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Dilan Pathirana introduces PEtab Select pypi.org/project/petab-…. Get in touch if you wish to try it out or contribute to the development.

From Paul Stapor L Simon Merkt 👨‍🔬👨‍💻👨‍🏫 Dilan Pathirana Daniel Weindl Jan Hasenauer CanPathPro Using mini-batch optimisation to train ODE models on large-scale datasets go.nature.com/32oikNE

Interested in projects in mathematical #modelling, #bioinformatics, or #deeplearning with applications in #immunology, #epidemiology and #metaflammation? Check out our open #PhDposition and #postdocjobs at the Rheinische Friedrich-Wilhelms-Universität Bonn. …ematics-and-life-sciences.uni-bonn.de/en/jobs

📜 Excited to share our new preprint on accounting for informativeness in heterogeneous data via inverse #ML models in likelihood-free #ABC parameter inference! ⬇️🧵 1/n biorxiv.org/content/10.110… Jan Hasenauer Computational Health Center LIMES Institute Bonn FitMultiCell

🎒Summer school: 𝐈𝐧𝐯𝐞𝐫𝐬𝐞 𝐩𝐫𝐨𝐛𝐥𝐞𝐦𝐬 𝐟𝐨𝐫 𝐦𝐮𝐥𝐭𝐢-𝐬𝐜𝐚𝐥𝐞 𝐦𝐨𝐝𝐞𝐥𝐬 💬With: Linda Petzold, Christiane Fuchs, Dennis Prangle , Stefan Engblom, Andreas Hellander ⏰August 22-26 📌@HCM_Bonn ✏️Details+register: hcm.uni-bonn.de/events/eventpa…

Interested in #InverseProblems, #ParameterEstimation, #StochasticModelling, or #MultiScale #Models? Then check out our workshop: hcm.uni-bonn.de/events/eventpa… Travel funding is available for selected participants. Application deadline: July 10

Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks biorxiv.org/cgi/content/sh… #biorxiv_sysbio

Accessibility of covariance information creates vulnerability in Federated Learning frameworks biorxiv.org/cgi/content/sh… #bioRxiv

Parametric uncertainty causes uncertain model predictions. But how to estimate prediction uncertainties? Elba Raimúndez, Jan Hasenauer, jrbanga & I have spent a few years comparing the best methods-and here are the results: ieeexplore.ieee.org/document/99173…

Dynamical information enables inference of gene regulation at single-cell scale New preprint with Michael P.H. Stumpf! biorxiv.org/content/10.110… tl;dr: estimates of cell dynamics (e.g. RNA velocity, optimal transport) can infer local, cell-specific GRNs (1/4)

We are organising an AMICI workshop as satellite event to the Bonn Conference on Mathematical Life Sciences. This workshop will provide an in-depth overview of the toolbox and its various functions and features. We look forward to seeing you there! docs.google.com/document/d/1OG…

BondGraphs.jl: Composable energy-based modelling in systems biology biorxiv.org/content/10.110…

👩‍💻We are happy to release #pyPESTO 0.3! 🥳 Parameter Estimation Toolbox for Systems Biology github.com/ICB-DCM/pyPESTO With quite a few new features: 🧵

📜Happy to present our preprint on #pyPESTO - our parameter estimation toolbox for systems biology and beyond! 🌿🥳 ➡️arxiv.org/abs/2305.01821 ⬇️🧵

AMICI 0.17.0 is out with SBML plugin and AlgebraicRule support and lots of other goodies: github.com/AMICI-dev/AMIC…. Thanks to Daniel Weindl, @fabfrohlich, Dilan Pathirana, polina.lakrisenko and Henrik Podéus for contributions!

Please RT: Two (3+y) postdoctoral research fellowships. If you want to work in a multidisciplinary team to study how cells make decisions please get in touch. Ideally you have a background in physics, maths, comp bio, but discipline hoppers also welcome. jobs.unimelb.edu.au/en/job/912480/…

New preprint “The timing of cellular events: a stochastic vs deterministic perspective” shows how first passage times of transcrIptional dynamic determine timing of cellular events. biorxiv.org/content/10.110… (with Lucy Han, Megan Coomer, Kaan Öcal, Ramon Grima)

Please RT: new MACSYS-CoE & Theory of Living Systems Webinar webinar by Prof. Bas Teusink theoryoflivingsystems.org/event-details/… on Wednesday 22nd of November at 3:30pm AEDT (GMT+11 - Syd/Mel/Can). Very much looking forward to our first whole cell modelling seminar.

Very excited (& nervous) to share what we've been working on the past many years. Only took 3 first authors (Schreuder the experimentalist, Dr Dawn Lin the analyst, and @syzmath the modeller) & co-senior Weber (computational, modeller, SynBio extraordinaire) biorxiv.org/content/10.110…