Tools

pyJUSBB

The PyJUSBB are bunch of python-based scripts that give a sample of individuals, identifies associations between summary measures of gray matter volume (extracted from preprocessed (with CAT12 software: http://www.neuro.uni-jena.de/cat/) T1Weighted data) and a broad range of behavioural scores. The tools further provide a ranking of the top correlating scores and assess stability of the outcomes within two independent sample of age and sex-matched individuals from the whole sample. The output is either a Figure or a CSV file.

Modelling and simulation

PyNN

PyNN (pronounced 'pine') is a simulator-independent language for building neuronal network models. In other words, you can write the code for a model once, using the PyNN API and the Python programming language, and then run it without modification on any simulator that PyNN supports (currently NEURON, NEST and Brian 2) and on a number of neuromorphic hardware systems. The PyNN API aims to support modelling at a high-level of abstraction (populations of neurons, layers, columns and the connections between them) while still allowing access to the details of individual neurons and synapses when required. PyNN provides a library of standard neuron, synapse and synaptic plasticity models, which have been verified to work the same on the different supported simulators. PyNN also provides a set of commonly-used connectivity algorithms (e.g. all-to-all, random, distance-dependent, small-world) but makes it easy to provide your own connectivity in a simulator-independent way. Even if you don't wish to run simulations on multiple simulators, you may benefit from writing your simulation code using PyNN's powerful, high-level interface. In this case, you can use any neuron or synapse model supported by your simulator, and are not restricted to the standard models.

Network level simulationModelling and simulation

PyramidalExplorer

It consists of a set of functionalities that allow possible regional differences in the pyramidal cell architecture to be interactively discovered by combining quantitative morphological information about the structure of the cell with implemented functional models. The key contribution of this tool is the morpho-functional oriented design that allows the user to navigate within the 3D dataset, filter and perform Content-Based Retrieval operations. As a case study, we present a human pyramidal neuron with over 9000 dendritic spines in its apical and basal dendritic trees. Using PyramidalExplorer, we were able to find unexpected differential morphological attributes of dendritic spines at particular compartments of the neuron, revealing new aspects of the morpho-functional organization of the pyramidal neuron.

Modelling and simulation

QCAlign

QCAlign was developed to support the use of the QUINT workflow for high-throughput studies. The QUINT workflow supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to a reference atlas.

Brain atlasesAnalysis

QuickNII

Software for 2D image registration to 3D atlas.

Brain atlasesData integration

Extract, quantify and analyse features from rodent histological images

The QUINT workflow comprises a suite of software designed to support atlas-based quantification. All the software have user interfaces, with no coding ability required. It generates object counts and percentage coverage per atlas-region, in addition to point clouds for visualising the features in 3D.

Brain atlases

Rat Brain Atlas

The Waxholm Space rat brain atlas is a detailed volumetric atlas of the rat brain, to which a wide range of anatomical and functional data have been registered, including detailed data showing cellular distributions, axonal pathways, and gene expression patterns. EBRAINS provides a visualization interface, enabling researchers to explore and compare different aspects of the rat brain in 3D space.

Brain atlases

Ratioscope

Genetically-encoded biosensors are heavily used in biology to monitor biological processes in real time within living cells. Many of such biosensors use two different emission wavelengths that change in opposite directions: the biological signal is measured as a change in the ratio of these two emissions. This so-called ratiometric quantification is standard and applies to many situations. Ratioscope, which runs in the Igor Pro environment, offers two packages: Ratio analysis of fluorescence images: image corrections, display in pseudocolor, measurements, kymograph, analysis of periodic activity, movies... Fusion module: statistics on series of experiments, to compare different experimental conditions; generate editor-ready graphs and plots.

Remote Connection Manager

The Remote Connection Manager (RCM) is an application that wraps vnc client. It allows HPC-users to perform remote visualization on HPC clusters. The tool offers to: Visualize the data produced on Cineca’s HPC systems (scientific visualization); Analyse and inspect data directly on the systems; Debug and profile parallel codes running on the HPC clusters. Debugging and profiling tools have to be interfaced to the compute nodes which execute the parallel code; they can benefit from tools enabling a graphic connection to the compute nodes. Scientific visualization can exploit the hardware (GPUs, memory and CPUs) available on the server side, enabling the user to remotely access their data and display them in an efficient way on their local client. The graphical interface of RCM allows the HPC users to easily create remote displays and to manage them (connect, kill, refresh).

Data analysis and visualisation

ReMoToo

ReMoToo is a system service that is able to stream the desktop to web remote clients, making it possible to have interactive sessions over remote high performance systems or even regular systems through a standard web browser. The key aspects of ReMoToo are the high quality visualization it provides as well as its low latency. To achieve it, ReMoToo uses video compression on the server side and sends the generated video stream to the client in a transparent and easy way. On the server side, several ReMoToo instances are managed by another service called ReMoLON. This service is in charge of the initiation, control and stop of ReMoToo visualization streams. The ReMoLON system service is connected through the ReMoLON_FrontEnd, a simple web server running on the login node/s. This FrontEnd is in charge of the user authentication and configuration of the ReMoToo instances through the ReMoLON system services.

