content management

Content Management : CMS (Content Management Systems), wiki...
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: 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): Rémy 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, édit 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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