nem 2.60.0 – Nested Effects Models

nem 2.60.0

:: DESCRIPTION

The package ‘nem‘ allows to reconstruct features of pathways from the nested structure of perturbation effects.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 nem

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Nov 1;24(21):2549-50. doi: 10.1093/bioinformatics/btn446. Epub 2008 Aug 21.
Analyzing gene perturbation screens with nested effects models in R and bioconductor.
Fröhlich H1, Beissbarth T, Tresch A, Kostka D, Jacob J, Spang R, Markowetz F.

TiMEx 0.99 – A Waiting Time Model for Mutually Exclusive Cancer Alterations

TiMEx 0.99

:: DESCRIPTION

TiMEx is a new generative probabilistic model for the de novo detection of mutual exclusivity patterns of various degrees across carcinogenic alterations.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 TiMEx

:: MORE INFORMATION

Citation:

TiMEx: a waiting time model for mutually exclusive cancer alterations.
Constantinescu S, Szczurek E, Mohammadi P, Rahnenführer J, Beerenwinkel N.
Bioinformatics. 2015 Jul 9. pii: btv400.

CellOrganizer 2.8.1 – Image-derived Models of Subcellular Organization and Protein Distribution

CellOrganizer 2.8.1

:: DESCRIPTION

The CellOrganizer project provides tools for :learning generative models of cell organization directly from images/ storing and retrieving those models in XML files/ synthesizing cell images (or other representations) from one or more models

::DEVELOPER

CellOrganizer TEam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac /  Linux
  • MatLab

:: DOWNLOAD

  CellOrganizer

:: MORE INFORMATION

Citation

Methods Cell Biol. 2012;110:179-93.
CellOrganizer: Image-derived models of subcellular organization and protein distribution.
Murphy RF.

CellBlender 3.5.0 – Blender addon for Creation, Simulation, Visualization, and analysis of 3D Cell Models

CellBlender 3.5.0

:: DESCRIPTION

CellBlender is an addon for Blender-2.6x to create computational cell biology models for use in MCell and potentially other cell simulation biophysics engines. In CellBlender 0.49 you can create geometric objects, assign surface regions to said objects, export the objects as MCell MDL geometry files, set MCell simulation parameters, import a time-series of MCell VIZ_OUTPUT, and interactively playback or render an animation of the VIZ_OUTPUT. MDL import along with other features will be added in future versions.

CellBlender is replacing PSC_DX and DReAMM as the primary tool to visualize MCell simulations.

::DEVELOPER

The National Center for Multiscale Modeling of Biological Systems (MMBioS)

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 CellBlender

:: MORE INFORMATION

Citation:

Stiles, JR, and Bartol, TM. (2001).
Monte Carlo methods for simulating realistic synaptic microphysiology using MCell.
In: Computational Neuroscience: Realistic Modeling for Experimentalists, ed. De Schutter, E. CRC Press, Boca Raton, pp. 87-127.

DNC-MIX – Model Distribution of Gene Expression Profile of Test Sample as Mixture of Distributions

DNC-MIX

:: DESCRIPTION

DNC-MIX models the distribution of the gene expression profile of a test sample as a mixture, with each component characterizing the expression levels in a class, and assigns a class label to each test sample

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DNC-MIX

:: MORE INFORMATION

Citation

Alexandridis, R., Lin, S., Irwin, M. (2004)
Class discovery and classification of tumor samples using mixture modeling of gene expression data.
Bioinformatics, 20, 2545-2552.

 

MAINMAST 1.0 – MAINchain Model trAcing using Spanning Tree from a EM map

MAINMAST 1.0

:: DESCRIPTION

MAINMAST is a de novo modeling protocol to build an entire protein 3D model directly from near-atomic resolution EM map.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

MAINMAST

:: MORE INFORMATION

Citation

De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge.
Terashi G, Kihara D.
J Struct Biol. 2018 Nov;204(2):351-359. doi: 10.1016/j.jsb.2018.07.013.

bnpsd 1.1.1 – Model and Simulate Admixed Populations

bnpsd 1.1.1

:: DESCRIPTION

bnpsd (Balding-Nichols Pritchard-Stephens-Donnelly) is an R package to model and simulate admixed populations

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

bnpsd

:: MORE INFORMATION

Citation

Ochoa, Alejandro, and John D. Storey. 2016a.
FST And Kinship for Arbitrary Population Structures I: Generalized Definitions.”
bioRxiv doi:10.1101/083915.

Ochoa, Alejandro, and John D. Storey. 2016b.
FST And Kinship for Arbitrary Population Structures II: Method of Moments Estimators.
bioRxiv doi:10.1101/083923.

Path2Models – Collection of Models automatically generated from Pathway Resources

Path2Models

:: DESCRIPTION

Path2Models automatically generates mathematical models from biological pathway representations using a suite of freely available software. Computed models from over 2600 organisms encoded in SBML and SBGN are available through the BioModels Database.

::DEVELOPER

BioModels team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Path2Models: large-scale generation of computational models from biochemical pathway maps.
Büchel F, et al.
BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.

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.

PSTAG 2.1.4a – Model Pseudoknot RNA Structure

PSTAG 2.1.4a

:: DESCRIPTION

PSTAG (Pair Stochastic Tree Adjoining Grammars) for RNA sequences including pseudoknotted structures.

::DEVELOPER

Sakakibara Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/WIndows

:: DOWNLOAD

 PSTAG

:: MORE INFORMATION

Citation:

Matsui, H, Sato, K. and Sakakibara, Y.,
Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures,
Bioinformatics, vol.21, no.11, pp.2611-2617, 2005