Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: scientific-computing

cid-harvard/pandas-to-postgres

Copy Pandas DataFrames and HDF5 files to PostgreSQL database

Language: Python - Size: 62.5 KB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 53 - Forks: 12

mynenik/kForth-32

32-bit Forth System for x86-linux

Language: Forth - Size: 6.53 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 19 - Forks: 2

equipez/setup_mex

This package provides scripts that attempt to facilitate setting up the MATLAB MEX.

Language: MATLAB - Size: 234 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 2 - Forks: 2

dmitry-kabanov/mardi-open-interfaces-new-attempt

Measure 2.2 “Open Interfaces” of the Mathematical Research Data Initiative (MaRDI) project

Language: C - Size: 551 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 1

gagolews/deepr

Deep R Programming (Open-Access Textbook)

Size: 105 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 85 - Forks: 1

ubermag/oommfc

OOMMF calculator.

Language: Python - Size: 25.6 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 46 - Forks: 18

Marcello-Sega/pytim

a python package for the interfacial analysis of molecular simulations

Language: Python - Size: 205 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 74 - Forks: 32

numericalalgorithmsgroup/dfols

Python-based Derivative-Free Optimizer for Least-Squares

Language: Python - Size: 9.76 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 37 - Forks: 14

cadojo/GeneralAstrodynamics.jl

Astrodynamics with units! Provides common astrodynamics calculations, plotting, and iterative Halo, Kepler, and Lambert solvers.

Language: Julia - Size: 2.26 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 20 - Forks: 3

ubermag/micromagneticdata

Python package for the analysis of micromagnetic data.

Language: Python - Size: 17.5 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 3 - Forks: 2

aeye-lab/pymovements

A python package for processing eye movement data

Language: Python - Size: 1.42 MB - Last synced: about 14 hours ago - Pushed: about 14 hours ago - Stars: 51 - Forks: 8

ubermag/micromagnetictests

Testing package for computational magnetism tools.

Language: Python - Size: 220 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 2

deepcharles/ruptures

ruptures: change point detection in Python

Language: Python - Size: 10.9 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1,466 - Forks: 161

vrtulka23/scinumtools

Essential tools for numerical scientific calculations, simulations and data analysis. Besides several useful tools, this package is featuring expression solver, physical units, material properties and dimensional input parameter modules.

Language: Python - Size: 1.53 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 5 - Forks: 0

SlicerCBM/SlicerCBM

Computational Biophysics for Medicine in 3D Slicer

Language: Python - Size: 5.28 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 13 - Forks: 2

open-cogsci/datamatrix

An intuitive, Pythonic way to work with tabular data

Language: Python - Size: 35.1 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 23 - Forks: 10

ubermag/discretisedfield

Python package for the analysis and visualisation of finite-difference fields.

Language: Jupyter Notebook - Size: 118 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 17 - Forks: 12

ubermag/ubermagutil

Utility package used across Ubermag.

Language: Python - Size: 333 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 5 - Forks: 2

ubermag/ubermagtable

Python package for manipulating tabular data.

Language: Python - Size: 1.92 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 6 - Forks: 2

ubermag/micromagneticmodel

Python-based domain-specific language for computational magnetism.

Language: Python - Size: 1.22 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 10 - Forks: 8

AMSC22-23/Eikonal-Cuda-Cesaroni-Tonarelli-Trabacchin

Eikonal CUDA implementation for the Advanced Methods for Scientific Computing (AMSC) Course @POLIMI

Language: C++ - Size: 17.1 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 1 - Forks: 0

RubixML/Tensor

A library and extension that provides objects for scientific computing in PHP.

Language: PHP - Size: 1.97 MB - Last synced: 6 days ago - Pushed: 2 months ago - Stars: 218 - Forks: 27

inducer/meshmode

High-order unstructured mesh representation and discrete function spaces

Language: Python - Size: 2.63 MB - Last synced: 4 days ago - Pushed: 9 days ago - Stars: 25 - Forks: 24

xitorch/xitorch

Differentiable scientific computing library

Language: Python - Size: 2.22 MB - Last synced: 4 days ago - Pushed: about 1 year ago - Stars: 129 - Forks: 18

ProjectPhysX/FluidX3D

The fastest and most memory efficient lattice Boltzmann CFD software, running on all GPUs via OpenCL.

