Lead-OR: A Multimodal Platform for Deep Brain Stimulation Surgery

Deep Brain Stimulation (DBS) electrode implant trajectories are stereotactically defined using preoperative neuroimaging. To validate the correct trajectory, microelectrode recordings (MER) can be used to match the neuroanatomy with expected neurophysiological activity patterns, commonly using up to five trajectories in parallel. However, understanding their location in relationship to basal ganglia anatomy can be challenging. Here we present a tool that integrates resources from stereotactic planning, neuroimaging, MER and high-resolution atlas data to create a real-time visualization of the implant trajectory. We show a general correspondence between features derived from neuroimaging and electrophysiological recordings and present example use cases that demonstrate the functionality of the tool. The software toolbox is made openly available, extendable and holds translational potential in the field of stereotactic neurosurgery.

OPAL—The Toolbox for the Integration and Analysis of IoT in a Semantically Annotated Way

Industrial Internet of Things (IIoT) applications are being used more and more frequently. Data collected by various sensors can be used to provide innovative digital services supporting increasing efficiency or cost reduction. The implementation of such applications requires the integration and analysis of heterogeneous data coming from a broad variety of sensors. To support these steps, this paper introduces OPAL, a software toolbox consolidating several software components for the semantically annotated integration and analysis of IoT-data. Data storage is realized in a standardized and INSPIRE-compliant way utilizing the SensorThings API. Supporting a broad variety of use cases, OPAL provides several import adapters to access data sources with various protocols (e.g., the OPC UA protocol, which is often used in industrial environments). In addition, a unified management and execution environment, called PERMA, is introduced to allow the programming language independent integration of algorithms.

A TROPICAL CYCLONE WIND, WAVE AND STORM TIDE RISK DESIGN AND WARNING TOOLBOX FOR AUSTRALIA

The paper will describe the development and operation of a comprehensive tropical cyclone wind, wave and storm tide risk design and warning software toolbox that covers all of tropical-influenced Australia, The toolbox is designed to provide both rapid assessment and detailed design capabilities for coastal, port, offshore and nearshore design, including projected future climate change. It also provides real-time emergency management functionality. The toolbox provides a probabilistic design framework that facilitates the essential need for sensitivity analysis of both inputs and outputs without pre-conceived risk thresholds. It provides the essential hazard component in a robust and verified context that can then, depending on the application, enable more focused and efficient deterministic modelling stages using models of choice.Recorded Presentation from the vICCE (YouTube Link): https://youtu.be/pssgiYdkEbM

BioCRNpyler: Compiling Chemical Reaction Networks from Biomolecular Parts in Diverse Contexts

Biochemical interactions in systems and synthetic biology are often modeled with Chemical Reaction Networks (CRNs). CRNs provide a principled modeling environment capable of expressing a huge range of biochemical processes. In this paper, we present a software toolbox, written in python, that complies high-level design specifications to CRN representations. This compilation process offers four advantages. First, the building of the actual CRN representation is automatic and outputs Systems Biology Markup Language (SBML) models compatible with numerous simulators. Second, a library of modular biochemical components allows for different architectures and implementations of biochemical circuits to be represented succinctly with design choices propagated throughout the underlying CRN automatically. This prevents the often occurring mismatch between high-level designs and model dynamics. Third, high-level design specification can be embedded into diverse biomolecular environments, such as cell-free extracts and in vivo milieus. Finally, our software toolbox has a parameter database, which allows users to rapidly prototype large models using very few parameters which can be customized later. By using BioCRNpyler, users can easily build, manage, and explore sophisticated biochemical models using diverse biochemical implementations, environments, and modeling assumptions.

Data-driven reduction of dendritic morphologies with preserved dendro-somatic responses

Dendrites shape information flow in neurons. Yet, there is little consensus on the level of spatial complexity at which they operate. We present a flexible and fast method to obtain simplified neuron models at any level of complexity. Through carefully chosen parameter fits, solvable in the least squares sense, we obtain optimal reduced compartmental models. We show that (back-propagating) action potentials, calcium-spikes and NMDA-spikes can all be reproduced with few compartments. We also investigate whether afferent spatial connectivity motifs admit simplification by ablating targeted branches and grouping the affected synapses onto the next proximal dendrite. We find that voltage in the remaining branches is reproduced if temporal conductance fluctuations stay below a limit that depends on the average difference in input impedance between the ablated branches and the next proximal dendrite. Further, our methodology fits reduced models directly from experimental data, without requiring morphological reconstructions. We provide a software toolbox that automatizes the simplification, eliminating a common hurdle towards including dendritic computations in network models.

Technical note: PaleoDataView – a software toolbox for the collection, homogenization and visualization of marine proxy data

We present a software toolbox that allows the efficient collection, management and maintenance of larger paleoceanographic data sets. The program combines a graphical user interface (GUI) with a simple document-based database and functionality for visualization, stratigraphy (visual alignment and radiocarbon calibration), age modelling and efficient ensemble time-series generation to create larger homogenous data compilations. Data can be imported from Excel or text files, are stored locally in netCDF format and can be easily exchanged between collaborating scientists. Within a data collection, data can be imported either to proxy-specific sub-collections or to a multi-proxy (“miscellaneous”) sub-collection that allows the import and management of any downcore data. A single age model is shared among all proxies of a core within a collection. The stand-alone software can be used with Windows and macOS and does not require web access. Installers of the current version for both Windows 10 and macOS including the C++ code can be downloaded from https://www.marum.de/Stefan-Mulitza/PaleoDataView.html (last access: 5 December 2019) along with a detailed user guide.