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Michael Schirner

Publications and source records attributed to Michael Schirner.

4 recordsLinked to original sources

SciOps: Achieving Productivity and Reliability in Data-Intensive Research

Scientists are increasingly leveraging advances in instruments, automation, and collaborative tools to scale up their experiments and research goals, leading to new bursts of discovery. Various scientific disciplines, including neuroscience, have adopted key technologies to enhance collaboration, reproducibility, and automation. Drawing inspiration from advancements in the software industry, we present a roadmap to enhance the reliability and scalability of scientific operations for diverse research teams tackling large and complex projects. We introduce a five-level Capability Maturity Model describing the principles of rigorous scientific operations in projects ranging from small-scale exploratory studies to large-scale, multi-disciplinary research endeavors. Achieving higher levels of operational maturity necessitates the adoption of new, technology-enabled methodologies, which we refer to as SciOps. This concept is derived from the DevOps methodologies that have revolutionized the software industry. SciOps involves digital research environments that seamlessly integrate computational, automation, and AI-driven efforts throughout the research cycle-from experimental design and data collection to analysis and dissemination, ultimately leading to closed-loop discovery. This maturity model offers a framework for assessing and improving operational practices in multidisciplinary research teams, guiding them towards greater efficiency and effectiveness in scientific inquiry.

q-bio.NC

TVB C++: A Fast and Flexible Back-End for The Virtual Brain

This paper introduces TVB C++, a streamlined and fast C++ Back-End for The Virtual Brain (TVB), a renowned platform and a benchmark tool for full-brain simulation. TVB C++ is engineered with speed as a primary focus while retaining the flexibility and ease of use characteristic of the original TVB platform. Positioned as a complementary tool, TVB serves as a prototyping platform, whereas TVB C++ becomes indispensable when performance is paramount, particularly for large-scale simulations and leveraging advanced computation facilities like supercomputers. Developed as a TVB-compatible Back-End, TVB C++ seamlessly integrates with the original TVB implementation, facilitating effortless usage. Users can easily configure TVB C++ to execute the same code as in TVB but with enhanced performance and parallelism capabilities.

q-bio.NC

The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

q-bio.OT

Brain Modelling as a Service: The Virtual Brain on EBRAINS

The Virtual Brain (TVB) is now available as open-source cloud ecosystem on EBRAINS, a shared digital research platform for brain science. It offers services for constructing, simulating and analysing brain network models (BNMs) including the TVB network simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional connectomes; multiscale co-simulation of spiking and large-scale networks; a domain specific language for automatic high-performance code generation from user-specified models; simulation-ready BNMs of patients and healthy volunteers; Bayesian inference of epilepsy spread; data and code for mouse brain simulation; and extensive educational material. TVB cloud services facilitate reproducible online collaboration and discovery of data assets, models, and software embedded in scalable and secure workflows, a precondition for research on large cohort data sets, better generalizability and clinical translation.

cs.CE