ANISEED

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 23/03/11
  • Minor correction: 12/04/12
Keywords

ANISEED : representing and modeling the ascidian development

This software was developed (or is under development) within the higher education and research community. Its stability can vary (see fields below) and its working state is not guaranteed.
  • Web site
  • System: UNIX-like, Windows, MacOS X
  • Current version: ANISEED V3.0 - 03/05/2007
  • License(s): GPL
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Olivier Tassy, Fabrice Daian, Delphine Dauga, Daniel Sobral, Pierre Khoueiry
  • Contact designer(s): Delphine.DAUGA@univmed.fr
  • Laboratory, service: IBDML

 

General software features

ANISEED (Ascidian Network for In situ Expression and Embryological Data) is a generic system designed to offer a representation of embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis).

The system was first applied to early ascidians (Ascidian NISEED). Ascidians, which are marine invertebrate chordates, are model organisms of choice because their embryos develop with a small number of cells and an invariant lineage, allowing their study a cellular level of resolution. Moreover, ascidians display a larval body plan similar to that of vertebrates suggesting that the study of these simple embryos will shed light on the more complex vertebrates.

The content of the ANISEED database can be explored via the Developmental Browser (http://aniseed-ibdm.univ-mrs.fr), which uses hub pages to organize key information about embryo anatomy, gene function, gene expression, regulatory interactions, and literature. Part of the ANISEED data can be displayed in their genomic context via a Gbrowse-based genome browser. In addition, a “3D Virtual Embryo” module is used both to map molecular or anatomical information onto interactive 3D embryo models, and to generate a quantitative description of the geometry of individual embryonic territories/cells and their topological arrangement, which are then imported into ANISEED. The maintenance of the system is facilitated by two sets of administration and curation tools

Context in which the software is used

ANISEED is the first integrated system for ascidians and is widely used in the growing community of ascidian laboratories. Over the past 2 years the system received 51,000 unique visitors, mainly from France, Japan, the USA, and Italy—all countries with strong ascidian communities. In addition, the generic nature of the system and its design principles may hold lessons for the future of model organism databases.

Publications related to the software

Tassy, O., Dauga, D., Daian, F., Sobral, D., Robin, F., Khoueiry, P., Salgado, D., Fox, V., Caillol, D., et al. Digital representation of embryonic development: the ANISEED system.
Genome Research 2010 Oct;20(10):1459-68

Sobral, D., Tassy, O., and Lemaire, P. Highly divergent gene expression programs can lead to similar chordate larval body plans.
Curr Biol. 2009 Dec 15;19(23):2014-9.

Tassy, O., Daian, F., Hudson, C., Bertrand, V., and Lemaire, P. A quantitative approach to the study of cell shapes and interactions during early chordate embryogenesis.
Curr Biol. 2006 Feb 21;16(4):345-58.