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

CreateFibril 2.5 – Build Atomic Resolution Models of Protein Fibrils

CreateFibril 2.5

:: DESCRIPTION

CreateFibril is a tool to build atomic resolution models of protein fibrils.

::DEVELOPER

CreateFibril team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 CreateFibril

:: MORE INFORMATION

Citation

Biophys J. 2013 Feb 5;104(3):683-93. doi: 10.1016/j.bpj.2012.12.037.
Computational assembly of polymorphic amyloid fibrils reveals stable aggregates.
Smaoui MR1, Poitevin F, Delarue M, Koehl P, Orland H, Waldispühl J.

MICC 1.0 – Model based Interaction Calling from ChIA-PET data

MICC 1.0

:: DESCRIPTION

MICC is an R package which provides methods to detect chromatin interactions from ChIA-PET data.

::DEVELOPER

MICC team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R

:: DOWNLOAD

 MICC

:: MORE INFORMATION

Citation

MICC: an R package for identifying chromatin interactions from ChIA-PET data.
He C, Zhang MQ, Wang X.
Bioinformatics. 2015 Jul 31. pii: btv445.

BkTree 20160124 – Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model

BkTree 20160124

:: DESCRIPTION

BkTree is an utility capable of predicting all familites of RNA nucleotide interactions, including base-base, base-phosphate, base-ribose, and base-stacking interactions, from the input query sequence (along with predicted or known canonical Watson-Crick base pairs).

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BkTree

:: MORE INFORMATION

Citation

Accurate Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model.
Ding L, Xue X, LaMarca S, Mohebbi M, Samad A, Malmberg RL, Cai L.
Bioinformatics. 2015 Apr 16. pii: btv210.

MEED – Model Expansion Experimental Design

MEED

:: DESCRIPTION

MEED is a tool for practical microarray experimental design that can suggest experiments so as to avoid ambiguity in the identification of regulatory relatrionships.

::DEVELOPER

Irit Gat-Viks laboratory.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WIndows/Linux
  • R
  • C++

:: DOWNLOAD

 MEED

:: MORE INFORMATION

Citation:

Szczurek E, Gat-Viks I, Tiuryn J, Vingron M:
Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments.
Mol Syst Biol 2009, 5:287.

CellDesigner 4.4.2 – Biochemical Networks Modeling Tool

CellDesigner 4.4.2

:: DESCRIPTION

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW).

::DEVELOPER

Systems Biology Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

CellDesigner ; Tutorial

:: MORE INFORMATION

CellDesigner is free to use >> License text

Citation