#sbml — Public Fediverse posts

een eerste update. De eerste donaties zijn binnen (dank!).

De planning gaat goed door. Er is een extra persoon aangesloten, de websites zijn wat bijgewerkt, er is een lijst gemaakt met pathways uit een standaardwerk die we kunnen toevoegen, en ik heb de data curatie pijplijn opgezet: https://www.wikipathways.org/sr24-curation/ (die ook de pathways in #SBML vertaalt)

#WikiPathways #SR24

new paper: "Making PBPK models more reproducible in practice" https://doi.org/10.1093/bib/bbae569

"We make a proposal aiming to harmonize abbreviations used in PBPK models.
To illustrate these recommendations, we present an original and reproducible PBPK model code in MATLAB, alongside an example of
MATLAB code converted to Systems Biology Markup Language format using MOCCASIN."

#SystemsBiology #bioinformatics #matlab #SBML #VHP4Safety

Dear #python community.

Is someone from #Madrid ( #spain ) here who is looking for a new #job opportunity in a global operating company (no agency or similar). I'm currently searching for a #python #fullstack developer who is familiar with #django. Ideally you should also have experience in development with chemistry software like #rdkit, #sbml (not a must). Job posting will be issued soon.
If you know someone please share

Ooh and you will have to work closely with me 😜

#jobs #FediHire

Version 1.2.0 of #pyNeuroML, the #Python package for working with #NeuroML models, has been released, brings more bugfixes and better support for #SBML

https://github.com/NeuroML/pyNeuroML/releases/tag/v1.2.0

#NeuroML #ComputationalNeuroscience #Neuroscience #Standardisation #FAIR

I spent a few months rebuilding a classic model from just its description in the original paper (von Dassow et al. 2000). Now I’ve added it to BioModels in standard formats so that everyone can use it https://www.ebi.ac.uk/biomodels/MODEL2304060001

I also wrote a manuscript about the experience and reproducibility. Soon to post as preprint.
#openscience #SBML #systemsbiology #COPASI @copasi

New preprint from Matthias König lab with a physiologically based pharmacokinetics model of Simvastatin therapy. https://doi.org/10.1101/2023.02.01.23285358

Great use of standard formats and repositories for #OpenScience and #reproducibility (#SBML etc).
I was able to load the flattened model into @copasi and run simulations , despite the paper using different software

New version of COPASI released (4.38 build 268).

Major bug fixes for OS X, improved handling of OMEX files, improved handling of units from #SBML files, and other bug fixes.

Get it now from http://copasi.org/Download/

#OpenSource #SystemsBiology #Chemistry #Modeling #Simulation