TMARKER v2.158 – Cell Nuclei Counting and Staining Estimation

TMARKER v2.158

:: DESCRIPTION

TMARKER assists in cell nuclei counting and staining estimation of pathological immunohistochemical TMA images and non-TMA images.

::DEVELOPER

NEXUS Personalized Health Technologies

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

  TMARKER

:: MORE INFORMATION

Citation

J Pathol Inform. 2013 Mar 30;4(Suppl):S2. doi: 10.4103/2153-3539.109804.
TMARKER: A free software toolkit for histopathological cell counting and staining estimation.
Schüffler PJ, Fuchs TJ, Ong CS, Wild PJ, Rupp NJ, Buhmann JM.

SuperFine – Supertree Estimation

SuperFine

:: DESCRIPTION

SuperFine is software for constructing supertrees from source phylogenies.

::DEVELOPER

The Warnow Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • Python

:: DOWNLOAD

 SuperFine

:: MORE INFORMATION

Citation:

SuperFine: fast and accurate supertree estimation.
Swenson MS, Suri R, Linder CR, Warnow T.
Syst Biol. 2012 Mar;61(2):214-27. doi: 10.1093/sysbio/syr092.

PrinCCes 1.09 – Protein Internal Channel & Cavity Estimation

PrinCCes 1.09

:: DESCRIPTION

PrinCCes is a free computer program for the automatic visualization of voids in proteins or protein complexes. The input of the program is the PDB (Protein Data Bank) file of the structure.

::DEVELOPER

Dr. Czirják Gábor

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 PrinCCes

:: MORE INFORMATION

Citation

J Mol Graph Model. 2015 Sep 16;62:118-127. doi: 10.1016/j.jmgm.2015.09.013
PrinCCes: Continuity-based geometric decomposition and systematic visualization of the void repertoire of proteins.
Czirják G

SPEDRE – Systematic Parameter Estimation in Data-Rich Environments for Cell Signaling Dynamics

SPEDRE

:: DESCRIPTION

SPEDRE is a method for estimating rate constants in a biochemical signaling network, and it is tailored for a special class of data-rich problems with observations of all species — problems that occur mainly when using proteomics technologies such as SILAC.

::DEVELOPER

Lisa Tucker-Kellogg’s Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W187-91. doi: 10.1093/nar/gkt459.
SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments.
Nim TH, White JK, Tucker-Kellogg L.

QMEAN – Server for Model Quality Estimation

QMEAN

:: DESCRIPTION

The QMEAN server provides access to two scoring functions for the quality estimation of protein structure models which allow to rank a set of models and to identify potentially unreliable region within these.

::DEVELOPER

Protein Structure Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Feb 1;27(3):343-50. doi: 10.1093/bioinformatics/btq662. Epub 2010 Dec 5.
Toward the estimation of the absolute quality of individual protein structure models.
Benkert P1, Biasini M, Schwede T.

RSEM v1.3.3 – RNA-Seq Expression Estimation by Expectation-Maximization

RSEM v1.3.3

:: DESCRIPTION

RSEM (RNA-Seq expression estimation by Expectation-Maximization) estimates gene and isoform expression levels from RNA-Seq data with a statistical model that takes into account reads that map to multiple positions.

::DEVELOPER

Colin DeweyBo Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RSEM

:: MORE INFORMATION

Citation

Li, B. and Dewey, C. N.
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
BMC Bioinformatics 2011, 12:323

SBML-PET-MPI 1.2 – Parallel Parameter Estimation Tool for SBML based Models

SBML-PET-MPI 1.2

:: DESCRIPTION

SBML-PET-MPI is a parallel parameter estimation tool for Systems Biology Markup Language (SBML) based models. The tool allows the user to perform parameter estimation, parameter uncertainty and identifiability analysis by collectively fitting multiple experimental data sets.

::DEVELOPER

Zhike Zi

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows with Cygwin/ Linux / Mac OsX

:: DOWNLOAD

 SBML-PET-MPI

:: MORE INFORMATION

Citation:

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.
Zi Z. (2011)
Bioinformatics. 2011 Apr 1;27(7):1028-9.

REDEMPTION 20150708 – Reduced Dimension Ensemble Modeling and Parameter Estimation

REDEMPTION 20150601

:: DESCRIPTION

REDEMPTION is a MATLAB toolbox for the identification of parameters and parameter ensembles of ODE models from time-series data.

:: DEVELOPER

Chemical and Biological Systems Engineering Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • MatLab

:: DOWNLOAD

 REDEMPTION

:: MORE INFORMATION

Citation

REDEMPTION: Reduced Dimension Ensemble Modeling and Parameter Estimation.
Liu Y, Manesso E, Gunawan R.
Bioinformatics. 2015 Jun 14. pii: btv365.

BEGFE 1.1 – Bayesian Estimation of Gene Family Evolution

BEGFE 1.1

:: DESCRIPTION

BEGFE implements a Markov Chain Monte Carlo algorithm to estimate the posterior probability distribution of the birth and death rate parameters and the numbers of gene copies at the internodes of the phylogenetic tree. In addition, BEGFE can simulate gene family data under the birth and death model.

::DEVELOPER

Phylogenetics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/ Windows

:: DOWNLOAD

BEGFE

:: MORE INFORMATION

Citation

Liu, L., L. Yu, V. Kalavacharla, Z. Liu.
A Bayesian model for gene family evolution.
BMC Bioinformatics. 2011, 12:426

FRST 1.2 – Protein Model Quality Estimation Method

FRST 1.2

:: DESCRIPTION

FRST serves to validate the energy of a protein structure. The server computes both an overall and a per-residue energy profile of a protein structure. The energy profile can be visualized in different ways, including a per-residue plot and a colored structure representation, accessible as a series of dynamic web pages.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FRST

:: MORE INFORMATION

Citation:

Silvio C.E. Tosatto.
The Victor/FRST Function for Model Quality Estimation.
Journal of Computational Biology 2005; 12(10):1316-1327