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.

Bionet 3.0a – Biological Cell Network Pathway Simulation

Bionet 3.0a

:: DESCRIPTION

Bionet is intended to provide a computational tool for modeling biological pathways or biosystem dynamics on multiple scales. At this time, manual descriptions of gene and protein interactions are described in text files with a simple format.The methodology in bionet is distinguished from previous qualitative modeling approaches in several ways. The goal was to develop a model that would allow experimental biologists to use the kind of qualitative data found in typical journal articles to describe the interaction of genes, proteins, and other cellular components to create computer models of large numbers of interacting parts. This arose from a practical need in our research to keep track of myriad components in pathway models that were built from data extracted from dozens of journal articles. Biologists already do this kind of mental modeling every time they make a new hypothesis; a tool was needed to aid in this reasoning. Secondly, with new sources of data becoming available, it was important to design a methodology that could be expanded in the future to integrate new data sources to refine models.

::DEVELOPER

Bionet Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

 Bionet

:: MORE INFORMATION

Citation

Bosl, W. J. (2007).
Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery.
BMC Syst Biol, 1, 13.

Pathview 1.24.0 – R package for Pathway based Data Integration and Visualization

Pathview 1.24.0

:: DESCRIPTION

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs.

::DEVELOPER

Weijun Luo <luo_weijun at yahoo dot com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 Pathview

:: MORE INFORMATION

Citation

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.
Luo W, Brouwer C.
Bioinformatics. 2013 Jul 15;29(14):1830-1. doi: 10.1093/bioinformatics/btt285.

visANT 5.50 – Integrative Visual Analysis Tool for Biological Networks & Pathways

visANT 5.50

:: DESCRIPTION

visANT is an integrative visual analysis tool for biological networks and pathways. VisANT is implemented as a java applet which can be run in most common browsers and has been test with Netscape, Internet Explorer with different versions on different platforms.

::DEVELOPER

VisANT Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux
  • JAVA

:: DOWNLOAD

visANT ; Manual

:: MORE INFORMATION

Citation

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.
Granger BR, Chang YC, Wang Y, DeLisi C, Segrè D, Hu Z.
PLoS Comput Biol. 2016 Apr 15;12(4):e1004875. doi: 10.1371/journal.pcbi.1004875

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W225-31. doi: 10.1093/nar/gkt401. Epub 2013 May 28.
VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies.
Hu Z1, Chang YC, Wang Y, Huang CL, Liu Y, Tian F, Granger B, Delisi C.

XTMS – Pathway Design in an eXTended Metabolic Space

XTMS

:: DESCRIPTION

XTMS, a web-based pathway analysis platform ,which provides full access to the set of pathways that can be imported into a chassis organism such as E. coli through the application of an Extended Metabolic Space modeling framework.

::DEVELOPER

Jean-Loup Faulon’s group at Micalis.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W389-94. doi: 10.1093/nar/gku362. Epub 2014 May 3.
XTMS: pathway design in an eXTended metabolic space.
Carbonell P, Parutto P, Herisson J, Pandit SB, Faulon JL.

PANDA XPLORER – Pathway AND Annotation Xplorer

PANDA XPLORER

:: DESCRIPTION

The PANDA (Pathway AND Annotation) Explorer: a data visualization tool capable of annotating genes with any data type and graphically displaying the result within the context of pathways.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package

:: DOWNLOAD

  PANDA XPLORER

:: MORE INFORMATION

Citation

PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data.
Hart SN, Moore RM, Zimmermann MT, Oliver GR, Egan JB, Bryce AH, Kocher JP.
PeerJ. 2015 May 19;3:e970. doi: 10.7717/peerj.970.

Pathway-PDT 20130806 – A Flexible Pathway Analysis Tool for Nuclear Families

Pathway-PDT 20130806

:: DESCRIPTION

Pathway-PDT uses the framework of Pedigree Disequilibrium Test (PDT) for general family data, to perform pathway analysis.

::DEVELOPER

Pathway-PDT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Pathway-PDT

:: MORE INFORMATION

Citation

Pathway-PDT: a flexible pathway analysis tool for nuclear families.
Park YS, Schmidt M, Martin ER, Pericak-Vance MA, Chung RH.
BMC Bioinformatics. 2013 Sep 4;14:267. doi: 10.1186/1471-2105-14-267