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Super-resolution microscopy has catalyzed valuable insights into the sub-cellular, mechanistic details of many different biological processes across a wide range of cell types. Fluorescence polarization spectroscopy tools have also enabled…
The BumpHunter algorithm is widely used in the search for new particles in High Energy Physics analysis. This algorithm offers the advantage of evaluating the local and global p-values of a localized deviation in the observed data without…
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…
The folding dynamics of proteins at the single molecule level has been studied with single-molecule force spectroscopy (SMFS) experiments for twenty years, but a common standardized method for the analysis of the collected data and for the…
This work presents the new template matching capabilities implemented in Pyxem, an open source Python library for analyzing four-dimensional scanning transmission electron microscopy (4D-STEM) data. Template matching is a brute force…
Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…
Modern time series analysis demands frameworks that are flexible, efficient, and extensible. However, many existing Python libraries exhibit limitations in modularity and in their native support for irregular, multi-source, or sparse data.…
The open-source python package diffpy.mpdf, part of the DiffPy suite for diffraction and pair distribution function analysis, provides a user-friendly approach for performing magnetic pair distribution function (mPDF) analysis. The package…
Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for…
A large scale collection of both semantic and natural language resources is essential to leverage active Software Engineering research areas such as code reuse and code comprehensibility. Existing machine learning models ingest data from…
PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, both to aid new method development, as well as for flexibility in computational workflow. The package provides a wide range…
Mathematical modeling is a powerful tool in rheology, and we present pyRheo, an open-source package for Python designed to streamline the analysis of creep, stress relaxation, oscillation, and rotation tests. pyRheo contains a comprehensive…
In recent years, there has been increasing interest in network diffusion models and related problems. The most popular of these are the independent cascade and linear threshold models. Much of the recent experimental work done on these…
The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add…
readPTU is a python package designed to analyze time-correlated single-photon counting data. The use of the library promotes the storage of the complete time arrival information of the photons and full flexibility in post-processing data…
Understanding how the brain functions is one of the biggest challenges of our time. The analysis of experimentally recorded neural firing patterns (spike trains) plays a crucial role in addressing this problem. Here, the PySpike library is…
We present PyOECP, a Python-based flexible open-source software for estimating and modeling the complex permittivity obtained from the open-ended coaxial probe (OECP) technique. The transformation of the measured reflection coefficient to…
We present PyXtal FF, a package based on Python programming language, for developing machine learning potentials (MLPs). The aim of PyXtal FF is to promote the application of atomistic simulations by providing several choices of structural…
Background: Fluorescent Timer proteins, which display time-dependent changes in their emission spectra, are invaluable for analyzing the temporal dynamics of cellular events at the single-cell level. We previously developed the…
Analysis of XRD diffraction patterns is one of the keystones of materials science and materials research. With the advancement of data-driven methods for materials design, candidate materials can be quickly screened for the study of a…