CAMP 3.3 – Conditional Allele Mouse Planner

CAMP 3.3

:: DESCRIPTION

CAMP has been created to help scientists set up a breeding strategy and calculate the costs of generating conditional knockout mice.

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

camp

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

CAMP

:: MORE INFORMATION

Citation

Hoffert JD, Pisitkun T, Miller RL.
Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles.
Transgenic Res. 2012 Jun;21(3):665-9. doi: 10.1007/s11248-011-9545-3.

pirnaPre 1.0.0 – piRNA Targets on mRNAs in Mouse

pirnaPre 1.0.0

:: DESCRIPTION

pirnaPre is a SVM classifier based on a combination of Miwi CLIP-Seq derived features and position derived features to predict potential targets of piRNAs on mRNAs.

::DEVELOPER

pirnaPre team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 pirnaPre

:: MORE INFORMATION

Citation

Computational identification of piRNA targets on mouse mRNAs.
Yuan J, Zhang P, Cui Y, Wang J, Skogerbø G, Huang DW, Chen R, He S.
Bioinformatics. 2015 Dec 16. pii: btv729.

AutoChrom3D v1 – Modeling and Visualization the 3D Structure of Human or Mouse Chromatin

AutoChrom3D v1

:: DESCRIPTION

AutoChrom3D was built for modeling and visualization the 3D structure of human or mouse chromatin. The 3D structure of chromatin is calculated and generated based on HiC data.

::DEVELOPER

Zhi-Luo Deng

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Perl
:: DOWNLOAD

  AutoChrom3D 

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Oct;41(19):e183. doi: 10.1093/nar/gkt745. Epub 2013 Aug 21.
The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling.
Peng C1, Fu LY, Dong PF, Deng ZL, Li JX, Wang XT, Zhang HY.

Netview – Explore the Human and Mouse Gene Regulatory Networks

Netview

:: DESCRIPTION

Netview is a free web tool that allow end users to explore the human and mouse gene regulatory networks. Users can query the system by providing a gene identifier and the boundaries of the subnetwork being explored. The system provides the list of interactions, the enriched Gene Ontology Terms together with a graphical representation of the subnetwork.

::DEVELOPER

di Bernardo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1101:179-96. doi: 10.1007/978-1-62703-721-1_10.
Reverse engineering transcriptional gene networks.
Belcastro V, di Bernardo D.

TFCat 1.0 – The Curated Catalog of Mouse and Human Transcription Factors

TFCat 1.0

:: DESCRIPTION

TFCat (Transcription Factor Catalog) is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature.

::DEVELOPER

The Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Genome Biol. 2009;10(3):R29. doi: 10.1186/gb-2009-10-3-r29.
TFCat: the curated catalog of mouse and human transcription factors.
Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach JC, Sladek R.

BioLegend CD Posters 1.4 / BioLegend Tools for iPad 1.4 – Information about Mouse and Human CD Molecules

BioLegend CD Posters 1.4 / BioLegend Tools for iPad 1.4

:: DESCRIPTION

BioLegend CD Posters / BioLegend Tools for iPad provides you with important information about your mouse and human CD Molecules, Cytokines and Chemokines.

BioLegend Tools for iPad also includes BioLegend pathway posters, an antibody usage calculator, and a lab timer. What’s more it is optimized for the iPad for speed and clarity.

::DEVELOPER

BioLegend

:: SCREENSHOTS

bcp

:: REQUIREMENTS

  • iPhone /  iPad

:: DOWNLOAD

 BioLegend CD Posters / BioLegend Tools for iPad

:: MORE INFORMATION

GRIMM 2.01 / MGR 2.03 – Multiple Genome Rearrangements / In Man and Mouse

GRIMM 2.01 / MGR 2.03

:: DESCRIPTION

GRIMM is a tool for analyzing rearrangements in pairs of genomes, including unichromosomal and multichromosomal genomes, and signed and unsigned data.

MGR is a tool for constructing phylogenies based on gene order for unichromosomal and multichromosomal genomes.

::DEVELOPER

Glenn Tesler , Guillaume Bourque

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GRIMM / MGR

:: MORE INFORMATION

Citation:

GRIMM: genome rearrangements web server.
Tesler G.
Bioinformatics. 2002 Mar;18(3):492-3.

webMGR: an online tool for the multiple genome rearrangement problem.
Lin CH, Zhao H, Lowcay SH, Shahab A, Bourque G.
Bioinformatics. 2010 Feb 1;26(3):408-10. Epub 2009 Dec 18.

ACEScan 1.0 – Prediction of Conserved Alternatively Spliced Exons from pairs of Conserved Mouse/Human Exons

ACEScan 1.0

:: DESCRIPTION

ACEScan is a webtool of identification and analysis of alternative splicing events conserved in human and mouse.

::DEVELOPER

Burge Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yeo, G., Van Nostrand, E., Holste, D., Poggio, T. and Burge, C. B. (2005).
Identification and analysis of alternative splicing events conserved in human and mouse.
Proc. Natl. Acad. Sci. USA 102, 2850-2855

MICE 1.4 – Mouse Information & Classification Entity

MICE 1.4

:: DESCRIPTION

MICE (Mouse Information and Classification Entity) is a program aimed at facilitating the monitoring of animals in their facility. It consists of a virtual facility in which scientists can perform all the tasks done in the real world (i.e., receiving animals, breeding, etc…). Each animal is recorded with all associated information (birth date, cage number, ID number, tail analysis number, parents, genetic status, genetic background and more), allowing for reliable tracking. Animals can be identified, grouped, sorted, moved…, according to any parameter of interest to the scientist, including associated comments. Crossings are automatically processed by the program, which determines the new genetic background, generation number, cage location and due date.

MICE reminds the user when births are expected, and entering the newborn animals only requires a few clicks (of the mouse!). The genealogy of each animal can be determined in two different ways, including a visual tree from which each ancestor’s information can be retrieved.

::DEVELOPER

P. Pognonec

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

MICE for Win ; for Mac

:: MORE INFORMATION

Citation:

MICE, a program to track and monitor animals in animal facilities. BMC Genetics 2001 Mar;2(1):4

Any comment and/or proposal concerning this application is welcome! Please contact P. Pognonec for additional information.