Language: C++ - Size: 20.7 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 3,217 - Forks: 258

openweathermap/deker-local-adapters

Local filesystem HDF5 storage for Deker

Language: Python - Size: 360 KB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 4 - Forks: 2

openweathermap/deker

Multidimensional arrays storage engine

Language: Python - Size: 5.33 MB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 17 - Forks: 5

andykee/lentil

Heart-healthy physical optics

Language: Python - Size: 7.93 MB - Last synced: 1 day ago - Pushed: 10 days ago - Stars: 12 - Forks: 4

numericalalgorithmsgroup/NAGPythonExamples

Examples and demos showing how to call functions from the NAG Library for Python

Language: Jupyter Notebook - Size: 21.4 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 56 - Forks: 22

CubicZebra/informatics

Framework of fast implementation data processing and operating pipelines

Language: Python - Size: 7.05 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 99 - Forks: 5

R-js/libRmath.js

Javascript Pure Implementation of Statistical R "core" numerical libRmath.so

Language: TypeScript - Size: 5.72 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 466 - Forks: 32

sinanislekdemir/payton

Payton! Kickstart any 3D OpenGL + GTK Ideas in a few seconds!

Language: Python - Size: 32.7 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 45 - Forks: 6

ddemidov/amgcl

C++ library for solving large sparse linear systems with algebraic multigrid method

Language: C++ - Size: 7.86 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 701 - Forks: 107

MineralsCloud/LinearElasticity.jl

Calculate linear elasticity for some crystals

Language: Julia - Size: 741 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 1 - Forks: 0

singularitti/SimpleIsing.jl

This repo implements the Metropolis–Hastings algorithm (MCMC method) and the Swendsen–Wang cluster algorithm for the Ising model

Language: TeX - Size: 2.73 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 0

singularitti/Spglib.jl

A Julia wrapper for the spglib C-API

Language: Julia - Size: 2.11 MB - Last synced: 8 days ago - Pushed: 11 days ago - Stars: 16 - Forks: 10

GuilhermePortella/IntroducaoCienciasComputacao

Introdução a matérias estudadas no curso de ciências da computação :ghost:

Language: JavaScript - Size: 6.16 MB - Last synced: 23 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

cadojo/PolynomialGTM.jl

An unofficial implementation of publicly available approximated polynomial models for NASA's Generic Transport Model aircraft.

Language: Julia - Size: 332 KB - Last synced: 9 minutes ago - Pushed: 2 months ago - Stars: 6 - Forks: 1

mmottl/gsl-ocaml

OCaml bindings to the GSL (GNU Scientific Library).

Language: OCaml - Size: 2.31 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 36 - Forks: 10

bioio-devs/bioio-ome-tiff

A BioIO reader plugin for reading Tiff files in the OME format.

Language: Python - Size: 59.6 KB - Last synced: 11 days ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

JaneliaSciComp/workstation

Janelia Workstation

Language: Java - Size: 98 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 20 - Forks: 11

usnistgov/fipy

FiPy is a Finite Volume PDE solver written in Python

Language: Python - Size: 453 MB - Last synced: 10 days ago - Pushed: about 1 month ago - Stars: 472 - Forks: 145

polsys/ennemi

Easy Nearest Neighbor Estimation of Mutual Information

Language: Python - Size: 1.81 MB - Last synced: 11 days ago - Pushed: about 1 month ago - Stars: 35 - Forks: 12

cogciprocate/ocl

OpenCL for Rust

Language: Rust - Size: 34.1 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 696 - Forks: 76

singularitti/PoissonSchrodingerSimulator.jl

This package implements the Lanczos algorithm and the conjugate gradient method on an irregular grid.

Language: TeX - Size: 3.39 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

storopoli/Why-Julia

Why Julia? A Gentle Pitch

Size: 3.46 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 10 - Forks: 0

MineralsCloud/CrystallographyBase.jl

This package contains some basic functionalities of Crystallography.jl

Language: Julia - Size: 1.6 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 4 - Forks: 0

singularitti/JackknifeAnalysis.jl

This code implements the Jackknife resampling algorithm.

