Chiminey: Reliable Computing and Data Management Platform in the Cloud

The enabling of scientific experiments that are embarrassingly parallel, long running and data-intensive into a cloud-based execution environment is a desirable, though complex undertaking for many researchers. The management of such virtual environments is cumbersome and not necessarily within the core skill set for scientists and engineers. We present here Chiminey, a software platform that enables researchers to (i) run applications on both traditional high-performance computing and cloud-based computing infrastructures, (ii) handle failure during execution, (iii) curate and visualise execution outputs, (iv) share such data with collaborators or the public, and (v) search for publicly available data.Comment: Preprint, ICSE 201

In Silico Simulation of Corticosteroids Effect on an NFkB- Dependent Physicochemical Model of Systemic Inflammation

During the onset of an inflammatory response signaling pathways are activated for "translating" extracellular signals into intracellular responses converging to the activation of nuclear factor (NF)-kB, a central transcription factor in driving the inflammatory response. An inadequate control of its transcriptional activity is associated with the culmination of a hyper-inflammatory response making it a desired therapeutic target. Predicated upon the nature of the response, a systems level analysis might provide rational leads for the development of strategies that promote the resolution of the response.A physicochemical host response model is proposed to integrate biological information in the form of kinetic rules and signaling cascades with pharmacokinetic models of drug action for the modulation of the response. The unifying hypothesis is that the response is triggered by the activation of the NFkB signaling module and corticosteroids serve as a template for assessing anti-inflammatory strategies. The proposed in silico model is evaluated through its ability to predict and modulate uncontrolled responses. The pre-exposure of the system to hypercortisolemia, i.e. 6 hr before or simultaneously with the infectious challenge "reprograms" the dynamics of the host towards a balanced inflammatory response. However, if such an intervention occurs long before the inflammatory insult a symptomatic effect is observed instead of a protective relief while a steroid infusion after inducing inflammation requires much higher drug doses.We propose a reversed engineered inflammation model that seeks to describe how the system responds to a multitude of external signals. Timing of intervention and dosage regimes appears to be key determinants for the protective or symptomatic effect of exogenous corticosteroids. Such results lie in qualitative agreement with in vivo human studies exposed both to LPS and corticosteroids under various time intervals thus improving our understanding of how interacting modules generate a behavior

Breaking down the boundaries to storing, sharing and publishing research data

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014General Track Papers and PanelsThe session was recorded and is available for watching (this presentation starts at 0:25:45)For several years Monash University have been employing the Data Curation Continuum as a conceptual model to understand the nature of research data workflows, and to put in place infrastructure that will enhance and enable these workflows. This paper describes a practical application of this model being undertaken by Monash University in collaboration with the Australian Synchrotron. It looks at the state of data management in this specific circumstance before the project began, the work undertaken and the challenges going forward. The paper demonstrates a solution that seeks to remove or minimise many of the boundaries faced when moving data within this continuum. The Store.Synchrotron service enables the archiving of data for the collecting researcher early and automatically (the Private Domain), facilitates controlled collaboration through tools provided (the Shared Domain), and provides a mechanism to make data publishable and freely available (the Public Domain) without the researcher needing to shift data from one place to another.Androulakis, Steve (Monash University, Australia)Bertling, Philip (Monash University, Australia)Groenewegen, David (Monash University, Australia)Harrison, Andrew (Monash University, Australia

KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins

KinetochoreDB is an online resource for the kinetochore and its related proteins. It provides comprehensive annotations on 1554 related protein entries in terms of their amino acid sequence, protein domain context, protein 3D structure, predicted intrinsically disordered region, protein–protein interaction, post-translational modification site, functional domain and key metabolic/signaling pathways, integrating several public databases, computational annotations and experimental results. KinetochoreDB provides interactive and customizable search and data display functions that allow users to interrogate the database in an efficient and user-friendly manner. It uses PSI-BLAST searches to retrieve the homologs of all entries and generate multiple sequence alignments that contain important evolutionary information. This knowledgebase also provides annotations of single point mutations for entries with respect to their pathogenicity, which may be useful for generation of new hypotheses on their functions, as well as follow-up studies of human diseases. Database URL: http://lightning.med.monash.edu/kinetochoreDB2

PolyQ 2.0:an improved version of PolyQ, a database of human polyglutamine proteins

Proteins with expanded polyglutamine (polyQ) repeats are involved in human neurodegenerative diseases, via a gain-of-function mechanism of neuronal toxicity involving protein conformational changes that result in the formation and deposition of β-sheet-rich aggregates. Aggregation is dependent on the context and properties of the host protein, such as domain context and location of the repeat tract. In order to explore this relationship in greater detail, here we describe PolyQ 2.0, an updated database that provides a comprehensive knowledgebase for human polyQ proteins. Compared with the previous PolyQ database, our new database provides a variety of substantial updates including detailed biological annotations and search options. Biological annotations in terms of domain context information, protein structural and functional annotation, single point mutations, predicted disordered regions, protein–protein interaction partners, metabolic/signaling pathways, post-translational modification sites and evolutionary information are made available. Several new database functionalities have also been provided, including search using multiple/combinatory keywords, and submission of new data entries. Also, several third-party plug-ins are employed to enhance data visualization in PolyQ 2.0. In PolyQ 2.0 the proteins are reclassified into 3 new categories and contain 9 reviewed disease-associated polyQ proteins, 105 reviewed non-disease polyQ proteins and 146 un-reviewed polyQ proteins (reviewed by UniProt curators). We envisage that this updated database will be a useful resource for functional and structural investigation of human polyQ proteins. Database URL: http://lightning.med.monash.edu/polyq2