marcorusc
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agentic_system_for_modelling Public
This repo stores agents definition for the orchestration of modelling tools.
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mcp-biomodelling-servers Public
A repository that stores all the MCP servers for creating biological mechanistic models. It includes server for NeKo, MaBoSS, PhysiCell/PhysiBoSS.
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Neko Public
Forked from sysbio-curie/Neko -
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PhysiCell-Studio Public
Forked from PhysiCell-Tools/PhysiCell-StudioPhysiCell Studio is a graphical tool to allow easy editing of a (XML) model, create initial positions of cells, run a simulation, and visualize results. To contribute, fork and make PRs to the deve…
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Supp_mat_MCP_orchestrator Public
This folder host the supplementary materials generated by different LLMs to test the MCP server orchestration with different output but same prompt input.
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PhysiCelldFBA_EMEWS Public
Forked from thalioo/COVID19Parameters exploration workspace for PhysiCelldFBA
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Materials_for_Presentation Public
Materials to start using MaBoSS, PhysiCell and NeKo
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Hatchling Public
Forked from CrackingShells/HatchlingThe user interface optimized for the MCP servers on Hatch!
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python-sdk Public
Forked from modelcontextprotocol/python-sdkThe official Python SDK for Model Context Protocol servers and clients
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UQ_PhysiCell Public
Forked from heberlr/UQ_PhysiCellThe goal of this package is to perform uncertainty quantification across the entire input space of PhysiCell models (including parameters, initial conditions, and rules) using either a single deskt…
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pyMaBoSS Public
Forked from colomoto/pyMaBoSSpython interface for the MaBoSS software
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python-loader Public
Forked from PhysiCell-Tools/python-loaderPython data loader for PhysiCell digital snapshots
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pc4_degradation Public
This is a sample project built with PhysiCell to simulate different kind of degradation at short and long range.
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PhysiBoSS Public
Forked from PhysiBoSS/PhysiBoSSPhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
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BacArena Public
Forked from euba/BacArenaagent based modelling
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PhysiCOOL Public
Forked from IGGoncalves/PhysiCOOLA generalized, model-agnostic framework for model calibration in PhysiCell.
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cluster_analysis Public
First part of the code to run PhysiBoSS on cluster and automatically analize the output
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Pypath_pipeline Public
Automatic network construction using omnipath and pypath
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perlin_ecm Public
PhysiCell project when ECM is initialized by a python script into a matlab files and loaded in physicell
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biomass Public
Forked from okadalabipr/biomassA Python Framework for Modeling and Analysis of Signaling Systems
Python Apache License 2.0 UpdatedFeb 17, 2023 -
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project_repo_ecm_simul Public
Project repository for the creation of jupyter notebook for PhysiCell simulation with extra cellular matrtix
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MaBoSS_test Public
Forked from sysbio-curie/MaBoSS_testPython GNU General Public License v3.0 UpdatedApr 27, 2020