GenoSkyline 1.2.1 – Tissue-specific Functional Annotation

GenoSkyline 1.2.1

:: DESCRIPTION

GenoSkyline functional annotations is currently available for 9 tissue/cell types. Pre-calculated GS scores for hg19 genome are available for download.

::DEVELOPER

Hongyu Zhao’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 GenoSkyline

:: MORE INFORMATION

Citation

Lu Q.*, Powles R.*, Wang Q., He B., and Zhao H.
Integrative tissue-specific functional annotations in the human genome provide novel insights on many complex traits and improve signal prioritization in genome wide association studies. (Submitted)

cellgraphs – Datastructure to Describe Cells in Tissue

cellgraphs

:: DESCRIPTION

Cellgraphs are a datastructure to describe cells in tissue.

::DEVELOPER

cellgraphs team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CellProfiler

:: DOWNLOAD

 cellgraphs

:: MORE INFORMATION

Citation

CD30 cell graphs of Hodgkin lymphoma are not scale-free – An image analysis approach.
Schäfer H, Schäfer T, Ackermann J, Dichter N, Döring C, Hartmann S, Hansmann ML, Koch I.
Bioinformatics. 2015 Sep 11. pii: btv542.

SERpredict – Predict Tissue or Tumor-Specific Exonised Repetitive element containing Isoforms

SERpredict

:: DESCRIPTION

SERpredict is an automated bioinformatics pipeline to predict tissue or tumor-specific repetitive element (RE)-containing isoforms in human and mouse DNA.

::DEVELOPER

HUSAR Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genet. 2007 Nov 6;8:78.
SERpredict: detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements.
Mersch B1, Sela N, Ast G, Suhai S, Hotz-Wagenblatt A.

CellSys 5.0 – Modular software for Physics-based Tissue Modelling in 3D

CellSys 5.0

:: DESCRIPTION

CellSys is a modular software tool for efficient off-lattice simulation of growth and organization processes in multicellular systems in two and three dimensions. It implements an agent-based model that approximates cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell.

::DEVELOPER

INRIA / IZBI Joint Research Group

:: SCREENSHOTS

CellSys

:: REQUIREMENTS

  •  Linux / WIndows

:: DOWNLOAD

 CellSys

:: MORE INFORMATION

Citation

A cell-based simulation software for multi-cellular systems.
Hoehme S, Drasdo D.
Bioinformatics. 2010 Oct 15;26(20):2641-2. doi: 10.1093/bioinformatics/btq437.

TST 1.4.2 – Tissue Simulation Toolkit

TST 1.4.2

:: DESCRIPTION

TST is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.

::DEVELOPER

The Biomodeling and Biosystems Analysis Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  •  Linux
  • C++ Compiler

:: DOWNLOAD

 TST

:: MORE INFORMATION

Citation

R M H Merks, & J A Glazier. (2005).
A cell-centered approach to developmental biology.
Physica A, 352(1), 113–130. doi:10.1016/j.physa.2004.12.028.

Gene Expression Barcode 3.0 – Determine the Genes Expressed for every Tissue and Cell Type in Humans and Mice

Gene Expression Barcode 3.0

:: DESCRIPTION

Gene Expression Barcode is designed to estimate which genes are expressed and which are unexpressed in a given microarray hybridization.

::DEVELOPER

Gene Expression Barcode team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

McCall et al.,
The Gene Expression Barcode 3.0: improved data processing and mining tools
Nucleic Acids Research. 2014 Jan;42:D938-D943.

arathGraphle – Functional Networks of Process, Tissue, and Developmental Stage Specific Interactions in Arabidopsis thaliana

arathGraphle

:: DESCRIPTION

ArathGraphle is an ensemble of genome-wide functional relationship networks predicted for A. thaliana using Bayesian integration of 60 experimental datasets. It is a hypothesis generation tool that integrates information from a variety of experiments to find consistent co-activities that might otherwise go unnoticed.

::DEVELOPER

Laboratory for Bioinformatics and Functional Genomics

:: SCREENSHOTS

ArathGraphle

:: REQUIREMENTS

  • Web Browser
  • Java

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Syst Biol. 2010 Dec 31;4:180. doi: 10.1186/1752-0509-4-180.
Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.
Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG.