Chapter 1. Overview

1. What is XooNIps ?

XooNIps is an easy-to-use software that can facilitates to build a database website for organizing enormous volume of information in various types of electronic formats, such as research papers, experrimental data, mathematical models, and programs along with the metadata, and to share them with users worldwide on the internet.

In other words, XooNIps is a neuroinformatics tool for neuroscientists who make full use of immense and complex materials, such as experimental data and programs of mathematical model.

Neuroinformatics is an emerging research field where neuroscience and informatics are combined to breakthrough the enigma of the brain. In November 2005, International Neuroinformatics Coordinating Facility (INCF) was established for facilitating international collaborations in this interdisciplinary field. Under these circumstances, the Laboratory for Neuroinformatics, RIKEN BSI, embarked on developing XooNIps which is now in public as an open source (free) software. Lately, it also has been used as an institutional repository system by universities and other institutions.

Main features:

  • By using XooNIps, even non-experts of computer systems can create a database.

  • XooNIps does not bother you with thinking of logic or structure of the website; thus allows you to concentrate on web designing.

  • XooNIps is mounted functions for quality control.

As of April 2007, the Neuroinformatics Japan Center (NIJC), RIKEN BSI, has taken over the responsibility for XooNIps operations including the maintenance of extended functions (add-ons).

2. Main features

2.1. Flexible database construction

2.1.1. Set up the operation environment

The site's operation environment, (ex. manner of user registration and item publication, etc.) can be easily set up by following the directions given on the Administration screen. You will simply choose the most appropriate one from the pulldown lists.

Administration screen

Figure 1.1. Administration screen


  • User registration

    • [Certification by moderators] (The moderator will check the profile of the new user).

    • [Certify automatically]

  • Item publication

    • [Certification by moderators] (The items will be peer reviewed)

    • [Certify automatically]

2.1.2. Publication levels / areas for different purposes

  • Public

    • Public area: The items registered in this area will be publicized broadly to the public.

    • To register items in the public area, it is necessary to request for the site moderator's certification.

  • Group

    • Group area: Access to this area is restricted to a group of registered users.

    • To register items and share them among the group, it is necessary to request for the group administrator's certification.

  • Private

    • Individual area: registered users (given a user ID and password) can use this area just like a personal folder.

2.1.3. CMS XOOPS(The base syste of XooNIps)

The following are the benefits from using XOOPS.

  • Reduce the costs for system construction and operation.

    • XOOPS is open software (enables free downloading).

  • Expand the functionality.

    • XOOPS modules offer wide varieties of site design.

  • Allow to change visual effects easily.

    • XOOPS templates (themes) enable to easily change the visual effects such as layout, etc.

CMS system

Figure 1.2. CMS system

2.2. Data classification

2.2.1. Data classification by item type

XooNIps is designed to support a variety of item types (12 different data formats). Besides, it provides advanced features to apply to emerging formats.

2.2.2. Index trees to classify / manage items

The items will be organized by the Index Tree. The Index Tree consists of the following publication areas: Public, Group and Private. Each of the areas consists of keywords so that the items can be logically and effectively sorted.


Figure 1.3. XooNIps

2.2.3. Data search

The following search options are available on XooNIps.

  • Directory search by index trees

    • Choose an index tag (public, group and private) to view the item list.

  • Keyword search

    • Choose a keyword at the default field.

  • Detail search

    • Specify a search condition on each item type field.

2.3. Quality-maintenance workflow

2.3.1. Certification system for new user registrations

To obtain a new account, the requester has to be checked / identified by the moderator to decide whether or not to certify the user as a registered user.

To prevent from malicious users.

User registration

Figure 1.4. User registration

2.3.2. Item peer-review system

The items to be registered and shared in the public and a group area have to be peer-reviewed by the moderator or group administrator. (Optional)

To manage quality control

peer-review system

Figure 1.5. peer-review system

2.4. Metadata distribution

2.4.1. Simultaneous search across different external database sites

  • Enable to obtain metadata complying with OAI-PMH

    • Mounted repository and harvester.

    • Metadata format

      • Apply to OAI-DC,JUNII,JUNII2

Metadata distribution

Figure 1.6. Metadata distribution

2.5. Variety of accessory functions

2.5.1. Improve the site operation efficiency

  • Import and export

    • Register items in the block

    • Download items in the block

  • Access log analysis

    • Download event logs

    • Download logs classified by event or period and present them in a graphic chart

    • Check the current status of users and registrations

2.5.2. Enhance incentive

  • Introducing user's profile

    • User's job title

    • Biography

    • Achievements

  • Ranking

    • New items

    • The most frequently browsed items

    • The most downloaded items

    • The user who publicized the most number of items

    • The most frequently used search keyword

Last updated: 2009/06/11