Language: TeX - Size: 1.86 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

AgentTorch/AgentTorch

large population models

Language: Jupyter Notebook - Size: 105 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 24 - Forks: 3

AIS-Package/aisp

This is an open source Python package that provides an implementation of techniques inspired by the artificial immune system, enabling the easy and intuitive use of algorithms based on immunology.

Language: Python - Size: 9.3 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 7 - Forks: 2

arrayfire/arrayfire

ArrayFire: a general purpose GPU library.

Language: C++ - Size: 19 MB - Last synced: 12 days ago - Pushed: about 1 month ago - Stars: 4,416 - Forks: 527

cggos/SciKit

Scientific Computing & Programming :bar_chart:

Language: Jupyter Notebook - Size: 2.55 MB - Last synced: 12 days ago - Pushed: 13 days ago - Stars: 1 - Forks: 2

sciexp/sciops

GitOps cluster template for scientific data analysis

Language: Shell - Size: 295 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 2 - Forks: 2

jackalkahwati/Stardrive_Simulation

Language: Python - Size: 103 KB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

PipInSpace/IonSolver

IonSolver is a magnetohydrodynamic simulation software featuring an extended Lattice Boltzmann method and GPU acceleration

Language: Rust - Size: 39.1 MB - Last synced: 1 day ago - Pushed: 13 days ago - Stars: 13 - Forks: 1

ddemidov/vexcl

VexCL is a C++ vector expression template library for OpenCL/CUDA/OpenMP

Language: C++ - Size: 22.8 MB - Last synced: 12 days ago - Pushed: about 2 years ago - Stars: 695 - Forks: 81

HSF/prmon

Standalone monitor for process resource consumption

Language: C++ - Size: 768 KB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 41 - Forks: 20

andthum/lintf2_ether_ana_postproc

Analysis postprocessing utilities for my molecular dynamics simulations of LiTFSI-Ether mixtures

Language: Python - Size: 1.2 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

bueler/p4pdes

C and Python examples from my book on using PETSc and Firedrake to solve PDEs

Language: C - Size: 4.5 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 178 - Forks: 66

glotzerlab/freud

Powerful, efficient particle trajectory analysis in scientific Python.

Language: C++ - Size: 80.5 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 258 - Forks: 47

inducer/numpde-notes

Slides/notes and Jupyter notebook demos for an introductory course of numerical methods for PDEs

Language: Jupyter Notebook - Size: 19.7 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 18 - Forks: 8

yt-project/yt_astro_analysis

yt astrophysical analysis modules

Language: Python - Size: 8.48 MB - Last synced: 14 days ago - Pushed: about 1 month ago - Stars: 20 - Forks: 21

ViniPetra/Computational-Science

Estudos de computação científica com Python

Language: Python - Size: 30.1 MB - Last synced: 15 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

scottshambaugh/monaco

Quantify uncertainty and sensitivities in your computer models with an industry-grade Monte Carlo library.

Language: Python - Size: 17.2 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 81 - Forks: 5

Einsums/Einsums

Provides compile-time contraction pattern analysis to determine optimal tensor operation to perform.

Language: C++ - Size: 24.8 MB - Last synced: 3 days ago - Pushed: 18 days ago - Stars: 33 - Forks: 7

tvanderbruggen/SciCpp

Language: C++ - Size: 1.36 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 5 - Forks: 0

leandrolcampos/specials

Special functions with hardware acceleration

Language: Mojo - Size: 327 KB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 23 - Forks: 0

Spinmob/spinmob

Rapid and flexible acquisition, analysis, fitting, and plotting in Python. Designed for scientific laboratories.

Language: Python - Size: 4.56 MB - Last synced: 15 days ago - Pushed: 4 months ago - Stars: 36 - Forks: 12

bioio-devs/bioio-base

Typing, base classes, and more for BioIO projects.

