Integromics™ | IT for Life Sciences

ArrayHub^TM is a LIMS (Laboratory Information Management System) which stores,
organizes and tracks a complete set of descriptive information for all tasks performed in
microarray experiments (sample preparation and tracking, extraction, labeling, array
creation, hybridization...) Furthermore, also the experiment's outcome data (images, raw
data, secondary analysis data files) can finally be stored and managed.

ArrayHub^TM supports data files for Affymetrix GeneChip^® brand platform; Applied
Biosystems 1700 Chemiluminescent Microarray Analyzer, cDNA, Oligonucleotide, and
custom microarray platforms.

ArrayHub^TM has been conceived to be the central repository of the microarray experiments
data in a laboratory. It can be connected with third-party analysis software (Bioconductor
R, Integromics anlysis applications, Spotfire, GeneSpring ...) to process raw data.

Experiment entities (samples, arrays, data files ...) can be annotated from ArrayHub^TM
using different annotation sources which can be public (GenBank, NetAffx™ Analysis
Center, Gene Ontology ...) or private to the laboratory.

ArrayHub^TM enables Core Facility organizations to provide a web based service
request system for requestors.

ArrayHub^TM data model has been created following MIAME (www.mged.org) guidelines to
ensure experiment information quality and also to allow users to publicize their data in
public databases as Array Express.

Benefits

Key Features

New Features

Customisations

System Requirements

BENEFITS

Due to their complexity, some laboratory workflows, such as microarray experiments, require
extended and customized database automation.

ArrayHub^TM has been conceived in order to ensure that microarray experimental information
is properly stored and organized. It provides for all the experimental information with secure
access, updates as well as a facile and safe sharing of coherent information (protocols,
instruments, projects, etc.) within the lab.

Sharing data with other users and/or submitting experimental information to public
repositories is a central demand by the research community. The MGED
(www.mged.org) consortium is establishing standards for microarray data annotation
and exchange. The consortium is also facilitating the creation of microarray databases
and related software implementing these standards. MGED promotes the joint use of
high quality and well annotated data within the life sciences community.
Thus, ArrayHub^TM has been designed following the MIAME guidelines proposed by the
MGED consortium.

ArrayHub^TM enables users to easily submit their experimental data and to retrieve, browse
and search the information in an efficient way.

KEY FEATURES

Fully MIAME compliant (www.mged.org):
- ArrayHub^TM relational data model is implemented according to the object model
  proposed by MIAME.
- Export ArrayHub^TM Experiments in MAGE - ML format.
- Import MAGE - ML experiments and protocols into ArrayHub^TM database.

Affymetrix^® GeneChip-compatible™ Data Management Software:
- Visualization and parsing capabilities for Affymetrix binary files (.DAT .CEL, .CHP)
- Affymetrix GeneChip^® Operating System (GCOS) integration.
- Affymetrix GeneChip^® Command Console integration.
- NetAffx™ Analysis Center integration. Keep your affymetrix annotation files and your
  chip definition files automatically up to date.

Workflow oriented data submission:
- An interactive Workflow panel helps to submit/view data depending on the experiment
  type that it's being considered
- Enables user to create their own workflows.
- Experiment progress monitoring
- User- friendly interface
- Enforce ontology vocabulary

Users Collaboration Capability:
- User - level sharing philosophy
- Read and Write permission management.
- Support for multi-disciplinary teams : lab technicians, bioinformatics ...
- Multiple administrators are allowed
- Extensible to enterprise-wide collaboration/ sharing

Security Features:
- Role based security policy.
- Passwords encryption
- Audit and Trail information is stored for existing and deleted entities (e.g. User and
  Date modification)
- Backup capabilties

Core Facility Web module:
- A framework which enables ArrayHub^TM LIMS Organizations to provide microarray
  experiment services to external users and organizations

Public database integration:
- ArrayHub^TM enables users to submit and publish their experiment results into public
  databases, such as ArrayExpress.
  It can export the ArrayHub^TM experiments to MAGE-ML and MAGE-TAB format.

Seamless integration with third-party analysis tools:
- Preprocessing tools integration: Bioconductor R, QFirst
- Analysis tools integration : Spotfire, Genespring

Experiment Design modeling:
- Define unlimited number of factors for your experiments
- Group Hybridizations depending on factor values

Support for multiple instruments data file formats:
- Support for Affymetrix GeneChip^® brand platform; Applied Biosystems 1700
  Chemiluminescent Microarray Analyzer, cDNA, Oligonucleotide, and custom
  microarray platforms.
  Enabling the creation and definition of parsing protocols to support any text file format.

Annotation Capability:
- Biomaterial, Arrays, Plates, Raw data files can be annotated from external sources
- Out-of-the-Box annotation sources: GenBank, Unigene, Gene Ontology, NetAffx™Analysis Center.
- Enable new annotation source integration.

Plate Management module:
- Graphical tool for plate creation (96 to 384-well plates)
- Plates annotation
- Sample-sheets generation.
- PCR and Plates merging transformation are handled.

Report Module:
- Custom Project PDF reports
- HTML-based Project summary reports

Extendible Data Model:
- A list of parameters can be added to any entity without custom programming in order to
  extend datamodel

Administration Module:
- Protocols, Instruments, Software and Locations administration

Powerful searching capabilities:
- Dynamic search engine to find objects by Textual Descriptors or Administrative
  Information.

Platform Independence & Back-end Compatibility:
- Operating system independent : Windows and Linux
- Oracle or MySQL databases backend

NEW FEATURES

- ArrayHub^TM Core Facility Web Module: a complete solution for microarray core facility
  organizations.
- Building of MAGE-TAB document based on an existing ArrayHub^TM project.Enables user
  to publish their experiment results into ArrayExpress public database.
- Enables secured access from your GeneSpring analysis software to your ArrayHub^TM
  stored projects.Avoid local copies of your files and minimize errors.
- Import MAGE-ML published protocols and array designs in your ArrayHub^TM LIMS.
  Speed up the ArrayHub^TM LIMS management tasks.

CUSTOMIZATIONS

We offer customized adaptation of ArrayHub^TM to your specific needs.Integration of a specific
workflow, specific data formats, data analysis scripts, PCR data and results, ... is all possible.

Please, talk to us and will make it possible!

SYSTEM REQUIREMENTS

The package is deployed as a Java application with a relational database backend.
The database supports the most popular management systems like MySQL™ or
Oracle™.

Platforms Supported: Windows O.S. (XP, 98, ME, 2000)
Minimum: 300 MHz Pentium, 128 MB RAM
Recommended: 1.5 GHz or faster Pentium IV, 512 or more MB RAM


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