Data analysis and visualisation

rgsl_odeiv2

An R package that solves a series of initial value problems in C via the GNU scientific library (ode solvers). The C code calls gsl_odeiv2 module functions to solve the problem or problems. The goal is to offload as much work as possible to the C code and keep the overhead minimal. That is why this package expects to solve a set of problems, rather than one, for the same model file (varying in e.g.: initial conditions, or parameters). The package contains 3 interface functions, they accept different ways of defining a set of problems,each with their own drawbacks and advantages. The interface functions are described in the following Sections. The ODE has to exist as a shared library (.so) file (currently in the current working directory: ?setwd and ?getwd ). There are some assumptions we make about the contents of the shared library file. Here we assume that the solutions serve some scientific purpose and the lab experiments come with observables, some measureable values that depend on the system's state (but are not the full state vector). We call the part of the model that calculates the observables ${ModelName}_func() (vfgen also calls them Functions of the model).

Data

rsHRF

This toolbox is aimed to retrieve the onsets of pseudo-events triggering an hemodynamic response from resting state fMRI BOLD voxel-wise signal. It is based on point process theory, and fits a model to retrieve the optimal lag between the events and the HRF onset, as well as the HRF shape, using a choice of basis functions (the canonical shape with two derivatives, (smoothed) Finite Impulse Response, mixture of gammas).

Data analysis and visualisation

RTNeuron

RTNeuron is a scalable real-time rendering tool for the visualisation of neuronal simulations based on cable models. Its main utility is twofold: the interactive visual inspection of structural and functional features of the cortical column model and the generation of high quality movies and images for presentations and publications. The package provides three main components: A high level C++ library. A Python module that wraps the C++ library and provides additional tools. The Python application script rtneuron-app.py A wide variety of scenarios is covered by rtneuron-app.py. In case the user needs a finer control of the rendering, such as in movie production or to speed up the exploration of different data sets, the Python wrapping is the way to go. The Python wrapping can be used through an IPython shell started directly from rtneuron-app.py or importing the module rtneuron into own Python programs. GUI overlays can be created for specific use cases using PyQt and QML.

Data analysis and visualisationModelling and simulation

SBtabVFGEN

Convert a model that has been hand written in the Sbtab format to VFGEN's format, NEURON's MOD file format, and optionally SBML (this is done if libsbml is installed with R bindings). This model conversion tool can be used by scientists working in the field of systems biology and all adjacent fields that work with ordinary differential equation (ODE) models. It can be helpful when collaborating with other researchers as it keeps the model separate from any programming language choice. The user writes the model in SBtab form, a simple, human readable format; afterwards this SBtab model can be converted to an ODE and further processed via vfgen (an alternative to vfgen is being worked on, if needed). The final result is code for the ODE right hand side function and analytical jacobian function (among other things) in the chosen programming language. This tool prepares a model M for use in numerical analysis application such as parameter estimation

Modelling and simulation

SCAIView-NEURO

SCAIView-NEURO is an semantic search engine especially built for translational neurodegeneration research. It supports literature mining in PubMed abstracts and PubMedCentral full text publications.

Data

Scalasca

Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks – in particular those concerning communication and synchronization – and offers guidance in exploring their causes. Scalasca supports the performance optimization of simulation codes on a wide range of current HPC platforms. Its powerful analysis and intuitive result presentation guides the developer through the tuning process. Scalasca targets mainly scientific and engineering applications based on the programming interfaces MPI and OpenMP, including hybrid applications based on a combination of the two. The tool has been specifically designed for use on large-scale systems including IBM Blue Gene and Cray XT, but is also well suited for small- and medium-scale HPC platforms.

Modelling and simulation

Score-P

Score-P is a software system that provides a measurement infrastructure for profiling, event trace recording, and online analysis of High Performance Computing (HPC) applications. It is being developed with the objective of creating a common basis for several complementary optimization tools in the service of enhanced scalability, improved interoperability, and reduced maintenance cost. Currently, it works with the analysis tools Cube, Extra-P, Periscope, Scalasca Trace Tools, Vampir, and Tau and is open for other tools.

Modelling and simulation

SDA

SDA (Simulation of Diffusional Association) is a Brownian dynamics simulation software package for the simulation of the diffusion of biomacromolecules in aqueous solution. SDA can be used to compute bimolecular diffusional association rate constants and to predict the structures of diffusional encounter complexes. It can also be used to simulate dilute or concentrated protein solutions and to investigate the adsorption of proteins to solid surfaces. SDA7 is available for standalone use and a subset of the functionality is implemented in the webSDA webserver.

Modelling and simulationMolecular and subcellular simulation

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