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MiMiR--an integrated platform for microarray data sharing, mining and analysis.

Tomlinson C, Thimma M, Alexandrakis S, Castillo T, Dennis JL, Brooks A, Bradley T, Turnbull C, Blaveri E, Barton G, Chiba N, Maratou K, Soutter P, Aitman T, Game L - BMC Bioinformatics (2008)

Bottom Line: The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication.MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia.The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microarray Centre, MRC Clinical Sciences Centre and Imperial College, Hammersmith Hospital, London, UK. chris.tomlinson@imperial.ac.uk

ABSTRACT

Background: Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data.

Results: A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.

Conclusion: The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

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Related in: MedlinePlus

The three-tier hardware and software architecture of MiMiR comprises a storage layer, an application services layer and an access/user interface layer (delimited by dashed lines). The MiMiR backend database is physically protected by two firewalls (FW) and is only accessible through the middle tier application servers (MDSA) which act as trusted middleware service and security gateway. The demilitarised zone (DMZ) sits between the two firewalls. All requests and retrieval of data to and from the web servers in the access layer are done in an encrypted format (marked 'https' with shaded arrows). MiMiR staff access internal tools for experimental annotation (GUI) using a less secure data transmission.
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Figure 1: The three-tier hardware and software architecture of MiMiR comprises a storage layer, an application services layer and an access/user interface layer (delimited by dashed lines). The MiMiR backend database is physically protected by two firewalls (FW) and is only accessible through the middle tier application servers (MDSA) which act as trusted middleware service and security gateway. The demilitarised zone (DMZ) sits between the two firewalls. All requests and retrieval of data to and from the web servers in the access layer are done in an encrypted format (marked 'https' with shaded arrows). MiMiR staff access internal tools for experimental annotation (GUI) using a less secure data transmission.

Mentions: In order to support the growing volume of stored data, the efficient mining capabilities and secure data access by multiple concurrent users, we modified the original MiMiR infrastructure and database schema [19]. A three-tier architecture comprising a data storage layer, an application services layer and a user interface layer was designed and implemented (Figure 1). This layered approach decouples (i.e. reduces the dependency of) the various software components from the MiMiR database which ensures high scalability and a flexible environment for software and applications development. The web and any other user-interface layer application servers are located in the de-militarised zone (DMZ) [21] which is protected by one firewall. A sophisticated middleware layer framework, called MiMiR Data Services Architecture (MDSA), was developed using Enterprise JavaBeans (EJB) to allow highly secure remote access to the data in MiMiR via a role/permissions-based security model. A list of registered users and role-specific permissions is maintained in the database to identify and grant access rights. All the client applications are accessible to registered users upon login with username and password. Clinical information stored in MiMiR can also be filtered according to ethical policies before being delivered back to the client or written into the clinical part of MiMiR.


MiMiR--an integrated platform for microarray data sharing, mining and analysis.

Tomlinson C, Thimma M, Alexandrakis S, Castillo T, Dennis JL, Brooks A, Bradley T, Turnbull C, Blaveri E, Barton G, Chiba N, Maratou K, Soutter P, Aitman T, Game L - BMC Bioinformatics (2008)

The three-tier hardware and software architecture of MiMiR comprises a storage layer, an application services layer and an access/user interface layer (delimited by dashed lines). The MiMiR backend database is physically protected by two firewalls (FW) and is only accessible through the middle tier application servers (MDSA) which act as trusted middleware service and security gateway. The demilitarised zone (DMZ) sits between the two firewalls. All requests and retrieval of data to and from the web servers in the access layer are done in an encrypted format (marked 'https' with shaded arrows). MiMiR staff access internal tools for experimental annotation (GUI) using a less secure data transmission.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2572073&req=5

Figure 1: The three-tier hardware and software architecture of MiMiR comprises a storage layer, an application services layer and an access/user interface layer (delimited by dashed lines). The MiMiR backend database is physically protected by two firewalls (FW) and is only accessible through the middle tier application servers (MDSA) which act as trusted middleware service and security gateway. The demilitarised zone (DMZ) sits between the two firewalls. All requests and retrieval of data to and from the web servers in the access layer are done in an encrypted format (marked 'https' with shaded arrows). MiMiR staff access internal tools for experimental annotation (GUI) using a less secure data transmission.
Mentions: In order to support the growing volume of stored data, the efficient mining capabilities and secure data access by multiple concurrent users, we modified the original MiMiR infrastructure and database schema [19]. A three-tier architecture comprising a data storage layer, an application services layer and a user interface layer was designed and implemented (Figure 1). This layered approach decouples (i.e. reduces the dependency of) the various software components from the MiMiR database which ensures high scalability and a flexible environment for software and applications development. The web and any other user-interface layer application servers are located in the de-militarised zone (DMZ) [21] which is protected by one firewall. A sophisticated middleware layer framework, called MiMiR Data Services Architecture (MDSA), was developed using Enterprise JavaBeans (EJB) to allow highly secure remote access to the data in MiMiR via a role/permissions-based security model. A list of registered users and role-specific permissions is maintained in the database to identify and grant access rights. All the client applications are accessible to registered users upon login with username and password. Clinical information stored in MiMiR can also be filtered according to ethical policies before being delivered back to the client or written into the clinical part of MiMiR.

Bottom Line: The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication.MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia.The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microarray Centre, MRC Clinical Sciences Centre and Imperial College, Hammersmith Hospital, London, UK. chris.tomlinson@imperial.ac.uk

ABSTRACT

Background: Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data.

Results: A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.

Conclusion: The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

Show MeSH
Related in: MedlinePlus