DeepFun – Tissue and Cell Type specific Deep Learning Sequence-based model to Decipher Noncoding Variant Effects.

DeepFun

:: DESCRIPTION

DeepFun is a deep-learning-based model for functional evaluation of genetic variants at the single-base resolution.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

Pei G, Hu R, Jia P, Zhao Z.
DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner.
Nucleic Acids Res. 2021 Jul 2;49(W1):W131-W139. doi: 10.1093/nar/gkab429. PMID: 34048560; PMCID: PMC8262726.

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

Hoehme Lab

:: 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.

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)

NASFinder – Identify Tissue-specific, Omics-determined Sub-networks

NASFinder

:: DESCRIPTION

The NASFinder (Network Activity Score Finder) is a web service for topological and functional analysis of sub-networks connecting an omics-determined module.

::DEVELOPER

The Microsoft Research – University of Trento Centre for Computational and Systems Biology

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • JRE

:: DOWNLOAD

NASFinder

:: MORE INFORMATION

Citation

Sci Rep, 6, 28851 2016 Jul 7
Systems View of Adipogenesis via Novel Omics-Driven and Tissue-Specific Activity Scoring of Network Functional Modules
Isar Nassiri et. al.

TST 1.4.3 – Tissue Simulation Toolkit

TST 1.4.3

:: 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.

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.

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