Tag Archives: Web

GlycoMine on R@CMon

Glycosylation is an ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes such as cellular communication, ligand recognition and subcellular recognition. It is estimated that greater than 50% of the entire human proteome is glycosylated. However, it is still a significant challenge to identify glycosylation sites, which requires expensive and laborious experimental research. Thus, bioinformatics approaches that can predict the glycan occupancy at specific sequons in protein sequences would be useful for understanding and utilising this very important PTM.

Predicted N-linked glycosylation sites from two case-study proteins using GlycoMine-Struct

Dr. Jiangning Song from the Department of Biochemistry and Molecular Biology at Monash University and his collaborators have designed and developed a bioinformatics tool – GlycoMine-Struct for predicting glycosylation sites. GlycoMine-Struct is a comprehensive tool for the systematic in-silico identification of N-linked and O-linked glycosylation sites in the human proteome. Through R@CMon, a dedicated cloud project with computational and storage resources has been provisioned to develop and host the GlycoMine-Struct tool. The flexible and scalable R@CMon-powered development environment enabled rapid prototyping, testing and re-deployment of the tool.

GlycoMine-Struct Main Page (http://glycomine.erc.monash.edu/Lab/GlycoMine_Struct/index.jsp#Introduction)

GlycoMine-Struct is now a publicly accessible web service, available to the wider research community. Users can now easily submit protein structure input files in PDB (Protein Data Bank) format to perform sites prediction on GlycoMine-Struct. Since it went public, GlycoMine-Struct has been accessed and used by thousands of local and international users, and still growing. A scientific reports paper has been published, highlighting the collaborative work done to develop GlycoMine-Struct, as an essential bioinformatics tool for improving the prediction of human glycosylation sites. The R@CMon team is actively supporting the GlycoMine-Struct project as it continues to serve the research community and develop performance improvements.

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.

Melbourne Weather Server on R@CMon

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Dr. Simon Clarke is a senior lecturer from the School of Mathematical Sciences at Monash University. He’s been granted permission by the Bureau of Meteorology to repackage its observational and forecasting Melbourne weather data for downstream analysis and visualisations. Weather data from the bureau is downloaded and processed at regular 10 minute intervals. Various metrics and visualisations are then computed using a custom-made MATLAB batch script developed in-house. The resulting output is then fed to a web server for public presentation with integrations to other external sites hosted by the bureau. The original weather server was housed on a “legacy” hosting platform, that had reached its end of life. The Melbourne weather server needed a new home.

Melbourne Weather Server

The R@CMon team engaged with Simon to scope the various weather server’s hosting requirements. Aside from the traditional LAMP-style type of hosting required, the server also needed direct access to MATLAB’s batch mode functionality. A new R@CMon-hosted instance was deployed on the Monash node of the NeCTAR Research Cloud. With it, a standard LAMP stack was also installed and configured. A Monash University-licensed installation of MATLAB has been made available onto the new weather server, allowing the downstream analysis of the raw data from the bureau to be conducted.

Melbourne Weather Server Visits for 2017

The new Melbourne weather server is now publicly accessible and available across world. The regular live feed is serving the Australian and international community providing live Melbourne weather observations and forecasts. With the support of the R@CMon team, it will continue to do so for more years to come.

Worm Strains Catalogue on R@CMon

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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.