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.

MiXCR 3.0.11 – Analysis of T- and B- cell Receptor Repertoire Sequencing data

MiXCR 3.0.11

:: DESCRIPTION

MiXCR is an universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data

::DEVELOPER

MiLaboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JRE
:: DOWNLOAD

 MiXCR

:: MORE INFORMATION

Citation:

Nat Methods. 2015 May;12(5):380-1. doi: 10.1038/nmeth.3364.
MiXCR: software for comprehensive adaptive immunity profiling.
Bolotin DA, Poslavsky S, Mitrophanov I, Shugay M3, Mamedov IZ, Putintseva EV, Chudakov DM.

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

CellTracker 1.0.3 – Cell Migration Detection

CellTracker 1.0.3

:: DESCRIPTION

is an image processing software to perform automated, semi-automated, and manual cell migration detection.

::DEVELOPER

CellTracker team

:: SCREENSHOTS

CellTracker

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • MatLab

:: DOWNLOAD

 CellTracker

:: MORE INFORMATION

Citation

CellTracker (not only) for dummies.
Piccinini F, Kiss A, Horvath P.
Bioinformatics. 2015 Nov 20. pii: btv686.

cellHTS2 2.35.0 / web cellHTS2 – Analysis of Cell-based RNAi Screens

cellHTS2 2.35.0 / web cellHTS2

:: DESCRIPTION

cellHTS2 is a software package implemented in Bioconductor/R to analyze cell-based high-throughput RNAi screens.

web cellHTS provides a user-friendly interface to cellHTS and a step-by-step tutorial how to use cellHTS for the analysis of high-throughput screening experiments.

::DEVELOPER

Boutros group & Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor
  • Java

:: DOWNLOAD

  cellHTS2 / web cellHTS2

:: MORE INFORMATION

Citation

Genome Biol. 2006;7(7):R66.
Analysis of cell-based RNAi screens.
Boutros M, Brás LP, Huber W.

Pelz., O., Gilsdorf, M., Boutros, M. (2010).
web cellHTS2: A web application for the analysis of high-throughput screening data.
BMC Bioinformatics 11:185.

CellProfiler 2.1.1 / CellProfiler Analyst 2.0 r11710 – Cell Image Analysis Software

CellProfiler  2.1.1

/ CellProfiler Analyst 2.0 r11710

:: DESCRIPTION

CellProfiler is a cell image analysis software which quantitatively measures phenotypes from thousands of images automatically, usually for high-throughput image-based cell screening experiments.CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

CellProfiler Analyst is free open-source software for exploring and analyzing large, high-dimensional image-derived data. It includes machine learning tools for identifying complex and subtle phenotypes.

::DEVELOPER

CellProfiler Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

CellProfilerCellProfiler Analyst

:: MORE INFORMATION

Citation:

Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM (2006)
CellProfiler: image analysis software for identifying and quantifying cell phenotypes.
Genome Biology 7:R100. PMID: 17076895

Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE (2008)
CellProfiler Analyst: data exploration and analysis software for complex image-based screens.
BMC Bioinformatics 9(1):482/doi: 10.1186/1471-2105-9-482. PMID: 19014601 PMCID: PMC2614436

LBIBCell 0.2 – Cell-Based Simulation Environment for Morphogenetic Problems

LBIBCell 0.2

:: DESCRIPTION

LBIBCell (Lattice Boltzmann Immersed Boundary) is a 2D simulation software to study the interplay between cell and tissue mechanics and biomolecular signaling.

::DEVELOPER

Computational Biology (CoBi)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LBIBCell

:: MORE INFORMATION

Citation

LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems.
Tanaka S, Sichau D, Iber D.
Bioinformatics. 2015 Mar 13. pii: btv147.

SmartCell v4.3 Beta3 – A Cell Network Simulation Program

SmartCell v4.3 Beta3

:: DESCRIPTION

SmartCell is a program developed to provide an idea of the evolution of a network in a whole, single cell. Based on stochastic algorithms, SmartCell needs multiple runs to have mean results.

::DEVELOPER

Serrano’s laboratory

:: SCREENSHOTS

SmartCell

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 SmartCell

:: MORE INFORMATION

Citation

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.
Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Tomás-Oliveira I, Serrano L.
Syst Biol (Stevenage). 2004 Jun;1(1):129-38.

Meta!Blast 2015.3 – Game to Explore the Complexities of Cell and Metabolic Biology

Meta!Blast 2015.3

:: DESCRIPTION

Meta!Blast is a real-time 3D action-adventure game that puts you in the pilot’s seat. Shrink down to microscopic size and explore the vivid, dynamic world of a soybean plant cell spinning out of control. Interact with numerous characters, fight off plant pathogens, and discover how important plants are to the survival of the human race. The eukaryotic cell is comprised of a dizzying array of molecules, proteins, and organelles. To understand the nature of these entities and their processes across both time and space can be a daunting task. The goal of Meta!Blast is to provide a medium that lends itself to the comprehension of cell and metabolic biology.

::DEVELOPER

Meta!Blast team

:: SCREENSHOTS

MetaBlast

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Meta!Blast 

:: MORE INFORMATION

Citation

Schneller W, Campbell PJ, Bassham D, Wurtele ES 2012.
Meta!Blast computer pipeline from science to 3D art to education.
Engineering of Virtual Reality, Eds: McDowall IE, Dolinsky M. International Society for Optics and Photonics. SPIE 828905. http://dx.doi.org/10.1117/12.911289