Tag: Cell

CPPsite 2.0 – Database of Cell Penetrating Peptides

CPPsite 2.0

:: DESCRIPTION

CPPsite is a database of experimentally validated Cell Penetrating Peptides (10-30 amino acids).This database maintains experimentally validated CPPs (linear & cyclic; modified & non-natural residues) and wide range of cargos (nucleic acids, proteins, nanoparticles, PNA) delivered in cells using these peptides.

::DEVELOPER

CPPsite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides.
Agrawal P, Bhalla S, Usmani SS, Singh S, Chaudhary K, Raghava GP, Gautam A.
Nucleic Acids Res. 2016 Jan 4;44(D1):D1098-103. doi: 10.1093/nar/gkv1266.

CellPPD – Designing of Cell Penetrating Peptides

CellPPD

:: DESCRIPTION

CellPPD is an in silico method, which is developed to predict and design efficient cell penetrating peptides (CPPs). The main dataset used in this method consists of 708 experimentally validated CPPs.

::DEVELOPER

CellPPD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

In silico approaches for designing highly effective cell penetrating peptides.
Gautam A, Chaudhary K, Kumar R, Sharma A, Kapoor P, Tyagi A; Open source drug discovery consortium, Raghava GP.
J Transl Med. 2013 Mar 22;11:74. doi: 10.1186/1479-5876-11-74.

SIM – Cell- and Gene-based Computer Model for Mammalian Somitogenesis

SIM

:: DESCRIPTION

SIM is a software of cell- and gene-based computer model for mammalian somitogenesis, simulating a gene regulatory network combining clock (Hes1/7) and gradient (Tbx6, Fgf8, Wnt3a) with Delta/Notch signaling resulting in dynamic gene expression patterns as observed in vivo finally leading to boundary formation.

::DEVELOPER

Institute of Experimental Genetics , German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

SIM

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java 

:: DOWNLOAD

 SIM

:: MORE INFORMATION

Citation

Tiedemann HB, Schneltzer E, Zeiser S, Hoesel B, Beckers J, Przemeck GKH, Hrabě de Angelis M. (2012).
From dynamic Expression patterns to Boundary Formation in the Presomitic mesoderm
PLoS Comput Biol 8(6): e1002586. doi:10.1371/journal.pcbi.1002586

ECC – Classification of Cells or other Biological Objects

ECC

:: DESCRIPTION

ECC (Enhanced CellClassifier) empowers the user with machine learning tools for classification of cells or other biological objects. If basic image analysis has already been completed by CellProfiler, ECC will calculate a model, apply and iteratively improve the model and analyse a whole plate or a set of plates. By doing this, complex image analysis tasks an be solved efficiently.

::DEVELOPER

 Lab of Prof. Wolf Dietrich Hardt

:: SCREENSHOTS

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • matlab

:: DOWNLOAD

 ECC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Jan 14;11:30. doi: 10.1186/1471-2105-11-30.
Enhanced CellClassifier: a multi-class classification tool for microscopy images.
Misselwitz B, Strittmatter G, Periaswamy B, Schlumberger MC, Rout S, Horvath P, Kozak K, Hardt WD.

iCell 3.2 – APP of 3D View inside a Cell

iCell 3.2

:: DESCRIPTION

iCell is a free education application that gives you a 3D view inside a cell. iCell gives students, teachers, and anyone interested in biology a 3D view inside a cell. Included are examples of three types of cells: animal, plant, and bacteria. Learn about the various parts of the cell, which biologists, biochemists, and DNA researchers at the HudsonAlpha Institute study and use to advance the limits of biotechnology.

::DEVELOPER

HudsonAlpha Institute for Biotechnology

:: SCREENSHOTS

:: REQUIREMENTS

  • Android / IPad / IPhone

:: DOWNLOAD

 iCell for IOS/ for Android

:: MORE INFORMATION

Braincells 1.1 – Follow Cell and Axon Movements in Image Sequences

Braincells 1.1

:: DESCRIPTION

Braincells? is a manual image analyzing program. The original purpose of this software was to follow cell and axon movements in image sequences.

::DEVELOPER

Daniel Kirilly (biodread@freemail.hu) ,Gabor Ivancsy (korelacio@freemail.hu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Braincells

:: MORE INFORMATION

GCellIQ 1.0 – Genomic Cell Image Quantitator

GCellIQ 1.0

:: DESCRIPTION

GCellIQ ( Genomic Cell Image Quantitator ) is user-friendly open-source software package that aims to provide an automated pipeline for processing large volumes of digital images generated from high-content screening (HCS), including those by RNAi or small compound screening. It’s suitable for batch processing large image dataset with little human interference.

::DEVELOPER

TMHRI Center for Bioengineering and Informatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

GCellIQ

:: MORE INFORMATION

Citation:

Li F, Zhou X, Zhu J, Ma J, Huang X, et al. (2007)
High content image analysis for human H4 neuroglioma cells exposed to CuO nanoparticles.
Bmc Biotechnology 7: p. 66.

VersaCount 1.02 / VersaCount Max! 0.6 – Assist with the Counting of Cells

VersaCount 1.02

:: DESCRIPTION

VersaCount is a simple application to assist with the counting of cells by microscopy. When used with a numeric keypad, it can significantly increase counting efficiency when compared with a traditional clicker. Although it was designed for malaria work, it can be customized for a wide variety of cell counting applications.

VersaCount Max is a greatly expanded version of VersaCount that includes more registers, more equations, and more customizability.

::DEVELOPER

Charlie Kim, Derisi Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

VersaCount

:: MORE INFORMATION

Citation

Charles C Kim and Joseph L DeRisi
VersaCount: customizable manual tally software for cell counting
Source Code for Biology and Medicine 2010, 5:1

Living Cell 3D Screensaver 1.3

Living Cell 3D Screensaver 1.3

:: DESCRIPTION

LIVING CELL 3D SCREENSAVER is really something spectacular! You will see how numerous particles move about performing their little but extremely important functions. Once you dive inside the nucleus you will be able to watch the DNA molecule rotating around its axis.These absolutely mind-boggling scenes are accompanied by mysterious music that was specially composed to enhance your viewing pleasure.The screensaver provides superb environment for getting acquainted with the challenging but extremely interesting content of cell biology.

::DEVELOPER

3D screensavers

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Living Cell 3D Screensaver

:: MORE INFORMATION

N/A

 

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