Tag: Model

GRaPe 1.0 – Generation of Generic Rate Equations for all Reactions in a Model

GRaPe 1.0

:: DESCRIPTION

GRaPe (Gene Reaction Protein Builder) was developed to enable the generation of generic rate equations for all reactions in a model. It encompasses an algorithm for estimating the concentration of proteins for a reaction to reach a particular steady state when kinetic parameters are unknown, and two robust methods for parameter estimation. It also allows for the seamless integration of gene expression or protein levels into a reaction and can generate equations for both transcription and translation.

::DEVELOPER

Pathways and biological systems modelling group , The University of Manchester

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

GRaPe

:: MORE INFORMATION

Citation

Adiamah DA, Handl J, Schwartz JM (2010).
Streamlining the construction of large-scale dynamic models using generic kinetic equations.
Bioinformatics 26: 1324-31.

MILLIPEDE 1.1.0 – Model for Identifying Transcription Factor Binding Sites

MILLIPEDE 1.1.0

:: DESCRIPTION

MILLIPEDE is a method that outperforms a leading recent method, centipede, marginally in human but dramatically in yeast (average auROC across 20 TFs increases from 74% to 94%). The sofware is based on logistic regression and thus benefits from supervision, but we show that partially and completely unsupervised variants perform nearly as well.

::DEVELOPER

Alex Hartemink

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R package

:: DOWNLOAD

 MILLIPEDE

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2013:80-91.
Using DNase digestion data to accurately identify transcription factor binding sites.
Luo K, Hartemink AJ.

Visualisation tools – Display 2-loop & 3-loop Arabidopsis Clock Models

Visualisation tools

:: DESCRIPTION

Visualisation tools display moving plots of 2 and 3D time series and limit cycles from our 2-loop and 3-loop Arabidopsis clock models.

::DEVELOPER

The Millar research group

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Visualisation tools

:: MORE INFORMATION

Citation

James C W Locke, Megan M Southern, László Kozma-Bognár, Victoria Hibberd, Paul E Brown, Matthew S Turner & Andrew J Millar
Extension of a genetic network model by iterative experimentation and mathematical analysis
Molecular Systems Biology 1:2005.0013

ADMIXMAP 3.8.3103 – Model Admixture using Marker Genotype data

ADMIXMAP 3.8.3103

:: DESCRIPTION

ADMIXMAP is a general-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus.

::DEVELOPER

Paul McKeigue

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ADMIXMAP

:: MORE INFORMATION

Citation

Design and analysis of admixture mapping studies.
Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM.
Am J Hum Genet. 2004 May;74(5):965-78. Epub 2004 Apr 14.

DBM – Dynamic Bayesian Markov model for Genotype Calling

DBM

:: DESCRIPTION

DBM is a Dynamic Bayesian Markov model for genotype calling, haplotype inference, de novo inference of population structure and local admixture for next-gen sequencing data.

::DEVELOPER

Yu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DBM

:: MORE INFORMATION

Citation

A dynamic Bayesian Markov model for phasing and characterizing haplotypes in next-generation sequencing.
Zhang Y.
Bioinformatics (2013) 29 (7): 878-885.

MIRACH 1.0 – Statistical Online Model Checker for Biological Pathway Models

MIRACH 1.0

:: DESCRIPTION

MIRACH , a Statistical Online Model Checker for Biological Pathway Models, based on the PLTLs formalism for expressing the rules/properties to be checked. MIRACH can currently check pathways models written either in CSML or SBML.

::DEVELOPER

Computational Biology Laboratory, School of Computing, National University of Singapore

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 MIRACH

:: MORE INFORMATION

Citation:

MIRACH: efficient model checker for quantitative biological pathway models.
Koh CH, Nagasaki M, Saito A, Li C, Wong L, Miyano S.
Bioinformatics. 2011 Mar 1;27(5):734-5. doi: 10.1093/bioinformatics/btq727. Epub 2011 Jan 5.

Judi 1.0 – Data and Model Integration for Biology

Judi 1.0

:: DESCRIPTION

Judi ( Java platform for unsupervised data and model integration ) is a software written in Java, with an aim to provide a user-friendly tool for general unsupervised data and model integration. For many problems in biology, such as gene function prediction and differentially expressed gene identification, and general feature selection problems, there are often multiple data sources available and/or multiple models/tools have been developed to solve the problem. The combination of evidences from multiple data sources and the integration of the output from different models will probably enhance our ability to solve the problem. Judi implements several algorithms and also provides a user-friendly interface to facilitate this process.

::DEVELOPER

Xuebing Wu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

  Judi

:: MORE INFORMATION

Citation

Xuebing Wu, Feng Zeng, Rui Jiang (2008)
Integrative inference of gene networks from expression data.
Poster at RECOMB Regulatory Genomics/Systems Biology/DREAM3, Oct 29-Nov 2, 2008. MA, USA

CMCompare 0.0.1 – Discriminatory Power of RNA Family Models

CMCompare 0.0.1

:: DESCRIPTION

The CMCompare program takes two Infernal covariance models and calculates the Link sequence and its Link score. The Link sequence is the sequence scored by both models highest at the same time. Two models with a high Link score are not well separated from each other.

::DEVELOPER

Ivo Hofacker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CMCompare

:: MORE INFORMATION

Citation

Discriminatory power of RNA family models
Höner zu Siederdissen, Christian and Hofacker, Ivo L.
Bioinformatics, 2010, 26, 453-459

FBA 2.0 – Flux Balance Analysis E.coli Model

FBA 2.0

:: DESCRIPTION

FBA (flux-balance analysis) is an software used in the analysis of metabolic behavior. FBA can be used to study metabolic systems.  The fundamental principle of FBA is the conservation of mass.

Another FBA website @ UCSD

::DEVELOPER

Jeremy S. Edwards & Bernhard Palsson

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

FBA

:: MORE INFORMATION

Citation:

Edwards JS, Ibarra RU, Palsson BO. (2001) Nat Biotechnol Feb;19(2):125-30 In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.

Edwards JS, Palsson BO (2000) Proc Natl Acad Sci May 9;97(10):5528-33. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.