WholeCellViz – Data Visualization for Whole-cell Models

WholeCellViz

:: DESCRIPTION

WholeCellViz is a web-based software program for visually analyzing whole-cell simulations.

::DEVELOPER

Karr Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

WholeCellViz

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 21;14:253. doi: 10.1186/1471-2105-14-253.
WholeCellViz: data visualization for whole-cell models.
Lee R1, Karr JR, Covert MW.

ModFit LT 5.0 – Flow Cytometry Modeling

ModFit LT 5.0

:: DESCRIPTION

ModFit LT follows the proud tradition of its predecessors – innovative features and unmatched flexibility to analyze even the most difficult DNA patterns. This is by far the most versatile DNA analysis software we have ever offered, featuring AutoDebris?, AutoAggregates?, AutoLinearity?, and exceptional batch processing. Powerful database support and an intuitive interface make this software a necessity in your laboratory. For fast, accurate analysis of DNA data files with report-ready screen layout, flexible databasing and user selectable analysis, look to ModFit LT™. This is the most comprehensive flow cytometric DNA Cell Cycle and Cell Proliferation analysis software available.

::DEVELOPER

Verity Software House

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

ModFit LT

:: MORE INFORMATION

Citation

Effects of resolution reduction on data analysis.
Hunsberger B, Bagwell CB, Herbert D, Bray C, Langweiler M.
Cytometry A. 2003 Jun;53(2):103-11.

X-CYT 1.3 – User-guided Automated Flow Cytometric Data Analysis

X-CYT 1.3

:: DESCRIPTION

X-Cyt follows a user-designed scheme and template to partition cytometric data in two or more dimensions for identifying cell populations of interest. In a small subset of samples, the user may try out several different partitioning schemes, and select one “optimal” partitioning to use as the template to guide the batch analysis of all samples.

::DEVELOPER

The Raychaudhuri Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R package

:: DOWNLOAD

 X-CYT

 :: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):19030-5. doi: 10.1073/pnas.1318322110. Epub 2013 Nov 4.
Application of user-guided automated cytometric data analysis to large-scale immunoprofiling of invariant natural killer T cells.
Hu X1, Kim H, Brennan PJ, Han B, Baecher-Allan CM, De Jager PL, Brenner MB, Raychaudhuri S.

CellOrganizer 2.8.1 – Image-derived Models of Subcellular Organization and Protein Distribution

CellOrganizer 2.8.1

:: 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
  • MatLab

:: DOWNLOAD

  CellOrganizer

:: MORE INFORMATION

Citation

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

BayesFlow 0.1 – Latent Modeling of Flow Cytometry Cell Populations

BayesFlow 0.1

:: DESCRIPTION

BayesFlow is a Bayesian hierarchical model, that models the variation across indivuals for clow cytometry data.

::DEVELOPER

Jonas Wallin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 BayesFlow

:: MORE INFORMATION

Citation

Erratum to: BayesFlow: latent modeling of flow cytometry cell populations.
Johnsson K, Wallin J, Fontes M.
BMC Bioinformatics. 2016 Mar 31;17(1):149.

flowFit 1.24.0 – Estimate Proliferation in Cell-tracking Dye Studies

flowFit 1.24.0

:: DESCRIPTION

flowFit is a Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments.

::DEVELOPER

flowFit team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 flowFit

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 2.
flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies.
Rambaldi D1, Pece S, Di Fiore PP.

CellFinder 1.5.1 – Study Annotations, Bibliography, Gene and Protein Expression in Stem Cells and Derivatives

CellFinder 1.5.1

:: DESCRIPTION

CellFinder maps validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Jan;42(Database issue):D950-8. doi: 10.1093/nar/gkt1264. Epub 2013 Dec 3.
CellFinder: a cell data repository.
Stachelscheid H1, Seltmann S, Lekschas F, Fontaine JF, Mah N, Neves M, Andrade-Navarro MA, Leser U, Kurtz A.

TIMER – Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells

TIMER

:: DESCRIPTION

TIMER (Tumor IMmune Estimation Resource) is a comprehensive resource for the clinical relevance of tumor-immune infiltrates, including B cells, CD4 and CD8 T cells, neutrophils, macrophages and dendritic cells.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Cancer Res. 2017 Nov 1;77(21):e108-e110. doi: 10.1158/0008-5472.CAN-17-0307.
TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells.
Li T, Fan J, Wang B, Traugh N, Chen Q, Liu JS, Li B, Liu XS.