GENS 2.3.1 – Simulate Gene-environment and Gene-gene Interactions

GENS 2.3.1

:: DESCRIPTION

GENS2 (Gene-Environment iNteraction Simulator) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered.

::DEVELOPER

Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli “Federico II”

:: SCREENSHOTS

::REQUIREMENTS

Linux/ MacOsX/Windows
Python

:: DOWNLOAD

GENS

:: MORE INFORMATION

Citation

Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2.
Pinelli M, Scala G, Amato R, Cocozza S, Miele G.
BMC Bioinformatics. 2012 Jun 14;13:132. doi: 10.1186/1471-2105-13-132.

SBRT 2.0.0 – The Systems Biology Research Tool

SBRT 2.0.0

:: DESCRIPTION

SBRT (Systems Biology Research Tool) is a software to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows / MacOsX
Java
glpk

:: DOWNLOAD

SBRT

:: MORE INFORMATION

Citation

The Systems Biology Research Tool: evolvable open-source software
Jeremiah Wright and Andreas Wagner
BMC Systems Biology 2008, 2:55

CABERNET 1.1 – A Cytoscape APP for Augmented Boolean Models of Gene Regulatory Networks

CABERNET 1.1

:: DESCRIPTION

CABERNET is a Cytoscape 3.2.0 app for the generation, the simulation, the analysis and the visualization of Boolean models of gene regulatory networks, particularly focused on the investigation of their robustness.

::DEVELOPER

Data and Computational Biology @ University of Milan – Bicocca.

:: SCREENSHOTS

::REQUIREMENTS

Linux/windows/MacOsX
Java
Cytoscape

:: DOWNLOAD

CABERNET

:: MORE INFORMATION

Citation

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks.
Paroni A, Graudenzi A, Caravagna G, Damiani C, Mauri G, Antoniotti M.
BMC Bioinformatics. 2016 Feb 4;17(1):64. doi: 10.1186/s12859-016-0914-z.

DREM 2.0.4 / mirDREM – Dynamic Regulatory Events Miner

DREM 2.0.4/ mirDREM

:: DESCRIPTION

The DREM (Dynamic Regulatory Events Miner) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static or dynamic transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them.

mirDREM supports the use of microRNAs in DREM

::DEVELOPER

Systems Biology Group – Carnegie Mellon University

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX / Windows
Java

:: DOWNLOAD

DREM , mirDREM

:: MORE INFORMATION

Citation

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data.
Schulz MH, Devanny WE, Gitter A, Zhong S, Ernst J, Bar-Joseph Z.
BMC Syst Biol. 2012 Aug 16;6(1):104.

MH Schulz, KV Pandit, CLL Cardenas, A Namasivayam, N Kaminsky and Z. Bar-Joseph.
Reconstructing dynamic miRNA regulated interaction networks
PNAS, August 28, 2013, doi: 10.1073/pnas.1303236110

epistasisGA – Detecting Gene-gene Interactions in Case-parent Triad or Affected/unaffected Sibling studies

epistasisGA

:: DESCRIPTION

The epistasisGA package implements the GADGETS approach for detecting gene-gene interactions in case-parent triad or affected/unaffected sibling studies.

GADGETS is genetic algorithm for detecting epistasis using nuclear families

::DEVELOPER

Michael Nodzenski

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
R

:: DOWNLOAD

epistasisGA

:: MORE INFORMATION

Citation:

Nodzenski M, Shi M, Krahn JM, Wise AS, Li Y, Li L, Umbach DM, Weinberg CR.
GADGETS: A genetic algorithm for detecting epistasis using nuclear families.
Bioinformatics. 2021 Nov 12:btab766. doi: 10.1093/bioinformatics/btab766. Epub ahead of print. PMID: 34788792.

Metabomxtr 1.29.0 – R package for Mixture-model Analysis of non-targeted Metabolomics Data

Metabomxtr 1.29.0

:: DESCRIPTION

The functions in Metabomxtr package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.

::DEVELOPER

Michael Nodzenski

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
R
BioConductor

Metabomxtr

:: MORE INFORMATION

Citation

Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data.
Nodzenski M, Muehlbauer MJ, Bain JR, Reisetter AC, Lowe WL Jr, Scholtens DM.
Bioinformatics. 2014 Jul 29. pii: btu509

XlinkCyNET 1.4.3 – Generate Residue-to-residue connections provided by XL-MS in PIN

XlinkCyNET 1.4.3

:: DESCRIPTION

XlinkCyNET is an open-source Java plugin that generates residue-to-residue connections provided by XL-MS in protein interaction networks. It provides an interactive interface for the exploration of cross-links and offers various options to display protein domains.

::DEVELOPER

The Liu Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX /Windows
Java
Cytoscape

:: DOWNLOAD

XlinkCyNET

:: MORE INFORMATION

Citation:

Lima DB, Zhu Y, Liu F.
XlinkCyNET: A Cytoscape Application for Visualization of Protein Interaction Networks Based on Cross-Linking Mass Spectrometry Identifications.
J Proteome Res. 2021 Apr 2;20(4):1943-1950. doi: 10.1021/acs.jproteome.0c00957. Epub 2021 Mar 9. PMID: 33689356.

NEXCADE 2.1 – Perturbation Analysis for Complex Networks

NEXCADE 2.1

:: DESCRIPTION

Nexcade (Network EXtinction casCADEs) is an automated and interactive program for analysing complex systems that can be conceptualized by networks, and represented as interconnected matrices of interactions. The analytical framework employs a graph theoretical approach for inducing various kinds of perturbations on networks such as extinction cascade simulations, focusing on the changes in topology and connectivity of the network as a function of the perturbation. Perturbations are induced in a user-defined manner followed by analysis of the resulting sub-networks.

::DEVELOPER

Suresh Babu & Dr. Gitanjali Yadav

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

NEXCADE

:: MORE INFORMATION

Citation

PLoS One. 2012;7(8):e41827. doi: 10.1371/journal.pone.0041827. Epub 2012 Aug 3.
NEXCADE: perturbation analysis for complex networks.
Yadav G1, Babu S.

MIMO 1.0 – Molecular Interaction Maps Overlap

MIMO 1.0

:: DESCRIPTION

MIMO addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information.

::DEVELOPER

Group of Clinical Genomic Networks

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MIMO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 May 15;14:159. doi: 10.1186/1471-2105-14-159.
MIMO: an efficient tool for molecular interaction maps overlap.
Di Lena P1, Wu G, Martelli PL, Casadio R, Nardini C.

JANet – Javascript AgeFactDB Network-viewer

JANet

:: DESCRIPTION

JANet is a specialized 3D Network Exploration and Visualization for Lifespan Data Exploration from AgeFactDB.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows /MacOsX
Java

:: DOWNLOAD

JANet

:: MORE INFORMATION

Citation

Hühne R, Kessler V, Fürstberger A, Kühlwein S, Platzer M, Sühnel J, Lausser L, Kestler HA.
3D Network exploration and visualisation for lifespan data.
BMC Bioinformatics. 2018 Oct 23;19(1):390. doi: 10.1186/s12859-018-2393-x. PMID: 30352578; PMCID: PMC6199797.