Arrêt de l'ensemble des services de la plateforme Migale à partir du lundi 3 avril 2017

La plateforme Migale sera indisponible du 3 au 10 avril 2017. Cette indisponibilité est dûe à l'arrêt du DataCenter Ile-de-France qui héberge l'infrastructure de la plateforme.

Merci d'avance de votre compréhension.

Pour toutes questions ou informations supplémentaires, merci de contacter help.migale@jouy.inra.fr.

Visualisation


VersionMAJ

circos

0.642013-01-20DownloadDoc
Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive.

Remarque
Run Unix # circosRun Web #

VersionMAJ

coot

0.72014-05-20DownloadDoc
Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.

Remarque Citing Coot and Friends If have found this software to be useful, you are requested (if appropriate) to cite: "Features and Development of Coot" P Emsley, B Lohkamp, W Scott, and K Cowtan Acta Cryst. (2010). D66, 486-501 Acta Crystallographica Section D-Biological Crystallography 66: 486-501
Run Unix # cootRun Web #

VersionMAJ

igv

2.3.672016-01-11DownloadDoc
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

Remarque To cite your use of IGV in your publication: James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011)
Run Unix # igvRun Web #

VersionMAJ

KronaTools

2.62016-01-13DownloadDoc
Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

Remarque
Run Unix # Run Web #

VersionMAJ

matrix2png

1.2.12011-05-30DownloadDoc
Matrix2png is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. Our group has found it useful for imaging all kinds of matrix-based data, not just microarray data.

Remarque If you use images created with matrix2png for publication or presentation, please cite:Pavlidis, P. and Noble W.S. (2003) Matrix2png: A Utility for Visualizing Matrix Data. Bioinformatics 19: 295-296 (abstract).Readers of the Bioinformatics application note: Here is the color version of the figure from the paper (pdf format).
Run Unix # matrix2pngRun Web #

VersionMAJ

phenix

1.8.12012-12-12DownloadDoc
PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods.

Remarque Citing PHENIX: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010).
Run Unix # phenixRun Web #

VersionMAJ

showVenn

1.02010-02-26DownloadDoc
Cet outil permet de manipuler des listes d'identifiants sous la forme d'un diagramme de Venn. On peut ainsi trouver les éléments en commun ou originaux de 5 listes différentes. En cliquant sur les différents territoires du diagramme, l'utilisateur récupère les identifiants qui correspondent au sous ensemble sélectionné.

Remarque
Run Unix # Run Web # http://tomcat.jouy.inra.fr/Venn/

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