Language: Python - Size: 1.36 MB - Last synced: 8 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

bioio-devs/bioio-ome-zarr

A BioIO reader plugin for reading Zarr files in the OME format.

Language: Python - Size: 69.3 KB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 1

Mateus-RB/MoleKing

MoleKing is a python module for chemists aiming to add common principles to python. This module adds new types of python variables, MoleKing_Molecule; MoleKing_Atom; MoleKing_SupraMolecule, and MoleKing_Output, alongside many features considered common knowledge among chemists.

Language: C++ - Size: 2.45 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 1 - Forks: 0

GIS4WRF/gis4wrf

QGIS toolkit 🧰 for pre- and post-processing 🔨, visualizing 🔍, and running simulations 💻 in the Weather Research and Forecasting (WRF) model 🌀

Language: Python - Size: 443 KB - Last synced: about 11 hours ago - Pushed: over 1 year ago - Stars: 158 - Forks: 35

alandefreitas/matplotplusplus

Matplot++: A C++ Graphics Library for Data Visualization 📊🗾

Language: C++ - Size: 38.3 MB - Last synced: 15 days ago - Pushed: about 1 month ago - Stars: 3,937 - Forks: 300

kailaix/ADCME.jl

Automatic Differentiation Library for Computational and Mathematical Engineering

Language: Julia - Size: 144 MB - Last synced: 8 days ago - Pushed: 7 months ago - Stars: 284 - Forks: 57

bioio-devs/bioio

Image reading, metadata management, and image writing for Microscopy images in Python

Language: Python - Size: 5.26 MB - Last synced: 15 days ago - Pushed: 17 days ago - Stars: 16 - Forks: 1

auto-differentiation/xad

Comprehensive automatic differentiation in C++

Language: C++ - Size: 1.21 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 215 - Forks: 15

maroba/findiff

Python package for numerical derivatives and partial differential equations in any number of dimensions.

Language: Python - Size: 2.35 MB - Last synced: 8 days ago - Pushed: 5 months ago - Stars: 397 - Forks: 58

jasmcaus/hazel

A Tensor Library written in C++.

Language: C++ - Size: 28.3 KB - Last synced: 16 days ago - Pushed: over 2 years ago - Stars: 3 - Forks: 25

storopoli/Julia_Scripts

Handy Julia Scripts

Language: Julia - Size: 1.79 MB - Last synced: 16 days ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

sourceduty/Experiments

📋 Experimental ideas, concepts and simulations.

Size: 28.3 KB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0

pabloinsente/sf_for_beh_ss

Introducing software development practices and tools for research in the behavioral and social sciences

Language: Jupyter Notebook - Size: 37.5 MB - Last synced: 16 days ago - Pushed: over 1 year ago - Stars: 9 - Forks: 1

wtanaka/ansible-role-scipy

Ansible role to install scipy -- scientific tools for Python

Size: 9.77 KB - Last synced: 16 days ago - Pushed: about 5 years ago - Stars: 2 - Forks: 0

wtanaka/ansible-role-numpy

Ansible role to install numpy for Python

Size: 10.7 KB - Last synced: 16 days ago - Pushed: about 5 years ago - Stars: 2 - Forks: 0

dpilger26/NumCpp

C++ implementation of the Python Numpy library

Language: C++ - Size: 114 MB - Last synced: 15 days ago - Pushed: 5 months ago - Stars: 3,384 - Forks: 542

Julia-Sydney/Julia-Sydney-Talks

A list of talks at the Julia Sydney Meetup

Language: Jupyter Notebook - Size: 3.74 MB - Last synced: 16 days ago - Pushed: about 5 years ago - Stars: 4 - Forks: 1

adtzlr/hyperelastic

Constitutive hyperelastic material formulations for FElupe.

