Phylo-HMRF – Comparing 3D Genome Organization in Multiple Species

Phylo-HMRF

:: DESCRIPTION

Phylo-HMRF (Phylogenetic Hidden Markov Random Field model) identifies evolutionary patterns of 3D genome based on multi-species Hi-C data.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

Phylo-HMRF

:: MORE INFORMATION

Citation

Cell Syst. 2019 Jun 26;8(6):494-505.e14. doi: 10.1016/j.cels.
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.
Yang Y, Zhang Y, Ren B, Dixon JR, Ma J.

SIMBA – Organization of the Yeast Molecular Network by Integrated Analysis of Genome-wide Data

SIMBA

:: DESCRIPTION

The SIMBA yeast site allows interactive exploration of a large scale compendium of data from diverse high throughput experiments. You can explore the behavior of your favorite gene or sets of genes, compare the activity of various functional modules in different experimental conditions or test the relations between gene expression programs, protein interactions and transcription factor binding profiles.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 SIMBA

:: MORE INFORMATION

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.

ARTO – Analysis of Replication Timing and Organization

ARTO

:: DESCRIPTION

ARTO (Analysis of Replication Timing and Organization) uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. The software takes raw time of replication (ToR) measurement signals as input and outputs for each genomic location an estimate of its ToR and an association to CTR (constant ToR region) or TTR (Temporal Transition Region).

::DEVELOPER

Laboratory of Computational Biology at the Technion.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

  ARTO

:: MORE INFORMATION

Citation

Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.
Farkash-Amar S, David Y, Polten A, Hezroni H, Eldar YC, Meshorer E, Yakhini Z, Simon I.
PLoS One. 2012;7(11):e48986.

SpotLink 1.0 – Proteomics tool for Organization and Visualization

SpotLink 1.0

:: DESCRIPTION

SpotLink is the tool for organizing proteomics raw data. The data includes 2D gel images, Mass Spectrometry (MS and MS/MS), protein expression profiles and etc.. The data is collected after a series of proteomics experiment and categorized by individual spot on gel.

::DEVELOPER

Primegens Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 SpotLink

:: MORE INFORMATION