Center for Reproducible Biomedical Modeling
Center for Reproducible Biomedical Modeling
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Inference of Large-Scale Boolean Models from Human-Curated Fully Annotated Process Description Diag.
Inference of Large-Scale Boolean Models from Human-Curated, Fully Annotated Process Description Diagrams: Focus on Rheumatoid Arthritis
Dr. Anna Niarakis, Professor of Computational Systems Biology at the University of Toulouse III-Paul Sabatier, specializes in complex human diseases, with a focus on autoimmune disorders. Her talk, "Inference of Large-Scale Boolean Models from Human-Curated, Fully Annotated Process Description Diagrams. Focus on Rheumatoid Arthritis," will introduce CaSQ, a tool developed to transform static molecular interaction maps (MIMs) into dynamic Boolean models. By converting detailed, annotated maps into standardized, interoperable models, Dr. Niarakis’s work aims to enhance understanding and reproducibility in disease modeling, with applications demonstrated in Rheumatoid Arthritis research.
#autoimmunediseases #booleanmodels #casq #computationalbiology #diseasemodeling #humaninteractionmaps #rheumatoidarthritis #systemsbiology #sciencelecture #scientificresearch
Переглядів: 63

Відео

On Steroids! Modeling 11-Oxygenated Androgen Levels in Chronic Kidney Disease
Переглядів 1916 годин тому
The Center for Reproducible Biomedical Modeling presents the second of four seminars in our fall 2024 seminar series, Building Models and Publishing Models. Abstract: Mathematical models are important tools for a quantitative understanding of biological systems. If they are based on biochemically realistic mechanisms they can make predictions on system dynamics in terms of the characteristics o...
Improving Reuse with Continuous Scientific Processes
Переглядів 70Місяць тому
The Center for Reproducible Biomedical Modeling presents the second of four seminars in our fall 2024 seminar series, Building Models and Publishing Models. This seminar features Dr. Rowan Cockett, CEO of Curvenote spoke on the future of science publishing. In this seminar, you will learn how his team enhances interactivity, computation, & reproducibility in scientific work, collaborating with ...
Using Bond Graphs to Ensure Thermodynamic Consistency in Biophysical Models
Переглядів 58Місяць тому
The Center for Reproducible Biomedical Modeling presents the first of four seminars in our fall 2024 seminar series, Building Models and Publishing Models. This seminar features Dr. Peter Hunter, FRS, FRSNZ, Director of the Auckland Bioengineering Institute. Dr. Hunter’s talk, "Using Bond Graphs to Ensure Thermodynamic Consistency in Biophysical Models," discusses how bond graphs provide a simp...
2024 Summer School - Day 5.1 Developing Multiscale Models of Microbes, Infection and Disease
Переглядів 485 місяців тому
2024 Summer School & Hackathon - Day 5.1 Elebeoba May, Associate Professor at the University of Wisconsin presents, "Developing Multiscale Models of Microbes, Infection and Disease" #multiscalemodels #multiscalemodeling #computationalbiology #bioinformatics #biology #biomodeling #biomodels #bistablemodeling #bistablemodels #reproducibility #reproducibilityresearch #science #systemsbiology
2024 Summer School - Day 5.2 - pyPESTO - A Modular and Scalable Tool for Parameter Estimation
Переглядів 485 місяців тому
2024 Summer School & Hackathon - Day 5.1 Paul Jost from the University of Bonn in Germany presents his talk on "pyPESTO - A Modular and Scalable Tool for Parameter Estimation". #pyPESTO, #parameterestimation #computationalbiology #bioinformatics #biology #biomodeling #biomodels #bistablemodeling #bistablemodels #reproducibility #reproducibilityresearch #science #systemsbiology
2024 Summer School - Day 5.3 - Towards Digital Twins of Acute Myeloid Leukemia Patients
Переглядів 565 місяців тому
2024 Summer School - Day 5.3 Boris Aguilar, Senior Researcher at the Institute for Systems Biology presents his talk, "Towards Digital Twins of Acute Myeloid Leukemia Patients". #myeloidleukemia #computationalbiology #bioinformatics #biology #biomodeling #biomodels #bistablemodeling #bistablemodels #reproducibility #reproducibilityresearch #science #systemsbiology
2024 Summer School - Day 5.5 - Coupling Chemical Network Models to Cell Tissue Models
Переглядів 725 місяців тому
2024 Summer School & Hackathon - Day 5.5 Indiana University professor James Glazier presents his talk, "Coupling Chemical Network Models to Cell Tissue Models: A short introduction to multicell agent-based modeling using CompuCell3D" #networkmodels #celltissuemodels #chemicalnetworkmodels #CompuCell3D #multicellmodeling #multicellmodels #computationalbiology #bioinformatics #biology #biomodelin...
2024 Summer School - Day 5.4 -
Переглядів 185 місяців тому
2024 Summer School & Hackathon - Day 5.4 Assistant Professor TJ Sego from the University of Florida presents his talk, "Reproducibility of Stochastic Simulation Results".
2024 Summer School & Hackathon - Day 4 - Model Credibility Hackathon
