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POLEVAL provides a software toolbox for collaborative, persistent and reproducible analysis of XPS experiments. It allows to treat, analyse and visualise the results of an extended experimental campaign in a single python notebook in a…
Movies of human induced pluripotent stem cell (hiPSC)-derived engineered cardiac tissue (microbundles) contain abundant information about structural and functional maturity. However, extracting these data in a reproducible and…
The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…
This work introduces a new software package `Sesame' for the numerical computation of classical semiconductor equations. It supports 1 and 2-dimensional systems and provides tools to easily implement extended defects such as grain…
BEFANA is a free and open-source software tool for ecological network analysis and visualisation. It is adapted to ecologists' needs and allows them to study the topology and dynamics of ecological networks as well as apply selected machine…
We present CONAN (COde for exoplaNet ANalysis), an open-source Python package for comprehensive analyses of exoplanetary systems. It provides a unified Bayesian framework to simultaneously analyze diverse exoplanet datasets to derive global…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
A key problem in automatic analysis and understanding of scientific papers is to extract semantic information from non-textual paper components like figures, diagrams, tables, etc. Much of this work requires a very first preprocessing step:…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
Deconvolution of cell mixtures in "bulk" transcriptomic samples from homogenate human tissue is important for understanding the pathologies of diseases. However, several experimental and computational challenges remain in developing and…
The level set tree approach of Hartigan (1975) provides a probabilistically based and highly interpretable encoding of the clustering behavior of a dataset. By representing the hierarchy of data modes as a dendrogram of the level sets of a…
BEANS software is a web based, easy to install and maintain, new tool to store and analyse data in a distributed way for a massive amount of data. It provides a clear interface for querying, filtering, aggregating, and plotting data from an…
GenoML is a Python package automating machine learning workflows for genomics (genetics and multi-omics) with an open science philosophy. Genomics data require significant domain expertise to clean, pre-process, harmonize and perform…
dlordinal is a new Python library that unifies many recent deep ordinal classification methodologies available in the literature. Developed using PyTorch as underlying framework, it implements the top performing state-of-the-art deep…
DepAnn is an interactive annotation tool for dependency treebanks, providing both graphical and text-based annotation interfaces. The tool is aimed for semi-automatic creation of treebanks. It aids the manual inspection and correction of…
Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. This is often impractical for non-bioinformaticians. Whilst the popular CELLxGENE software provides an…
Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistical insights into biological functions. Currently, high-throughput data are usually visualized on top of predefined…
In recent years, x-ray speckle tracking techniques have emerged as viable tools for wavefront metrology and sample imaging applications. These methods are based on the measurement of near-field images. Thanks to the simple experimental…