xlink-kme-sbml
Kinetic crosslink simulations using SBML and Tellurium
Science Score: 44.0%
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Low similarity (9.8%) to scientific vocabulary
Repository
Kinetic crosslink simulations using SBML and Tellurium
Basic Info
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Metadata Files
README.MD
Kinetic Simulation Framework for Crosslinks
Build & run kinetic crosslink simulations
2023-09 Kai-Michael Kammer
Kinetic simulation of the crosslink formation. Using SBML (https://sbml.org) to build the model and Tellurium for running the simulation (https://tellurium.readthedocs.io/en/latest/).
This package is meant to build kinetic models. For simulating & analyzing kinetic models see https://github.com/stengel-laboratory/xlink-kme-sbml-analysis
Installation
This package requires Tellurium and simplesbml installed. Also required is the prottools package from https://github.com/stengel-laboratory/prot-tools
The easiest way to install is to first follow the instructions for the prottools package.
Having done so, the missing packages can be installed in the exisiting conda environment with
conda activate prot_tools
conda install scipy matplotlib python-libsbml jinja2 plotly
pip install tellurium simplesbml
Note that at least on Fedora 35 Tellurium needs ncurses-libs and ncurses-compat-libs installed:
sudo dnf install ncurses-libs ncurses-compat-libs
This package is missing on Fedora >= 37, so you'll have to symlink the following files
sudo ln -s /usr/lib/libtinfo.so.6 /usr/lib/libtinfo.so.5
sudo ln -s /usr/lib/libform.so.6 /usr/lib/libform.so.5
sudo ln -s /usr/lib/libncurses.so.6 l/usr/lib/ibncurses.so.5
sudo ln -s /usr/lib64/libtinfo.so.6 /usr/lib64/libtinfo.so.5
sudo ln -s /usr/lib64/libform.so.6 /usr/lib64/libform.so.5
sudo ln -s /usr/lib64/libncurses.so.6 l/usr64/lib/ibncurses.so.5
Usage
The
sbml_prot_template.py
file provides an example on how to use this package. It will accept a pdb file and further parameter files prepared by the prot_tools package. The output will be a kinetic model in the SBML format to use in simulations.
Owner
- Name: stengel-laboratory
- Login: stengel-laboratory
- Kind: organization
- Repositories: 1
- Profile: https://github.com/stengel-laboratory
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: Kinetic Simulation Framework for Crosslinks
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Kai-Michael
family-names: Kammer
email: kai-michael.kammer@uni-konstanz.de
affiliation: Universität Konstanz
orcid: 'https://orcid.org/0009-0006-9122-0480'
repository-code: 'https://github.com/stengel-laboratory/xlink-kme-sbml'
abstract: Kinetic crosslink simulations using SBML and Tellurium
keywords:
- cross-linking
- chemical kinetics
- mass spectrometry
license: GPL-3.0
commit: 4c8a9a60c80b020468566fe2cbf770b686917b9a
date-released: '2024-07-12'
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Dependencies
- numpy *
- pandas *
- tellurium *