Language: Python - Size: 566 KB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 5 - Forks: 0

LarsonLaugh/toyband

A Landau level simulator

Language: Python - Size: 9.81 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 0 - Forks: 0

peekxc/primate

Implicit matrix function and trace estimator

Language: Python - Size: 21.8 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 5 - Forks: 0

WebdeveloperIsaac/Arthmeticarrangerfcc

Free Code Camp Scientific Computing With Python Projects and Problem Solutions

Language: Python - Size: 49.8 KB - Last synced: 16 days ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0

egemenimre/satmad

Satellite Mission Analysis and Design

Language: Python - Size: 1.58 MB - Last synced: 7 days ago - Pushed: about 1 year ago - Stars: 36 - Forks: 5

wigging/computing-julia

Examples of the Julia programming language

Language: Julia - Size: 147 KB - Last synced: 16 days ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

Roger-luo/tutorial-julialang

A Tutorial to Julia Language

Language: Julia - Size: 6.84 KB - Last synced: 16 days ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

glentner/dataphile

Data analytics library for Python and suite of open source, command line based data ops tools.

Language: Python - Size: 351 KB - Last synced: 16 days ago - Pushed: over 1 year ago - Stars: 12 - Forks: 3

inducer/numerics-notes

Slides/notes and Jupyter notebook demos for an introductory course of numerical analysis/scientific computing

Language: Jupyter Notebook - Size: 7.27 MB - Last synced: 4 days ago - Pushed: 5 months ago - Stars: 43 - Forks: 11

caseresearch/code-review

⛔️ [DEPRECATED] A repo for code review sessions at CAS. ⛔️ [DEPRECATED] See

Language: HTML - Size: 7.96 MB - Last synced: 16 days ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 41

InPhyT/inphyt.github.io

Special repository hosting the InPhyT website.

Language: HTML - Size: 185 MB - Last synced: 17 days ago - Pushed: 5 months ago - Stars: 2 - Forks: 1

stdlib-js/google-summer-of-code

Google Summer of Code resources.

Size: 251 KB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 24 - Forks: 5

junyuan-chen/NonlinearSystems.jl

Solve nonlinear systems of equations and nonlinear least squares in Julia

Language: Julia - Size: 158 KB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 4 - Forks: 1

wmayner/pyemd

Fast EMD for Python: a wrapper for Pele and Werman's C++ implementation of the Earth Mover's Distance metric

Language: C++ - Size: 422 KB - Last synced: about 23 hours ago - Pushed: about 1 year ago - Stars: 473 - Forks: 64

ubermag/ubermag

Meta package for the Ubermag project.

Language: Python - Size: 1.42 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 36 - Forks: 11

Related Keywords
scientific-computing 1,398 python 437 machine-learning 108 science 92 numerical-methods 81 data-science 80 python3 76 physics 72 mathematics 66 numpy 62 hpc 62 cpp 57 julia 55 linear-algebra 53 simulation 53 matlab 53 numerical-analysis 45 data-analysis 43 deep-learning 43 freecodecamp 40 high-performance-computing 38 statistics 37 parallel-computing 37 optimization 37 scientific-visualization 36 visualization 35 rust 35 scipy 33 fortran 31 gpu 31 math 29 differential-equations 29 cuda 29 c 28 scientific 26 jupyter-notebook 26 c-plus-plus 24 data-visualization 24 computational-science 24 partial-differential-equations 24 matrix 23 astronomy 23 jupyter 22 tensor 21 xarray 21 linux 20 pytorch 20 mpi 20 javascript 20 algorithms 20 opencl 20 image-processing 19 science-research 19 numerical-computation 19 finite-element-methods 19 hacktoberfest 19 dask 18 astrophysics 18 java 17 scientific-workflows 17 bioinformatics 17 r 17 computational-physics 17 docker 16 microscopy 16 chemistry 16 freecodecamp-project 16 open-source 16 tutorial 16 gpu-computing 16 python-3 16 finite-elements 15 cloud-computing 15 automatic-differentiation 15 materials-science 15 go 15 matplotlib 15 monte-carlo-simulation 15 image-metadata 15 analysis 15 openmp 15 scientific-formats 15 julia-language 15 windows 15 macos 15 php 15 programming 15 numerical-calculations 14 micromagnetics 14 golang 14 scientific-machine-learning 13 distributed-computing 13 ode-solver 13 pde-solver 13 scientific-research 13 latex 13 binder 13 pde 13 molecular-dynamics 13 bioio 13