Переглядів 515 місяців тому
Dr. Joe Hellerstein and Lucian Smith lead a participatory hackathon where several models of COVID-19 are discussed, and their credibility is analyzed. Breakout Room #1 with Dr. Hellerstein: A group analysis of the credibility of two papers: “A data-driven model to describe and forecast", by Paiva et al. and “SEIR model for COVID-19 dynamics incorporating the environment and social distancing" b...
2024 Summer School & Hackathon - Day 3.1 - An Overview of Model Calibration and Parameter Estimation
Переглядів 1055 місяців тому
Dr. Joe Hellerstein discusses the 'landscape' of how parameters fit the data, and search strategies for finding the best fits. #computationalbiology #bioinformatics #biology #biomodeling #biomodels #bistablemodeling #bistablemodels #modelcalibration #parameterestimation #reproducibility #reproducibilityresearch #science #systemsbiology
2024 Summer School & Hackathon - Day 3.2 - Oscillators and Signaling Pathways
Переглядів 465 місяців тому
Dr. Sauro discusses modifying bistable models to become oscillators, analyzing oscillating models, and signal pathways. #oscillators #oscillatingmodels #signalpathways #computationalbiology #bioinformatics #biology #biomodeling #biomodels #bistablemodeling #bistablemodels #reproducibility #reproducibilityresearch #science #systemsbiology #tellurium
2024 Summer School & Hackathon - Day 3.3 - Model Annotation
Переглядів 415 місяців тому
Dr. John Gennari discusses the use and importance of model annotation, and using the Antimony Web Editor to view and modify model annotations. #antimony #antimonywebeditor #computationalbiology #bioinformatics #biology #biomodeling #biomodels #bistablemodeling #bistablemodels #modelannotations #reproducibility #reproducibilityresearch #science #systemsbiology
2024 Summer School & Hackathon - Day 2.4 - Studying Bistability
Переглядів 455 місяців тому
Creating and analyzing bistable models using Tellurium. computationalbiology #bioinformatics #biology #biomodeling #biomodels #bistablemodeling #bistablemodels #reproducibility #reproducibilityresearch #science #systemsbiology #tellurium
2024 Summer School & Hackathon - Day 2.3 Advanced Antimony
Переглядів 375 місяців тому
More complicated models using Antimony, including multicompartment models and fancy events. #antimony #computationalbiology #bioinformatics #biology #biomodeling #biomodels #chatgpt #reproducibility #reproducibilityresearch #science #systemsbiology
2024 Summer School & Hackathon - Day 2.2 - SBML and Biomodels
Переглядів 695 місяців тому
2024 Summer School & Hackathon - Day 2.2 - SBML and Biomodels
2024 Summer School & Hackathon - Day 2.1 - Introduction to Tellurium (Part 2)
Переглядів 545 місяців тому
2024 Summer School & Hackathon - Day 2.1 - Introduction to Tellurium (Part 2)
2024 Summer School & Hackathon - Day 1.4 Introduction to Tellurium
Переглядів 605 місяців тому
2024 Summer School & Hackathon - Day 1.4 Introduction to Tellurium
2024 Summer School & Hackathon - Day 1.2 Introduction to Modeling
Переглядів 815 місяців тому
2024 Summer School & Hackathon - Day 1.2 Introduction to Modeling
2024 Summer School & Hackathon - Day 1.3 Introduction to Antimony
Переглядів 685 місяців тому
2024 Summer School & Hackathon - Day 1.3 Introduction to Antimony
2024 Summer School & Hackathon - Day 1.1 Welcome and Introduction to Python
Переглядів 1915 місяців тому
2024 Summer School & Hackathon - Day 1.1 Welcome and Introduction to Python
pyPESTO: A Modular and Scalable Tool for Parameter Estimation for Dynamic Models - Paul Jost
Переглядів 1065 місяців тому
pyPESTO: A Modular and Scalable Tool for Parameter Estimation for Dynamic Models - Paul Jost
Reproducibility and FAIR Principles: The Case of a Segment Polarity Network Model - Pedro Mendes
Переглядів 675 місяців тому
Reproducibility and FAIR Principles: The Case of a Segment Polarity Network Model - Pedro Mendes
Multiscale Multicellular Modeling Challenges and Opportunities
Переглядів 289Рік тому
Multiscale Multicellular Modeling Challenges and Opportunities
2023 Kinetic Modeling Virtual Course - Part 5: Metabolic Control Analysis - Herbert Sauro
Переглядів 430Рік тому
2023 Kinetic Modeling Virtual Course - Part 5: Metabolic Control Analysis - Herbert Sauro
2023 Kinetic Modeling Virtual Course & Hackathon: Part 1 & 2 - Herbert Sauro & Michael Kochen
Переглядів 468Рік тому
2023 Kinetic Modeling Virtual Course & Hackathon: Part 1 & 2 - Herbert Sauro & Michael Kochen
2023 Kinetic Modeling Virtual Course & Hackathon - Part 3: Parameter Fittings - Joseph Hellerstein
Переглядів 157Рік тому
2023 Kinetic Modeling Virtual Course & Hackathon - Part 3: Parameter Fittings - Joseph Hellerstein
2023 Kinetic Modeling Virtual Course - Part 4: Intro to BioModels & Systems Biology Standards
Переглядів 117Рік тому
2023 Kinetic Modeling Virtual Course - Part 4: Intro to BioModels & Systems Biology Standards
Harmony 2023: FAIRSPACE - Part III
Переглядів 13Рік тому
Harmony 2023: FAIRSPACE - Part III
Harmony 2023: FAIRSPACE - Part II
Переглядів 9Рік тому
Harmony 2023: FAIRSPACE - Part II

