EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.

Evaluation and FMEA of Fabrication Techniques for Metallic Grating Couplers on Polymer Substrates with Low Glass Transition Temperatures

The main task is to analyze the state of the art of grating couplers production and low-cost polymer substrates. Then to provide a recommendation of a new or adapted process for the production of metallic gratings on polymer sheets, based on a Failure Mode and Effect Analysis (FMEA). In order to achieve that, this thesis is divided into four chapters. After the first introductory chapter, the second section provides details about the state-of-the-art in optical technology platforms with focus on polymers and their main features for the aimed application, such as flexibility, low cost and roll to roll compatibility. It defines then the diffraction gratings and their specifications and closes with the explanation of adhesion mechanisms of inorganic materials on polymer substrates. The third chapter discusses processing of grating couplers. It introduces the basic fabrication methods and details a selection of current fabrication schemes found in literature with an assessment of their potential use for the desired application. The last chapter is a FMEA analysis of the retained fabrication process, called Flip and Fuse, in order to check its capability to realize the grating structure.