Tag Archives: Database

HIVed Database on R@CMon

Measuring the changes in gene expressions levels and determining differential expressed genes during the processes of human immunodeficiency virus (HIV) infection, replication and latency is instrumental in further understanding HIV infections. These measurements or studies are vital in developing strategies for virus eradication from the human body. Dr. Chen Li, a research fellow from the Immunoproteomics Laboratory at Monash University has developed a novel compendium of comprehensive functional genes annotations from genes expressions and proteomics studies. The genes in the compendium have been carefully curated and shown to be differentially expressed during HIV infection, replication and latency.

The HIVed Online Database, Front Page

The R@CMon team assisted with the deployment of the online database – HIVed on the Monash node of the NeCTAR Research Cloud. The system has been running on R@CMon and serving the public community for more than a year. HIVed is considered to be the first fully comprehensive database that combines datasets from a wide range of experimental studies that have been carefully curated using a variety of experimental conditions. The datasets are further enriched by integrating it with other public databases to provide additional annotations for each data points. The HIVed online database has been developed to facilitate the functional annotation and experimental hypothesis HIV related genes with an intuitive web interface which enables dynamic display or presentation of common threads across HIV latency and infection conditions and measurements. The work done for the development of HIVed has been recently published into Scientific Reports and the Immunoproteomics Laboratory has plans to incorporate new experimental studies and external annotations into the HIVed database as they become available.

Worm Strains Catalogue on R@CMon

Associate Professor Roger Pocock is the head of the Neuronal Development and Plasticity Laboratory at Monash University. Roger’s lab investigates the various fundamental mechanisms that factors in brain development using the Caenorhabditis elegans organism as a model system. Roger joined Monash University in 2014, bringing with him a comprehensive catalogue of worm strains data that has been carefully curated for years from his previous laboratory at the University of Copenhagen. The strains catalogue is held in a FileMaker database, that the laboratory members regularly update and query for current and new strains’ entries.

C. elegans as a model system, Neuronal Development and Plasticity Laboratory

FileMaker (and its derivatives) is commercial software for creating custom applications for a variety target platforms (e.g. web, iPad, Windows, Mac). The worm strains catalogue from Roger’s lab was the first FileMaker-based database deployment on R@CMon. The R@CMon team were able to install and configure a fully-licensed and latest version of FileMaker Pro on the Monash node of the NeCTAR Research Cloud inside a dedicated tenancy (i.e. computational and storage resources) provisioned for the lab. The FileMaker software itself has been deployed on a Monash-licensed Windows Server instance, which has access to the latest system and security updates from Microsoft.

Worm Strains Catalogue Entry

The FileMaker WebDirect feature has been enabled on the new server to allow easy access to the strains catalogue from standard web browsers via internet, without any need for additional programming or software installation on the user’s client machine. Proper HTTPS have been prepared and enabled on new the WebDirect interface. Since then, and with the ongoing support of R@CMon, the catalogue has grown to include  external collaborators’ models that are derived from other strains.

The Proteome Browser on R@CMon

The Proteome Browser (TPB) is a web portal that integrates human protein data and information. It provides an up-to-date view of the proteome (the entire library of proteins that can be expressed by cells or organisms – like us!) across large gene sets to support human proteome characterisation as part of the Chromosome-centric Human Proteome Project (C-HPP). Pertinent genomic and protein data from multiple international biological databases are assembled by TPB in a searchable format supporting C-HPP’s global proteomics effort.

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TPB’s primary report of chromosome-ordered genes visualised using traffic light colour system.

TPB’s framework extracts biological data from numerous sources, maps it into the genome, and performs categorisation on the results based on quality and information content. The result (level of evidence) is presented by TPB using a simple point matrix coded by traffic light system (green – highly reliable evidence, yellow – reasonable evidence, red – some evidence is available or black – there is no available evidence). TPB uses hierarchical data types to group similar information from different experiment types.

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TPB’s summary report for the chosen chromosome.

TPB is supported by Monash University, Monash eResearch Centre (MeRC)Chromosome-centric Human Proteome Project (C-HPP)Australia/New Zealand Chromosome 7 Consortium and the Australian National Data Service (ANDS). Researchers are now using TPB in various proteomic-related discoveries.

The R@CMon cloud team recently provided assistance to migrate The Proteome Browser web service to be hosted on the Monash node of the NeCTAR Research Cloud. TPB is using persistent storage (Volumes) granted via a VicNode computational storage allocation to house its underlying database. TPB’s new home will ensure it has stable and scalable long-term hosting supported by the NeCTAR and RDSI federal research infrastructure programmes.