Related papers: pyMBE: the Python-based Molecule Builder for ESPRe…
Predicting protein complex structures is essential for protein function analysis, protein design, and drug discovery. While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the…
We have developed PyTIE (Python Topological Indices Expressions) which is defined as the collections of Python packages such as PyTIE D, PyTIE DS, PyTIE SMS DE, and PyTIE SMS DSE, which are open-source software packages and cross-platform…
We develop an open-source python workflow package, $py$GWBSE to perform automated first-principles calculations within the GW-BSE (Bethe-Salpeter) framework. GW-BSE is a many body perturbation theory based approach to explore the…
PySDM is an open-source Python package for simulating the dynamics of particles undergoing condensational and collisional growth, interacting with a fluid flow and subject to chemical composition changes. It is intended to serve as a…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…
Automated molecular simulations are used extensively for predicting material properties. Typically, these simulations exhibit two regimes: a dynamic equilibration part, followed by a steady state. For extracting observable properties, the…
We present a new software pipeline -- PyMorph -- for automated estimation of structural parameters of galaxies. Both parametric fits through a two dimensional bulge disk decomposition as well as structural parameter measurements like…
Computed tomography perfusion (CTP) and magnetic resonance perfusion (MRP) are widely used in acute ischemic stroke assessment and other cerebrovascular conditions to generate quantitative maps of cerebral hemodynamics. While commercial…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources…
This paper is a guide to the installation and use of the Python package PYESSENCE. PYESSENCE is designed to evolve linear perturbations to Coupled Quintessence models with a arbitrary number of cold dark matter (CDM) fluids and dark energy…
Unmodelled searches and reconstruction is a critical aspect of gravitational wave data analysis, requiring sophisticated software tools for robust data analysis. This paper introduces PycWB, a user-friendly and modular Python-based…
We present PyCCE, an open-source Python library to simulate the dynamics of spin qubits in a spin bath, using the cluster-correlation expansion (CCE) method. PyCCE includes modules to generate realistic spin baths, employing coupling…
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes.…
Programming by example (PBE) is an emerging programming paradigm that automatically synthesizes programs specified by user-provided input-output examples. Despite the convenience for end-users, implementing PBE tools often requires strong…
We present ChemXploreML, a modular desktop application designed for machine learning-based molecular property prediction. The framework's flexible architecture allows integration of any molecular embedding technique with modern machine…
Sparse linear algebra is a cornerstone of many scientific computing and machine learning applications. Python has become a popular choice for these applications due to its simplicity and ease of use. Yet high performance sparse kernels in…
Peptide self-assembly prediction offers a powerful bottom-up strategy for designing biocompatible, low-toxicity materials for large-scale synthesis in a broad range of biomedical and energy applications. However, screening the vast sequence…
FCMpy is an open source package in Python for building and analyzing Fuzzy Cognitive Maps. More specifically, the package allows 1) deriving fuzzy causal weights from qualitative data, 2) simulating the system behavior, 3) applying machine…
In this paper, we present a new gas-grain chemical code for interstellar clouds written in pure Python (GGCHEMPY). By combining with the high-performance Python compiler Numba, GGCHEMPY is as efficient as the Fortran-based version. With the…