simbTUM 3.0a – Simulation of Stochastic processes and ODE models in Biology

simbTUM 3.0a

:: DESCRIPTION

simbTUM allows to define ODE-models or stochastic compartemental models of biological processes, to simulate, to fit data and to do some statistics (fitting and statistics for deterministic models only).

::DEVELOPER

Institute of Computational Biology, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

simbTUM

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 simbTUM

:: MORE INFORMATION

jagn 1.02 – Java-Based Model for Artificial Gene Networks Generation

jagn 1.02

:: DESCRIPTION

jagn is a software for an Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data, which can be used by computational methods to recover the network topology, and then, analyse the results based on complex networks measurements/topology.

::DEVELOPER

Fabrício Martins Lopes

:: SCREENSHOTS

jagn

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  jagn

:: MORE INFORMATION

Citation:

Lopes, Fabrício M.; Cesar-Jr, Roberto M.; Costa, Luciano da F.
Gene expression complex networks: synthesis, identification and analysis.
Journal of Computational Biology, v. 18, p. 1353-1367, 2011.

Sunflower 1.1.0 – Model for Natural Selection in Promoters

Sunflower 1.1.0

:: DESCRIPTION

Sunflower is an evolutionary model for promoters, analogous to the commonly used synonymous/nonsynonymous mutation models for protein-coding sequences.

::DEVELOPER

Michael M. Hoffman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Sunflower

:: MORE INFORMATION

Citation

Hoffman MM, Birney E. 2010.
An effective model for natural selection in promoters.
Genome Res. 20(5):685-692.

HAPMIXMAP 1.0 – Model HapMap Haplotypes

HAPMIXMAP 1.0

:: DESCRIPTION

HAPMIXMAP is a program for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program developed by Scheet and Stephens (2006).  The program models unphased genotype data on unrelated individuals, and fits a model in which linkage disequilibrium is generated by K independent Poisson arrival processes corresponding to K modal haplotype states.  This corresponds to the observation that typically 2-4 common haplotypes account for most of the allelic diversity in any haplotype block, and that rarer haplotypes are typically slight variants of these modal haplotypes.  The block-like structure of haplotypes in the genome, corresponding to ancestral recombination hotspots, is modelled by allowing the arrival rate to vary across the genome.

::DEVELOPER

Paul McKeigue

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HAPMIXMAP

:: MORE INFORMATION

phylolm 2.6.2 – R package for Fitting Phylogenetic Linear Regression models

phylolm 2.6.2

:: DESCRIPTION

phylolm is an R package providing a function for fitting phylogenetic linear regression models. The likelihood is calculated with an algorithm that is linear in the number of tips in the tree. The package also provides a function for simulating continuous traits along the tree.

::DEVELOPER

Lam Si Tung Ho

:: REQUIREMENTS

  • Linux/windows/ MacOsX
  • R Package

:: DOWNLOAD

 phylolm

:: MORE INFORMATION

Citation

Syst Biol. 2014 Feb 4. [Epub ahead of print]
A linear-time algorithm for Gaussian and non-Gaussian trait evolution models.
Ho LS, Ané C.

FiltRest3D – Filtering Protein Models by Fuzzy Restraints

FiltRest3D

:: DESCRIPTION

FiltRest3D is a software for scoring and ranking of models according to their agreement with user-defined restraints.Automatic methods for protein structure prediction (fold-recognition, de novo folding, and docking programs) produce large sets of alternative models. These large model sets often include many native-like structures, which are scored as high as false positives. Such native-like models can be more easily identified based on data from experimental analyses used as structural restraints (e.g. identification of nearby residues by crosslinking, chemical modification, site-directed mutagenesis, deuterium exchange coupled with mass spectrometry etc.)

FiltRest3D Web Server

::DEVELOPER

Bujnicki Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

FiltRest3D

:: MORE INFORMATION

Citation

Michal J. Gajda,Irina Tuszynska1, Marta Kaczor, Anastasia Yu. Bakulina and Janusz M. Bujnicki
FILTREST3D: discrimination of structural models using restraints from experimental data
Bioinformatics (2010) 26 (23): 2986-2987

SMOG 2.4.2 / OpenSMOG 1.1 – Structure-based Models for Biomolecules

SMOG 2.4.2 / OpenSMOG 1.1

:: DESCRIPTION

SMOG is a versatile software package for generating structure-based models.SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD.

OpenSMOG : Simulating SMOG models in OpenMM

::DEVELOPER

SMOG team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SMOG / OpenSMOG

:: MORE INFORMATION

Citation

de Oliveira AB Jr, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC.
SMOG 2 and OpenSMOG: Extending the limits of structure-based models.
Protein Sci. 2021 Oct 16. doi: 10.1002/pro.4209. Epub ahead of print. PMID: 34655449.

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.
Noel JK, Levi M, Raghunathan M, Lammert H, Hayes RL, Onuchic JN, Whitford PC.
PLoS Comput Biol. 2016 Mar 10;12(3):e1004794. doi: 10.1371/journal.pcbi.1004794

nondetects 2.22.0 – Model and Impute non-detects in qPCR data

nondetects 2.22.0

:: DESCRIPTION

nondetects is a suit of methods to model and impute non-detects in the results of qPCR experiments.

::DEVELOPER

Matthew N. McCall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 nondetects

:: MORE INFORMATION

Citation

On non-detects in qPCR data.
McCall MN, McMurray HR, Land H, Almudevar A.
Bioinformatics. 2014 Apr 23. pii: btu239

ZIBR v0.1 – Zero-Inflated Beta Random Effect model

ZIBR v0.1

:: DESCRIPTION

ZIBR is a package for fitting zero-inflated mixed-effects models for repeated measureed microbiome data.

::DEVELOPER

Hongzhe Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

ZIBR

:: MORE INFORMATION

Citation

Chen EZ, Li H.
A two-part mixed-effects model for analyzing longitudinal microbiome compositional data.
Bioinformatics. 2016 Sep 1;32(17):2611-7. doi: 10.1093/bioinformatics/btw308. Epub 2016 May 14. PMID: 27187200; PMCID: PMC5860434.

Cromwell 1.0 – The New Model Processor for Mass Spectrometry Data

Cromwell 1.0

:: DESCRIPTION

Cromwell is an implementation of our algorithms for low-level processing of mass spectrometry proteomics data. Cromwell represents our third attempt (at least) to find a method to process spectra that both works quickly and achieves reasonably good results.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab

:: DOWNLOAD

 Cromwell

:: MORE INFORMATION

Citation

Cancer Inform. 2005;1:41-52.
Understanding the characteristics of mass spectrometry data through the use of simulation.
Coombes KR, Koomen JM, Baggerly KA, Morris JS, Kobayashi R.