MAF MicroArray Facility: a LIMS with extended support for Nylon based microarrays

If you have an account, you may connect to our locally installed version of MAF: From the Internet: MAF@TAGC/inter From the Intranet: MAF@TAGC/intra If you don't have an account but wish to visit MAF, please use the guest login: user: guest password: we1come [note that the third symbol is the digit 'one']

MAF functionalities

Background High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option. GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. Results MAF (MicroArray Facility) is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it supports the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking), data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. Conclusions MicroArray Facility is a complete data management system for microarray producers and end-users. Although particular care has been devoted to adequately model Nylon based microarrays, spotted cDNA slides and oligo-chips are also supported. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for shared facilities and industry service providers alike.

Documentation

Academic User Manual (37 pages) Publication (under review)

Software Availability

Project name: MicroArray Facility (MAF) Project home page: http://tagc.univ-mrs.fr/bioinformatics/maf/ Operating system(s): Platform independent Programming language: Perl, SQL Other requirements: Web Server (e.g. Apache), RDBMS (Oracle or PostgreSQL), MAGEstk License: Royalty free, non-exclusive, non-transferable INSERM license for academics     To obtain copies of the MicroArray Facility SQL and Perl scripts as well as ELOGE genomic data for database population, please mail two signed copies of the INSERM licence above to the attention of P. Hingamp at the laboratory address shown to the left. Any restrictions to use by non-academics: Discovery Software license from IPSOGEN SAS

Financial Support

This software project was funded in part by the European Commission, contract-no. QLRI-CT-2001-00015 (TEMBLOR) under the RTD programme "Quality of Life and Management of Living Resources"

Contacts

ELOGE is a joint venture between IPSOGEN SAS and TAGC. At TAGC, please contact .