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)
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."
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 π
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
BioModels Database has launched a new competition for early career researchers β https://www.ebi.ac.uk/biomodels/competition/model-of-the-year-2024
Deadline is Feb. 29, 2024.
My colleagues at the EBI have published a paper about the 2023 BioModels Model of the Year competition:
https://www.frontiersin.org/articles/10.3389/fsysb.2024.1363884/abstract
Mathematical modelling is a pivotal tool in deciphering the complexities of biological systems and their control mechanisms, providing substantial benefits for industrial applications, and answering relevant biological questions. The BioModels' Model of the Year 2023 competition was established to recognize and highlight exciting modelling-based research in life science, particularly by nonindependent early career researchers. It further aims to endorse reproducibility and FAIR principles of model sharing among these researchers. This article delineates the competition's criteria for participation and selection, introduces the award recipients, and provides an overview of their contribution. Their models provide crucial insights into cell division regulation, protein stability, and cell fate determination, illustrating the role of mathematical modelling in advancing biological research.
The next HARMONY (Hackathon on Resources for Modeling in Biology) will be held in in April in London. More information is available now about registration & scheduling.
https://co.mbine.org/events/
#SystemsBiology #ComputationalBiology #SBML
I spent a few months rebuilding a classic model from just its description in the original paper (von Dassow et al. 2000). Now Iβve 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
Kingsley Uyi Idehen
Egon Willighagen
BiGCaT Bioinformatics
Sebastian Muthwill
Darren Wilkinson
Ankur Sinha "FranciscoD"
Mike Hucka
Pedro Mendes