Dataset Information

Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.

ABSTRACT: We describe the ways in which Galaxy, a web-based reproducible research platform, can be used for web-based sharing of complex computational models. Galaxy allows users to seamlessly customize and run simulations on cloud computing resources, a concept we refer to as Models and Simulations as a Service (MaSS). To illustrate this application of Galaxy, we have developed a tool suite for simulating a high spatial-resolution model of the cardiac Ca(2+) spark that requires supercomputing resources for execution. We also present tools for simulating models encoded in the SBML and CellML model description languages, thus demonstrating how Galaxy's reproducible research features can be leveraged by existing technologies. Finally, we demonstrate how the Galaxy workflow editor can be used to compose integrative models from constituent submodules. This work represents an important novel approach, to our knowledge, to making computational simulations more accessible to the broader scientific community.

SUBMITTER: Walker MA

PROVIDER: S-EPMC4788737 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.

Walker Mark A MA Madduri Ravi R Rodriguez Alex A Greenstein Joseph L JL Winslow Raimond L RL

Biophysical journal 20160301 5

We describe the ways in which Galaxy, a web-based reproducible research platform, can be used for web-based sharing of complex computational models. Galaxy allows users to seamlessly customize and run simulations on cloud computing resources, a concept we refer to as Models and Simulations as a Service (MaSS). To illustrate this application of Galaxy, we have developed a tool suite for simulating a high spatial-resolution model of the cardiac Ca(2+) spark that requires supercomputing resources f ...[more]

PMID: 26958881

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Project description:Background Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of “on-demand” Galaxy instances over the cloud. By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses. The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server’s initial configuration and deployment. Results “Laniakea@ReCaS”, the first instance of a Laniakea-based service, is managed by ELIXIR-IT and was officially launched in February 2020, after about one year of development and testing that involved several users. Researchers can request access to Laniakea@ReCaS through an open-ended call for use-cases. Ten project proposals have been accepted since then, totalling 18 Galaxy on-demand virtual servers that employ ~ 100 CPUs, ~ 250 GB of RAM and ~ 5 TB of storage and serve several different communities and purposes. Herein, we present eight use cases demonstrating the versatility of the platform. Conclusions During this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research. Laniakea@ReCaS provides a proof of concept of how enabling access to appropriate, reliable IT resources and ready-to-use bioinformatics tools can considerably streamline researchers’ work.

Project description:Computational modeling and simulation have become essential tools in the quest to better understand the brain's makeup and to decipher the causal interrelations of its components. The breadth of biochemical and biophysical processes and structures in the brain has led to the development of a large variety of model abstractions and specialized tools, often times requiring high performance computing resources for their timely execution. What has been missing so far was an in-depth analysis of the complexity of the computational kernels, hindering a systematic approach to identifying bottlenecks of algorithms and hardware. If whole brain models are to be achieved on emerging computer generations, models and simulation engines will have to be carefully co-designed for the intrinsic hardware tradeoffs. For the first time, we present a systematic exploration based on analytic performance modeling. We base our analysis on three in silico models, chosen as representative examples of the most widely employed modeling abstractions: current-based point neurons, conductance-based point neurons and conductance-based detailed neurons. We identify that the synaptic modeling formalism, i.e. current or conductance-based representation, and not the level of morphological detail, is the most significant factor in determining the properties of memory bandwidth saturation and shared-memory scaling of in silico models. Even though general purpose computing has, until now, largely been able to deliver high performance, we find that for all types of abstractions, network latency and memory bandwidth will become severe bottlenecks as the number of neurons to be simulated grows. By adapting and extending a performance modeling approach, we deliver a first characterization of the performance landscape of brain tissue simulations, allowing us to pinpoint current bottlenecks for state-of-the-art in silico models, and make projections for future hardware and software requirements.

Project description:Background:There are few specialist paediatric Chronic Fatigue Syndrome (CFS/ME) services in the UK. Therefore, the distance some families have to travel to reach these services can be a barrier to accessing evidence-based treatment. Videoconferencing technology such as Skype provides a means of delivering sessions remotely. This study aimed to explore the views of children and young people, their parents, and healthcare professionals of treatment delivered by videoconferencing in a specialist paediatric CFS/ME team. Method:To explore the experiences of the participants, a qualitative design was selected. Twelve young people (age 9-18), and 6 parents were interviewed about their experience of treatment sessions delivered via videoconferencing within a specialist CFS/ME service. A focus group explored the views of healthcare professionals (N?=?9) from the service. Thematic analysis was used. Results:Three themes were identified from the data: "Challenges and concerns", "Benefits" and "Treatment provision". Challenges and concerns that participants identified were; difficulties experienced with technology; a sense of a part of communication being lost with virtual connections; privacy issues with communicating online and feeling anxious on a screen. Participants felt that benefits of videoconferencing were; improving access to the chronic fatigue service; convenience and flexibility of treatment provision; a sense of being more open online and being in the comfort of their own home. In terms of treatment provision participants talked about videoconferencing as a part of a hierarchy of communication; the function of videoconferencing within the context of the chronic fatigue service; additional preparation needed to utilise videoconferencing and an assumption that videoconferencing is "part of young people's lives". Conclusions:Although the experience of sessions provided by videoconferencing was different to sessions attended in person, participants tended to be positive about videoconferencing as an alternative means of accessing treatment, despite some barriers. Videoconferencing could be an additional option within an individualised care plan, but should not be an alternative to face to face support.

Dataset Information

Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.

Publications

Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models.

Similar Datasets

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