FOCUS 0.29 – A model to Identify Organisms present in Metagenomes

FOCUS 0.29

:: DESCRIPTION

FOCUS, an innovative and agile composition based using non-negative least squares to profile and report abundant organisms present in me-tagenomic samples and their relative abundance without sequence length dependencies.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Python

:: DOWNLOAD

 FOCUS

:: MORE INFORMATION

Citation:

Silva, G. G. Z., D. A. Cuevas, B. E. Dutilh, and R. A. Edwards, 2014
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.
PeerJ, 2, e425, doi:10.7717/peerj.425.

MOABS 1.3.2 – Model based Analysis of Bisulfite Sequencing data

MOABS 1.3.2

:: DESCRIPTION

MOABS is a comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data

::DEVELOPER

Wei Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MOABS

:: MORE INFORMATION

Citation:

Genome Biol. 2014 Feb 24;15(2):R38. doi: 10.1186/gb-2014-15-2-r38.
MOABS: model based analysis of bisulfite sequencing data.
Sun D, Xi Y, Rodriguez B, Park HJ, Tong P, Meong M, Goodell MA, Li W.

SMOG 2.0.3 – Structure-based Models for Biomolecules

SMOG 2.0.3

:: 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

EBChangePoint 0.1.0 – Empirical Bayes Change-point Model

EBChangePoint 0.1.0

:: DESCRIPTION

EBChangePoint could efficiently pool information across genes to improve detection efficiency.

::DEVELOPER

EBChangePoint team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 EBChangePoint

:: MORE INFORMATION

Citation:

An empirical Bayes change-point model for identifying 3′ and 5′ alternative splicing by next-generation RNA sequencing.
Zhang J, Wei Z.
Bioinformatics. 2016 Feb 11. pii: btw060.

CellOrganizer 2.4 – Image-derived Models of Subcellular Organization and Protein Distribution

CellOrganizer 2.4

:: 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

:: DOWNLOAD

  CellOrganizer

:: MORE INFORMATION

Citation

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

GraphiteLifeExplorer 20120731 – Model in 3D Assemblies of Proteins and DNA

Graphite-LifeExplorer 20120731

:: DESCRIPTION

GraphiteLifeExplorer (G-LE,  former Graphite-MicroMégas) is a software for the building and visualization of macromolecular assemblies. Its main feature is the capability to create (and export) 3D models of DNA in a highly intuitive manner.

::DEVELOPER

Samuel Hornus

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  GraphiteLifeExplorer

:: MORE INFORMATION

Citation

Easy DNA modeling and more with GraphiteLifeExplorer
Samuel Hornus, Bruno Levy, Damien Larivière, Eric Fourmentin
Research article published 07 Jan 2013 PLOS ONE

MMB 2.15 – Model the Structure and Dynamics of Macromolecules

MMB 2.15

:: 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).

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

Lee Lab 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.

B-NEM – Boolean Nested Effect Models

B-NEM

:: DESCRIPTION

B-NEM combines the use of downstream effects with the higher resolution of signalling pathway structures in Boolean Networks.

::DEVELOPER

B-NEM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 B-NEM

:: MORE INFORMATION

Citation

Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models.
Pirkl M, Hand E, Kube D, Spang R.
Bioinformatics. 2015 Nov 17. pii: btv680.