de.NBI Project

MetaProtServ – de.NBI partner project

The German Network for bioinformatics infrastructure (de.NBI) aims to consistently provide bioinformatics software and computing resources to the research community.

The de.NBI partner project MetaProtServ complements the research activities of three de.NBI centers. The researches of BiGi are experienced in microbial genome, metagenome, and postgenome research. Metaproteomics provides functional data complementing metagenomics and metatranscriptomics that can be integrated into BiGi’s multi-omics pipelines for a holistic understanding of microbial communities. The establishment of the MPA as a webservice for the scientific community requires computing and storage resources that are offered at BiGi.  As a long-term perspective the MetaProteomeAnalyzer can be fully integrated into cloud computing resources provided by BiGi.

Development of the web-based MPA version for cloud environments

The MetaProteomeAnalyzer (MPA) is a Java-Application using the popular LAMP-Stack to store protein and spectrum data. The MPA is split into a Server and a Client. The server stores the data in an SQL database and manages protein database searches submitted through the Client. The Client contains the graphical user interface that enables the user to submit files for searches, retrieve metadata on proteins from UniProt and through BLAST similarity searches, create metaproteins and view and export results.

In the first step towards providing the MPA as a full cloud-based web service, the latest version of the MPA is hosted on a Server at the OVGU, accessible by Remote-Desktop for users using their MPA-Account from whitelisted locations. This allows for better maintenence and user support, while eliminating issues arising from inadequate computer hardware that is required to deal with the increasing complexity of mass spectrometry data.

In order to provide the MPA as a full cloud-based solution, the software is reimplemented to adapt to new Web 4.0 technologies. The centerpiece of this remimplementation is the replacement of the LAMP stack with the SMACK stack.