Smoldyn is a particle-based biochemical simulator for modeling molecular diffusion, surface interactions, and chemical reactions
☆30May 23, 2026Updated last month
Alternatives and similar repositories for Smoldyn
Users that are interested in Smoldyn are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results☆43Updated this week
- Generates simulated confocal data from a ground truth signal☆11Aug 16, 2022Updated 3 years ago
- Benchmarking and metadata tracking. CLI and Python integration. Extensible, with distributed/cluster support.☆20Jun 18, 2026Updated 2 weeks ago
- Code for reproducing results from the paper "RNA velocity and protein acceleration from single-cell multiomics experiments."☆11Feb 1, 2020Updated 6 years ago
- Blastocyst-like structures generated from human pluripotent stem cells☆13Sep 25, 2022Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Registry of containerized biosimulation tools that support a standard command-line interface☆15May 28, 2026Updated last month
- Python interface for running COMETS simulations and analyzing the results☆16May 19, 2026Updated last month
- ☆17Apr 9, 2021Updated 5 years ago
- Integrated Genome Modeling (IGM): multi-modal data-driven simulator of genome structures☆12Jun 15, 2023Updated 3 years ago
- Spatial RNA velocity☆10Oct 3, 2024Updated last year
- Static analyzer for dynamics of Automata Networks☆12Feb 3, 2021Updated 5 years ago
- Data Mining project☆10Jan 10, 2024Updated 2 years ago
- C++ basecode and python scripting interface☆19Mar 20, 2025Updated last year
- ☆17Mar 2, 2024Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆19Oct 27, 2021Updated 4 years ago
- Relates to the article by Lioy, Cournac et al., Cell, 2018 (Functional partitioning of a bacterial chromosome through the interplay of nu…☆11Aug 19, 2020Updated 5 years ago
- Data analysis pipeline for scNT-seq (single-cell metabolically labeled new RNA tagging sequencing)☆16Jun 9, 2026Updated 3 weeks ago
- The PomBase community curation tool☆19Updated this week
- Collection of search spaces for hyperparameter optimization in the mlr3 ecosystem☆14Aug 16, 2025Updated 10 months ago
- R implementation of Robust Rank Aggregation algortihm☆12Jun 8, 2022Updated 4 years ago
- ☆10Dec 3, 2019Updated 6 years ago
- Materials used by previous Turing related workshop events☆19Dec 10, 2025Updated 6 months ago
- ☆13Dec 20, 2025Updated 6 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Scripts to perform active learning as described in the referenced article.☆13Sep 17, 2025Updated 9 months ago
- epigenome analysis to rank transcription factors☆15Dec 19, 2019Updated 6 years ago
- A tool for semantics-based annotation and composition of biosimulation models☆20Jun 24, 2026Updated last week
- Phylodynamic inference☆23May 15, 2020Updated 6 years ago
- ☆18Sep 6, 2022Updated 3 years ago
- Dose response curves and DIP rates for cell proliferation data in Python☆16Updated this week
- ExTrack MLE for diffusive noisy single-particle tracks☆16Jun 24, 2026Updated last week
- The Automatic Mycorrhiza Finder (AMFinder) allows for automatic computer vision-based identification and quantification of AM fungal colo…☆27Nov 3, 2023Updated 2 years ago
- Matrix digital rain in P5.JS & Canvas☆11Sep 22, 2019Updated 6 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- ☆24Oct 11, 2024Updated last year
- an R wrapper for the Gnu Scientific Library☆19Apr 11, 2026Updated 2 months ago
- This repository contains HCA Benchmarking codes☆26Nov 11, 2019Updated 6 years ago
- ☆23Mar 29, 2023Updated 3 years ago
- This repository aims to serve as an index of the work described at Salmen & De Jonghe et. al 2022☆25Feb 21, 2022Updated 4 years ago
- python simulation interface for molecular modeling. To cite this software publication: https://www.sciencedirect.com/science/article/pii/…☆13Aug 24, 2016Updated 9 years ago
- University of Groningen PhD thesis template☆17Apr 6, 2022Updated 4 years ago