Tools

The Jupyter Notebook

Jupyter notebook is a language-agnostic HTML notebook application for Project Jupyter. In 2015, Jupyter notebook was released as a part of The Big Split™ of the IPython codebase. IPython 3 was the last major monolithic release containing both language-agnostic code, such as the IPython notebook, and language specific code, such as the IPython kernel for Python. As computing spans across many languages, Project Jupyter will continue to develop the language-agnostic Jupyter notebook in this repo and with the help of the community develop language specific kernels which are found in their own discrete repos.

Data

The Virtual Brain

The Virtual Brain (TVB) is an open-source platform for constructing and simulating personalised brain network models. The TVB-on-EBRAINS ecosystem includes a variety of prepackaged modules, integrated simulation tools, pipelines and data sets for easy and immediate use on EBRAINS. Process your large cohort databases and use these results to develop potential medical treatments, therapies or diagnostic procedures.

Modelling and simulationWhole-brain simulation

The Virtual Brain Web-App

Access the TVB GUI from the Internet and simulate brain network models on HCP. TheVirtualBrain is a framework for the simulation of the dynamics of large-scale brain networks with biologically realistic connectivity. TheVirtualBrain uses tractographic data (DTI/DSI) to generate connectivity matrices and build cortical and subcortical brain networks. The connectivity matrix defines the connection strengths and time delays via signal transmission between all network nodes. Various neural mass models are available in the repertoire of TheVirtualBrain and define the dynamics of a network node. Together, the neural mass models at the network nodes and the connectivity matrix define the Virtual Brain. TheVirtualBrain simulates and generates the time courses of various forms of neural activity including Local Field Potentials (LFP) and firing rate, as well as brain imaging data such as EEG, MEG and BOLD activations as observed in fMRI. TheVirtualBrain is foremost a scientific simulation platform and provides all means necessary to generate, manipulate and visualize connectivity and network dynamics. In addition, TheVirtualBrain comprises a set of classical time series analysis tools, structural and functional connectivity analysis tools, as well as parameter exploration facilities. An overview over TVB-on-EBRAINS services is provided in the preprint https://arxiv.org/abs/2102.05888

Modelling and simulationWhole-brain simulation

Threading Building Blocks

Intel® Threading Building Blocks (Intel® TBB) is a widely used C++ library for shared memory parallel programming and heterogeneous computing (intra-node distributed memory programming). The library provides a wide range of features for parallel programming that include: Generic parallel algorithms Concurrent containers A scalable memory allocator Work-stealing task scheduler Low-level synchronization primitives Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. It does not require any special compiler support and has ports to multiple architectures that include Intel® architectures and ARM.

Modelling and simulation

Tide

Tide (Tiled Interactive Display Environment) is a distributed application that can run on multiple machines to power display walls or projection systems of any size. Its user interface is designed to offer an intuitive experience on touch walls. It works just as well on non touch-capable installations by using its web interface from any web browser. Tide helps users with: Presenting and collaborating on a variety of media such as high-resolution images, movies and pdfs. Sharing multiple desktop or laptop screens using the DesktopStreamer application. Sketching new ideas by drawing on a whiteboard and browsing websites. Interacting with content streamed from remote sources such as high-performance visualisation machines through the Deflect protocol. In particular all Equalizer-based applications as well as Brayns ray-tracing engine have built-in support. Viewing high-resolution, immersive stereo 3D streams on compatible hardware.

