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

MMB 2.19 – Model the Structure and Dynamics of Macromolecules

MMB 2.19

:: DESCRIPTION

MMB (a contraction of MacroMolecule Builder) was previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein as well as RNA. Aside from the renaming, MMB 2.3 differs from RNABuilder 2.2 in two important ways. Release 2.3 has fully overhauled guts. It uses the BiopolymerClassContainer, a much cleaner programming construct which will make future upgrades and extensions more efficient. As of release 2.3.4, we link against new Molmodel binaries which have more efficient tracking of atoms in rigid regions. This yields a two-fold speed improvement and four-fold lower memory requirement for many problems. Also in this release, some rarely used features have been removed, but these were never in the tutorial literature so their absence should go largely unnoticed. The default input file name is now commands.dat rather than contacts.dat. A couple of somewhat obscure bugs were fixed. The error messages are more informative, and more aggressively prevent the user from risky or incorrect construction of the input file.

::DEVELOPER

MMB Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • VMD

:: DOWNLOAD

 MMB

:: MORE INFORMATION

Citation:

Samuel Coulbourn Flores, Russ B. Altman.
Structural insights into Pre-Translocation Ribosome Motions.
In Proceedings of Pacific Symposium on Biocomputing’2011. pp.205~216 (2011)

Samuel Flores and Russ Altman,
Turning limited experimental information into 3D models of RNA,
RNA 16(9):1769-78 (2010).

SMOG 2.2 – Structure-based Models for Biomolecules

SMOG 2.2

:: 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.

::DEVELOPER

SMOG team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SMOG

:: MORE INFORMATION

Citation

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