these combinatorial interactions to quantify various biological pathways or networks in a comparative sense, and to determine how they change in different individuals experiencing the same disease process.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Matlab

:: DOWNLOAD

 DIRAC

:: MORE INFORMATION

Citation

Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC).
Eddy JA, Hood L, Price ND, Geman D.
PLoS Comput Biol. 2010 May 27;6(5):e1000792.