Data analysis and visualisation

TVB Brain Atlas Viewer

A viewer that allows users to view brain atlasses on top of a 3d brain model. The Brain Atlas Viewer allows users to inspect the location and shape of different brain regions and their associated function. Brain regions can be selected by anatomy or by function. Descriptions are available in English, Arabic, Hebrew, and German. Regions are annotated with their function. TVB Brain Atlas Viewer is an interactive software that can be operated via touch screen. It was part of the HBP Travelling Exhibition that started in July 2019 at Bloomfield Museum in Jerusalem organized by the HBP Museum Program (SP11). An overview over TVB-on-EBRAINS services is provided in the preprint https://arxiv.org/abs/2102.05888

Whole-brain simulationModelling and simulationBrain atlases

TVB-HPC

TVB-HPC provides a framework for generating high-performance computational kernels which can be run on HPC systems with or without hardware accelerators for large scale parameter fitting of brain models An overview over TVB-on-EBRAINS services is provided in the preprint https://arxiv.org/abs/2102.05888

Whole-brain simulationModelling and simulation

TVB image processing pipeline

The TVB pipeline allows neuroscientists to automatically extract structural connectomes from diffusion-weighted MRI data and functional connectomes from fMRI data based on a number of state-of-the-art methods for image processing, tractography reconstruction and connectome generation. Pipeline output can be directly uploaded to The Virtual Brain neuroinformatics platform for large-scale brain simulation. Further pipeline outputs include: raw tractography output (track streamlines), structural (coupling weights and distances) and functional connectomes, region-wise fMRI time series, M/EEG region-wise source activity time series. The pipeline supports the following atlasses: AAL, AAL2, Craddock200, Craddock400, Desikan Killiany, Destrieux, Human Connectome Project Multimodal Parcellation and Perry512. The pipeline is available as a Docker container based on the BIDS MRtrix3 App containing environment and software for connectome extraction (e.g. FreeSurfer, FSL, MRtrix). The container makes use of parallelized software that can be run with multiple threads locally or on supercomputers. Input data must be provided in BIDS format. As a minimum, dwMRI and strucutral MRI scans need to be provided. In addition, the pipeline can process fMRI (region-wise fMRI time courses and functional connectomes), EEG and MEG data (region-wise source activity time courses).

Whole-brain simulationModelling and simulation

UG4

UG4 (Unstructured Grids 4) is an extensive, flexible, cross-platform open source simulation framework for the numerical solution of systems of partial differential equations. Using Finite Element and Finite Volume methods on hybrid, adaptive, unstructured multigrid hierarchies, UG4 allows for the simulation of complex real world models (physical, biological etc.) on massively parallel computer architectures. UG4 is implemented in the C++ programming language and provides grid management, discretization and (linear as well as non-linear) solver utilities. It is extensible and customizable via its plugin mechanism. The highly scalable MPI based parallelization of UG4 has been shown to scale to hundred thousands of cores. Simulation workflows are defined either using the Lua scripting language or the graphical VRL interface https://vrl-studio.mihosoft.eu/. Besides that, UG4 can be used as a library for third-party code. Several examples are provided in the Examples application that can be used for simulations of the corresponding phenomena but also serve as demonstration modules for implementing user-defined plugins and scripts. By developing custom plugins, users can extend the functionality of the framework for their particular purposes. The framework provides coupling facilities for the models implemented in different plugins. Key elements of UG4 are: Efficient solvers on distributed, adaptive multigrid hierarchies. A flexible component based discretization system. Efficient support for massively parallel computer architectures. Full scripting support. A modular plugin based architecture.

Modelling and simulation

UQSA

Uncertainty quantification via ABC-MCMC with copulas as well as global sensitivity analysis for ODE models in systems biology. This R package can approximate the posterior probability density of Parameters for Ordinary Differential Equation models. The ABC sampler used here is developed to be fairly model agnostic, but the supplied tool set and R functions specifically target ODEs as they are fast enough to simulate to permit Bayesian methods. Bayesian methods for parameter estimation are resource intensive and therefore require some consideration of efficiency in simulation. Other modeling frameworks exist, with benefits of higher accuracy in specific scenarios (e.g. low molecule count), or reduced complexity (rule based models). We have written a sibling library for R that facilitates the simulation of systems biology specific models using the GNU scientific library solvers (and models written in C). With powerful enough computing hardware, or small enough models, these frameworks can be combined with this package. We write models using the SBtab format and automatically generate C-code as well as R-code for them, the R-code can be used with deSolve (an R package) while the C-code is compatible with gsl_odeiv2 solvers. Code generation is done via SBtabVFGEN (an R package) and vfgen (a standalone software). In addition, we are writing our own substitution for vfgen, to avoid single points of failure. But the model setup phase can be completely sidestepped by writing the C-code manually (or generating it in any other way).

