A repository that stores all the MCP servers for creating biological mechanistic models. It includes server for NeKo, MaBoSS, PhysiCell/PhysiBoSS.
☆16Jul 2, 2026Updated 2 weeks ago
Alternatives and similar repositories for mcp-biomodelling-servers
Users that are interested in mcp-biomodelling-servers are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- This page hosts NeKo, a python package that allow the user to automatically build gene regulatory networks from any databases.☆21Updated this week
- PhysiCell Studio is a graphical tool to allow easy editing of a (XML) model, create initial positions of cells, run a simulation, and vis…☆40Jul 1, 2026Updated 2 weeks ago
- PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks☆35Updated this week
- Fast reconstruction of spatial networks from bioimages.☆26Mar 27, 2026Updated 3 months ago
- The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks☆27Jul 3, 2026Updated 2 weeks ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch.…☆208Updated this week
- Computational framework for dataset integration☆12Jul 21, 2023Updated 3 years ago
- ☆14Feb 24, 2020Updated 6 years ago
- FunctionaL Omics Processing platform☆13Jul 25, 2024Updated last year
- Python implementation of Underdamped Langevin Inference, a method to infer the dynamical equation of underdamped stochastic systems from …☆17Jun 20, 2025Updated last year
- Method for plotting histograms on a curve using a West Transform☆10Apr 26, 2022Updated 4 years ago
- Boolean Network Modeling☆41Jan 31, 2020Updated 6 years ago
- SignalingProfiler is a pipeline that builds signaling networks to cellular phenotypes from multiomics data.☆15Mar 26, 2026Updated 3 months ago
- Using Large Language Models to Simulate Multiple Humans and Replicate Human Subject Studies☆12Oct 6, 2023Updated 2 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- UniFORM: Towards Universal ImmunoFluorescence Normalization for Multiplex Tissue Imaging☆18Jul 30, 2025Updated 11 months ago
- Matilda is a multi-task framework for learning from single-cell multimodal omics data. Matilda leverages the information from the multi-m…☆22Jul 7, 2026Updated last week
- Python package for biodatafuse project.☆16Apr 22, 2026Updated 2 months ago
- TFregulomeR reveals transcription factors’ context-specific features and functions☆15Apr 18, 2022Updated 4 years ago
- A tool for creating Python implementations of SBML models.☆15Oct 5, 2022Updated 3 years ago
- A Python Framework for Modeling and Analysis of Signaling Systems☆30Jul 13, 2026Updated last week
- A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.☆18Mar 11, 2026Updated 4 months ago
- Landscape Single Cell Entropy☆23Aug 24, 2020Updated 5 years ago
- Transfer Learning-enabled context-aware microbial source tracking☆16Oct 4, 2022Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- ☆12Feb 16, 2024Updated 2 years ago
- Muon for Julia☆28Updated this week
- Analysis of RNAseq data from (host-associated) microbial mixtures☆12Nov 25, 2019Updated 6 years ago
- Assembly and intrahost / low-frequency variant calling for viral samples☆15Feb 12, 2020Updated 6 years ago
- Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.☆32Jun 10, 2025Updated last year
- R package for computing Association Plots☆17Nov 4, 2024Updated last year
- cz-benchmarks is a package for standardized evaluation and comparison of machine learning models for biological applications.☆56Dec 19, 2025Updated 7 months ago
- Quantum Gene Regulatory Networks with Application to Single-cell Data☆26Feb 28, 2025Updated last year
- Code for "Feature selection methods affect the performance of scRNA-seq data integration and querying"☆33Mar 15, 2025Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- ☆18Feb 19, 2021Updated 5 years ago
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆35Apr 9, 2026Updated 3 months ago
- mSWEEP High-resolution sweep metagenomics using fast probabilistic inference☆17Nov 19, 2025Updated 8 months ago
- Multiscale simulation of multi-cellular system☆30Jul 31, 2020Updated 5 years ago
- [Adv. Sci. 2025] PRO-LDM: A Conditional Latent Diffusion Model for Protein Sequence Design and Functional Optimization☆15Jul 11, 2025Updated last year
- A public MuSpAn page for community discussions and issue reporting.☆23Jun 17, 2026Updated last month
- A collection of 280+ Boolean networks from various sources useful for benchmarking or testing.☆24May 29, 2026Updated last month