Systems biologist using @JuliaLanguage to scale up #sysbio models.
Zurich
Joined September 2019
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Paul Lang retweeted
📢
We offer a #postdoc position on the topic "ENHANCING THE COMPUTATIONAL BIOLOGY OF MICROORGANISMS AND PLANTS WITH NEW METHODS OF ARTIFICIAL INTELLIGENCE AND SUPERCOMPUTING ”
Part of @Momentum_CSIC
⏳30/08/2024
More information at momentum.csic.es/
Join the next #JuliaLang #SysBio community call!
🗓️ April 23, 5pm UTC
🔗Link: forms.gle/XSWAV4VoBrnkz3K78
🎤 Speakers:
Aayush Sabharwal: SymbolicIndexingInterface.jl
Augustinas Sukys: Neural approximations of the chemical master eqn
Emily Nieves: Bayesian chemical reaction NNs
Paul Lang retweeted
🌟 Inviting early career researchers to showcase your mathematical model of a biological system at the BioModels' Model of the Year 2024 competition! Submit your exciting work, gain recognition, and win cash prize! Deadline: Feb 29, 2024. More info: ebi.ac.uk/biomodels/competit…
Paul Lang retweeted
Institutional Innovation and FROs in @Nature! Let's shake up incentive design in science, shall we?
nature.com/articles/d41586-0…
Co authored with @AdamMarblestone @MWCvitkovic @tkalil2050 @C9Martin @SGRodriques
featuring @SchmidtFutures @Convergent_FROs and @AsteraInstitute
"Reusable rule-based #CellCycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells" is out in @PLOSCompBiol !
📜Manuscript: journals.plos.org/ploscompbi…
⚙️#SBML: github.com/paulflang/cell_cy…
Thank you David Penas, @julio_r_banga, @dweindl and Bela Novak!
Join the Julia Systems Biology community calls!
🗓️ December 13, 6 pm UTC
🔗 Call link: forms.gle/oiec6FN2AwSBRXEY8
🎤 Speakers:
- Torkel Loman: Integration of Catalyst.jl with #JuliaLang #sysbio packages.
- @sPersson96 : Parameter estimation with PEtab.jl.
Paul Lang retweeted
We are having pizza and discuss Systems Biology in room 32-G451 from 6pm!! 🍕🧬💻 come join @PF_Lang , @ChrisRackauckas and me 👋 #juliacon #julialang @JuliaConOrg
I am very excited that our preprint "Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells" is now available on @biorxiv_sysbio . Many thanks to the co-authors David Penas, @julio_r_banga , @dweindl and Bela Novak.
Our model builds on existing #CellCycle and #sysbio research and aims at improving the following aspects:
- scope and detail of the modelled cell cycle reaction network
- information content of the validation data
- parameter estimation procedure
- model reusability
The work would not have been possible without @BioNetGen, immunofluorescence imaging data from @WStallaert and colleagues from the @purvislab, reCAT, #PEtab
and saCeSS. Big shout to the developers of these tools and @jonrkarr, @johnsekar86 and @FS_Heldt for the inspiration.
Paul Lang retweeted
#sysbio tool developers and users! "Systems biology: community needs, plans, and visions" @JuliaConOrg! Brainstorm future developments and collaborate with top players in the field. #SciML #JuliaLang
Apply now: forms.gle/icu9Fp1cNPPvCJsW7
More info: pretalx.com/juliacon2023/tal…
Paul Lang retweeted
Here we show how #julialang enables new biology
nature.com/articles/s41592-0…
Thanks to @Roesch_E @jgreener64 @adamlmaclean @nassarhuda @ChrisRackauckas Tim Holy, our eagle eyed reviewers & @rita_strack @naturemethods for superb support!
I love a good mountaineering analogy 😎
Paul Lang retweeted
#AlphaCode—a new #AI system for developing computer code developed by @DeepMind—can achieve average human-level performance in solving programming contests.
Learn more this week in Science: scim.ag/Nn
Paul Lang retweeted
#emed2022 @PF_Lang on building reusable mammalian cell cycle models using @bionetgen, #reCAT for reconstructing sim data, validation data from Stallaert et al biorxiv.org/content/10.1101/… and #PEtab @JanHasenauer
for parameter optimization. Nice piece of work github.com/paulflang/cell_cy…
Paul Lang retweeted
📢NEW COURSE Learn how to make COBRA methods scale to problem sizes that require the use of #hpc
Miroslav Kratochvil from @uni_lu will explain COBREXA.jl, a toolkit for working with complex metabolic models
REGISTER 👇
ow.ly/UzLx50L0E2s
@EBItraining
Paul Lang retweeted
Parametric uncertainty causes uncertain model predictions. But how to estimate prediction uncertainties? Elba Raimúndez, @JanHasenauer, @julio_r_banga & I have spent a few years comparing the best methods-and here are the results: ieeexplore.ieee.org/document…
Excited to present a rule-based #CellCycle model that explains location and dynamics of 16 observables at #ICSB2022 ! Check out the #SBML, @bionetgen and #PEtab model specifications on GitHub (bit.ly/3COdtEM). Feel free to improve/extend model or data with a PR.
#sysbio
For those interested in the experimental data, this is the publication. Big thank you to @WStallaert and colleagues from the @purvislab!👍
teapawt.net/WStallaert/status/1461…