КОМЕНТАРІ

  • @twt298
    @twt298 4 місяці тому

    incredible I just found this video and is amazing the way how the speaker explain everything

  • @claudioc.ramirez550
    @claudioc.ramirez550 Рік тому

    Wonderful class...very good !!..My mass got transformed. Thanks a lot !!

  • @luciansmith9315
    @luciansmith9315 Рік тому

    Slides Available at docs.google.com/presentation/d/1h8nx7dd-Ejb4Hsrks0CdF-l01z-lVQt4/edit

  • @DanKolis
    @DanKolis Рік тому

    Endless iteration of stuff like this is duplication, sure. But mostly one can 'eat' import' etc from other ones reasonably well. Its not such a serious issue when the whole thing is so incomplete anyway. When an IDE exists so non-programmers can see speculation work enough to generate some forward progress, even fairly wonky ones, what sorts of files should lurk describing nature is pretty unclear. So, its a big fat land of best guesses. That's the way it is. The big reckoning is contingent on trying hard to do the best thing, and not pay too much attention really to every single similar one 'out there'.

  • @almightyseahorse665
    @almightyseahorse665 4 роки тому

    This is really fascinating. Hope to see more from Mr Gerkin!

  • @jinwang3643
    @jinwang3643 5 років тому

    Amazing share! Thank both professors for inspirations. Really interesting research! Thank the host for organizing!

  • @chrismofer
    @chrismofer 5 років тому

    fascinating and useful stuff, thank you for posting!

  • @aditikonar2411
    @aditikonar2411 5 років тому

    What is it's significance?

  • @Mr_i_o
    @Mr_i_o 5 років тому

    If you want to see a presentation, we will have to correct that. The Demo Gods were merciful!?