database

Database
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 02/01/12
  • Minor correction: 02/01/12

Datum : web application for sharing data from databases

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:
  • License(s): GPL - v2
  • Status: internal use, under development
  • Support: maintained, ongoing development
  • Designer(s): Olivier Maury
  • Contact designer(s): Olivier.Maury (chez) grignon.inra.fr
  • Laboratory, service:

 

General software features

Datum is a web application, so a server-based software for use with a web browse. It aims sharin data from databases and information related to these databases:

  • sharing data and files, with access rights (management of users and permissions)
    • browsing tables and data from the database
    • data reports with charts (defined with SQL queries)
    • dynamic charts
  • display of the database schema
  • integration of datasets (CSV files)
  • project information : news, little CMS feature
  • user history, internationalisation, help, database management, statistics, ...

Some databases use specific module to :

  • change the interface layout
  • create template files for the integration
  • add specific integrations and data extractions

One software instance can manage several databases.
A daemon can run asynchronous tasks, as data extraction, without blocking the page display.

Datum is based on the PHP framework, Yii.

Context in which the software is used

Developed for one project, the application was made generic to interface the database of the research unit.

So, this common code base is used by several projects in the "Biosphere-Atmosphere" research team at INRA "Environnement et Grandes Cultures" and for the information system of SOERE PRO (Systems of observation and long-term experimentation for environmental research on organic wast products).

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 13/09/11
  • Minor correction: 28/09/11

SIGDEF : system for the management and distribution of software licenses

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.
  • System:
  • Current version: 1.0 - 02/05/2011
  • License(s): GPL, CeCILL - En Ă©tude.
  • Status: internal use, under development
  • Support: maintained, no ongoing development
  • Designer(s): IRD - DSI - Service Informatique Scientifique : StĂ©phane DEBARD (conception), Geoffrey PASCAL (conception et dĂ©veloppement)
  • Contact designer(s): stephane.debard@ird.fr
  • Laboratory, service:

 

General software features

SIGDEF is a generic designed application to deliver and manage licences. This tool is intended for IT support services. Two interfaces (one for users and another for administrators) allow to send orders to activate software licenses and to manage them easily.

1 - User Interface:

  • Identification (with a directory, a .htaccess file) or no identification.
  • Choice of the software and its version (management of both individual or grouped orders), choice of the installation of the application(s) following validation instructions.
  • Downloading documents related to usage and access rights (agreements, contracts, letters ...).
  • Summary and acceptance of the users' charter.

2 - Administrator Interface:

  • Control and validation of submitted orders (control of the user information and the user choices).
  • Email license sending after validation, validation may be done ​​by one or several services.
  • Synthesis and search of current orders, committed or sent.

Future work:
- Export raw results of the synthesis of commands.
- Specific requests and crossing data to make assessments on the controls.

The documentation is complete: installation, utilization and assessment, including the design documentation (database, workflow).

Context in which the software is used

Software editors allow software vendors to group the purchasing of licenses for several software packages in order to reduce costs. Companies delegate license management to the IT support services. These licenses are often distributed with the help of ID or activation files provided to the manager without the support of monitoring or management tools.

SIGDEF provide tools for the license management and deployment on a large scale.

SIGDEF is currently used in production (for more than one year) to manage licenses in Geographic Information Systems.
Two independent teams of the same ISD use this application to validate and distribute the licenses to their users (200 users).

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

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:
  • 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:

 

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.

Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 01/08/13
  • Minor correction: 01/08/13

CASSIS : analysis and treatment of astrophysical data

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:
  • Current version: 3.4 - August 1, 2013
  • License(s): not yet chosen
  • Status: stable release
  • Support: maintained, ongoing development
  • Designer(s): Jean-Michel Glorian, Mickael Boiziot, Samuel Adam, Romaric Benech, Cedric Chappert, Ludovic Deveaux, Damien Faral, Thomas Floquet, Sebastien Fort, Alexandre Girard, Nicolas Guegan, Alain Klotz, Rose Neriere, Guillaume Pelouas, Brice Quillerie, Ngoc thach Ta, Laure Tamisier, Samuel Thiriot.
  • Contact designer(s): Jean-Michel@irap.omp.eu
  • Laboratory, service:

 

General software features
  • Display of astrophysical spectra
  • Identification of lines of transitions of molecules
  • Creation of LTE and Radex theoretical spectra
  • Use of atomic and molecular databases JPL, CDMS, NIST

  • Coded in Java, use sqlite Card Plume

Context in which the software is used
Publications related to the software
  • Pagani, Vastel, Hugo et al., 2009, A&A 494, 623, "Chemical modeling of L183 (L134N): an estimate of the ortho/para H2 ratio"
  • Hezareh, Houde, McCoey et al., 2008, ApJ 684, 1221, "Simultaneous Determination of the Cosmic Ray Ionization Rate and Fractional Ionization in DR 21(OH)"
Higher Edu - Research dev card
Development from the higher education and research community
  • Creation or important update: 31/03/10
  • Minor correction: 16/09/10

ChemAzTech : chemical product library & management software

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:
  • Current version: 0.6a - 07-30-2010
  • License(s): GPL
  • Status: beta release, under development
  • Support: maintained, ongoing development
  • Designer(s): RĂ©my Dernat (CNRS, IBMM). Contributions are wellcome.
  • Contact designer(s): remy(_dot_)dernat(_at_)univ-montp1(_dot_)fr
  • Laboratory, service:

 

General software features

Chemical product library & management software

This software includes lots of features. Main objective is to involve a maximum of people around a single interface, avalaible from a browser. It's a freely OpenSource and powerfull tool based on existing OpenSource chemical softwares.
You can download and see documentation and sources on sourceforge : http://chemaztech.sourceforge.net

Main features :

  •  Manage chemical products (with structures, place of storage, references, experiment number...).
  •  Draw, Ă©dit structures with JChemPaint.
  •  See your molecules 3D with JMol, in 2D with JChemPaint (java) or with the python librairy OASA (SVG pictures)
  •   Search by sub-structures with MyChem.
  •  Automated threatment for mol properties, with Smiles codes, Inchi with MyChem.
  •   Import molecules from a single MOL file, or CDX (ChemDraw)** or all a database from a SDF file (eg : from ISIS/Base) **
  •   Extract CSV, export as PDF or XLS(X)...
  •  Manage storage and accounting.
  •  Manage users and groups and a visibility level for products

** These softwares are not OpenSource but are very usefull in chemistry.

Other softwares used by ChemAzTech are OpenSource, under GPL or LGPL for JMol and
JChemPaint (JChemPaint is associated to Chemistry Development Kit (CDK)).
Thus, I can use them as building blocks for ChemAzTech, without forgetting OpenBabel, which is an important component of MyChem and which I use to convert files CDX and the MOL into MOL2 for 3D visualization .

On plume : OpenBabel

Context in which the software is used

First of all, this software needs a LAMP (Linux Apache MySQL PHP) server with OpenBabel and MyChem. Then you will have to install java and python (+ OASA library). It's a powerfull software for the management of chemical products, but as you can see, you need a lot a lot of features on your server to install it.

It's a beta software. Use it at your own risks.

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