SBGN-ED 1.6 – Editing, Translating and Validating of SBGN Maps

SBGN-ED 1.6

:: DESCRIPTION

SBGN-ED is a VANTED Add-on which allows to create and edit all three types of SBGN maps, that is Process Description, Entity Relationship and Activity Flow, to validate these maps according to the SBGN specifications, to translate maps from the KEGG and MetaCrop pathway databases into SBGN, and to export SBGN maps into several file and image formats.
SBGN (Systems Biology Graphical Notation) is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SBGN-ED

:: MORE INFORMATION

Citation

Tobias Czauderna, Christian Klukas and Falk Schreiber
Editing, Validating, and Translating of SBGN Maps
Bioinformatics (2010)doi: 10.1093/bioinformatics/btq40

Meta-All 1.2 – Store and Access Information about Metabolic Pathways

Meta-All 1.2

:: DESCRIPTION

Meta-All is a software that allows to store and access information about metabolic pathways, including reaction kinetics, detailed locations, environmental circumstances and taxonomic information.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  Meta-All

:: MORE INFORMATION

Citation

S. Weise, I. Grosse, C. Klukas, D. Koschuetzki, U. Scholz, F. Schreiber and B.H. Junker.
Meta-All: a system for managing metabolic pathway information.
BMC Bioinformatics, 7:e465, 2006.

VANTED 2.6.5 – Visualization and Analysis of Networks containing Experimental Data

VANTED 2.6.5

:: DESCRIPTION

VANTED (Visualisation and Analysis of Networks containing Experimental Data) is an open source software that offers the possibility to load and edit graphs, which may represent biological pathways or functional hierarchies. It allows to integrate different *omics data into the functional context and provides a variety of functions for data mapping and processing, statistical analysis, and visualisation. With the VANTED Add-on interface it is easily possible to extend the functionality of the software.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 VANTED

:: MORE INFORMATION

Citation

Klukas and Schreiber (2010)
Integration of -omics data and networks for biomedical research with VANTED.
Journal of Integrative Biology, 7(2)

Björn H. Junker, Christian Klukas and Falk Schreiber (2006)
VANTED: A system for advanced data analysis and visualization in the context of biological networks.
BMC Bioinformatics, 7:109

CELLmicrocosmos 4.2 PathwayIntegration – Localization and Visualization of Protein-Interaction Networks in a Virtual Cell

CELLmicrocosmos 4.2 PathwayIntegration

:: DESCRIPTION

The CELLmicrocosmos PathwayIntegration (CmPI) was developed to support and visualize the subcellular localization prediction of protein-related data such as protein-interaction networks.

::DEVELOPER

the Bioinformatics / Medical Informatics department at Bielefeld University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 CmPI

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Feb;11(1):1340005. doi: 10.1142/S0219720013400052. Epub 2013 Feb 18.
Subcellular localization charts: a new visual methodology for the semi-automatic localization of protein-related data sets.
Sommer B1, Kormeier B, Demenkov PS, Arrigo P, Hippe K, Ates Ö, Kochetov AV, Ivanisenko VA, Kolchanov NA, Hofestädt R.

HumanNet v2 – Human Gene Networks for Disease Research

HumanNet v2

:: DESCRIPTION

HumanNet is a human functional gene network by integrating diverse types of omics data using Bayesian statistics framework and demonstrated its ability to retrieve disease genes.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

HumanNet v2: human gene networks for disease research.
Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I.
Nucleic Acids Res. 2019 Jan 8;47(D1):D573-D580. doi: 10.1093/nar/gky1126.

Catapult – Associating new Genes with Traits, Phenotypes, and Diseases

Catapult

:: DESCRIPTION

Catapult (Combining dATa Across species using Positive-Unlabeled Learning Techniques), is a supervised machine learning method that uses a biased support vector machine where the features are derived from walks in a heterogeneous gene-trait network.

::DEVELOPER

the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Catapult

:: MORE INFORMATION

Citation:

Prediction and validation of gene-disease associations using methods inspired by social network analyses.
Singh-Blom UM, Natarajan N, Tewari A, Woods JO, Dhillon IS, Marcotte EM.
PLoS One. 2013 May 1;8(5):e58977. doi: 10.1371/journal.pone.0058977.

JiffyNet – Jiffy (instant) Gene Network Modeler for newly Sequenced Species

JiffyNet

:: DESCRIPTION

JiffyNet specifically designed to instantly construct genome-scale protein networks based on associalogs (functional associations transferred from a template network by orthology) for a query species with only protein sequences provided.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Eiru Kim, Hanhae Kim, Insuk Lee.
JiffyNet: a web-based instant protein network modeler for newly sequenced species,
Nucl. Acids Res. (1 July 2013) 41 (W1): W192-W197

RIDDLE – Network-assisted Gene Set Analysis

RIDDLE

:: DESCRIPTION

RIDDLE (Reflective diffusion and local extension)is a network-based method for characterizing gene sets. It asks if an input query set is significantly “close” to a known pathway or disease set in the human functional network.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea and the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 26;13(12):R125. doi: 10.1186/gb-2012-13-12-r125.
RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network.
Wang PI, Hwang S, Kincaid RP, Sullivan CS, Lee I, Marcotte EM.

MORPHIN – Model Organisms Projected on a Human Integrated Gene Network

MORPHIN

:: DESCRIPTION

MORPHIN is a web-based bioinformatics tool to study human diseases using model organism genes.

::DEVELOPER

Network Biomedicine Laboratory  at Yonsei University, Korea and the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.
Hwang S, Kim E, Yang S, Marcotte EM, Lee I.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W147-53. doi: 10.1093/nar/gku434.

Paintomics 3 v0.4.5 – Painting Omics Data in Biological Pathways

Paintomics 3 v0.4.5

:: DESCRIPTION

 Paintomics is a web tool for the integration and visualization of transcriptomics and metabolomics data.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 1;27(1):137-9. Epub 2010 Nov 23.
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.
García-Alcalde F, García-López F, Dopazo J, Conesa A.