Modelling and simulation

Vaa3D

Vaa3D is a handy, fast, and versatile 3D/4D/5D Image Visualization and Analysis System for Bioimages and Surface Objects. It also provides many unique functions that you may not find in other software. It is Open Source, and supports a very simple and powerful plugin interface and thus can be extended and enhanced easily. Vaa3D is cross-platform (Mac, Linux, and Windows). This software suite is powerful for visualizing large- or massive-scale (giga-voxels and even tera-voxels) 3D image stacks and various surface data. Vaa3D is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes Vaa3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, Vaa3D streamlines the workflow of visualization-assisted analysis. Vaa3D can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales... it comes with a number of plugins and toolboxes. Importantly, you can now write your own plugins to take advantage of the Vaa3D platform, possibly within minutes!

Data analysis and visualisation

VIOLA

VIOLA (Visualization Of Layer Activity) is a lightweight, open-source, web-based, and platform-independent application combining and adapting modern interactive visualization paradigms, such as coordinated multiple views, for massively parallel neurophysiological data. It gives an insight into spatially resolved time series such as simulation results of neural networks with 2D geometry. With the multiple coordinated views, an explorative and qualitative assessment of the spatiotemporal features of neuronal activity can be performed upfront of a detailed quantitative data analysis of specific aspects of the data.

Data analysis and visualisation

Vishnu

DC Explorer, Pyramidal Explorer and Clint Explorer are the core of an application suite designed to help scientists to explore their data. Vishnu is a communication framework that allows them to interchange information and cooperate in real-time. It provides a unique access point to the three applications and manages a database with the users’ data sets.

Data

ViSimpl

ViSimpl involves two components: SimPart and StackViz. SimPart is a three-dimensional visualizer for spatio-temporal data that allow spatio/temporal analysis of the simulation data, using particle-based rendering. StackViz illustrates how the electrophysiological variables evolve over time and provides a temporal representation of the data at different aggregation levels. They allow users to visually discriminate the activity of different groups of neurons, and provide detailed information about individual neurons of interest. These components share synchroniszed playback control of the simulation being analyzsed and work together as linked views, although they are loosely coupled and can also be used independently. They are ready to be used with BlueConfig Datasets among other file formats such as specific HDF5 and CSV. VisSimpl can be coupled with NeuroScheme for adding functionality such as navigate through the underlying structure of the data using symbolic representations and different levels of abstraction.

Modelling and simulationCellular level simulationData analysis and visualisation

VisuAlign

Software for 2D image registration to 3D atlas.

Brain atlasesData integration

Viziphant

Viziphant is a Python module for easy visualization of Neo objects and Elephant results. It provides a high-level API to easily generate plots and interactive visualizations of neuroscientific data and analysis results. This API uses and extends the same structure as in Elephant to ensure intuitive usage for scientists that are used to Elephant.

Data analysis and visualisation

voluba – Alignment of high-resolution volumes of interest

Using voluba, you can upload an image file to a private storage space and register it interactively to a reference space in your web browser. Currently, voluba supports the BigBrain model, Waxholm rat template and Allen mouse template as reference spaces. voluba is compatible with siibra-explorer, so you can directly inspect your aligned data superimposed with brain region maps and other datasets. You can also submit your anchoring result to EBRAINS curation support for sharing.

Brain atlasesData integration

voluba-mriwarp – Aligning human MRI volumes to atlas space

voluba-mriwarp enables you to integrate human whole-brain MRI scans into the detailed anatomical context of the Human Brain Atlas on your local computer. The tool automatically performs registration based on predefined parameters. The results can be used to assign anatomical locations to brain regions of the atlas. To perform a more detailed analysis, you can export assignments to a PDF report together with linked features like receptor densities or brain connectivity.

Brain atlasesData integration

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