Upcoming workshops

    • 17 Jun 2024
    • 21 Jun 2024
    • University of Glasgow

    BIOREME have teamed up with Innovate UK Business Connect and SofTMech to host a study group in mathematical modelling for respiratory medicine.
    We are delighted to invite participants to register for our upcoming mathematical study group with confirmed challenges from industry and clinicians more details here -> https://www.bioreme.net/events-all/studygroup-2024

    When: 17th - 21st June 2024
    Where: University of Glasgow

    Cost: There is no cost to participate. Lunch and refreshments are provided throughout the event. Accommodation in University of Glasgow Student Accommodation can be provided at no cost. Please indicate this on your registration form.

    Deadline: 17th May 2024 (unless capacity is reached before this date).

    Who is this for? We encourage researchers with a range of expertise to register for this event, including applied mathematics, computational modelling, statistics, data science, physics and engineering. We welcome researchers at all career stages from PhD students through to academic staff. This hands-on workshop offers a great opportunity to apply your skills to a new area, get some experience working with an industrial or clinical partner on a real-world problem, and potentially discover exciting new research collaborations

    Challenge 1: Can audio recordings be used to detect leaks in mechanical insufflation exsufflation (MIE) treatments
    Presented by Dr Toby Stokes and Dr Michelle Chatwin, BREAS Medical

    Challenge 2: Using data collected from Structured Light Plethysmography to
    differentiate Breathing Pattern Disorder from normal breathing
    Presented by Dr Emily Fraser and Mathew Bulpett, Oxford University Hospital

    Challenge 3: Searching for exhaled breath volatile biomarkers: How can we correct for environmental contamination?
    Presented by Dr Ran Wang and Prof Stephen Fowler

    To find out more, please get in touch at contact@bioreme.net

    • 9 Jul 2024
    • 12 Jul 2024
    • Leeds, UK
    The L24EEDs workshop "Mathematical modelling of microbial communities: cooperation, dynamics, and resistance" will be held in Leeds, UK from 9th-12th July 2024.

    This international workshop will bring together members of different communities (maths, biology, ecology, physics, and computing) who use different tools to address questions ranging from fundamental issues on the role of fluctuations in evolutionary processes to the modelling of antibiotic resistance, and the evolution of cooperative behaviour. The event is sponsored by the UK Engineering and Physical Sciences Research Council and the Leeds School of Mathematics

    There is no registration fee, but registration is mandatory (deadline: 31/05/24), and the number of places is limited. There is limited funding to contribute to the travel expenses of PhD students and early career researchers.

    Further details of the workshop, including confirmed keynote speakers, programme, registration, and how to submit contributed talks (deadline: 12/04/24) can be found on the L24EEDs website.

    Thank you and best wishes,
    Mauro Mobilia, Lluís Hernández-Navarro & Matthew Asker
    (Organisers of the L24EEDs workshop)

    • 28 Jul 2024
    • 11 Aug 2024
    • Virtual

    Announcing the 19th Annual Multicell Virtual-Tissue Modeling Online Summer School and Hackathon -- Indiana University, Bloomington. July 28th – August 4th, 2024 (Workshop) and August 9th – August 11th, 2024 (Hackathon).

    Please forward this announcement to anyone that you think might be interested.
    We are pleased to announce the 19th Annual Multicell Virtual-Tissue Modeling Online Summer School and Hackathon -- 2024, which will take place between Sunday, July 28th and Sunday August 4th, 2024. We would very much appreciate your help in letting your colleagues and students know about this opportunity.

    This year’s workshop will take place over one seven-day week. The workshop will focus on the basics of building virtual tissue models modeling using CompuCell3D, as well as exploration of more advanced modeling topics using the many features and capabilities of the CompuCell3D software. A two-day model-building Hackathon in which attendees work in teams to build a functioning model of their problem of interest will be hosted on the weekend following the workshop (August 9–11). For first-time participants, attendance in the workshop is required for participation in the Hackathon. Previous workshop attendees or returning hackathon participants may contact us directly for admission into only the hackathon.

    Summer school attendance guarantees admission to the Model-Building Hackathon. The Hackathon will group attendees by topic of interest. Experienced modelers will be embedded within each group. Workshop instructors will be available to assist Hackathon participants throughout the two-day session. Everyone will leave with a functioning core model that they can further customize, or even potentially develop into a publication!

    For more information, please see our announcements at https://compucell3d.org/Workshop24

    To register, please visit: https://tinyurl.com/CC3D2024

    More information on CompuCell3D is available at https://compucell3d.org/.

    Try out some example models online at NanoHub: https://compucell3d.org/Models-nanoHub.

    AUDIENCE: Mathematical Biologists, Computational Biologists, Experimental Biologists, Medical Scientists, Bioengineers, and Biophysicists, ranging from undergraduates to senior faculty, with a current or potential interest in mechanistic modeling of biological systems. The course covers multicellular modeling, which applies to developmental and tissue biology, tissue engineering, developmental diseases like cancer, in-host modeling of infection and immune response, and tissue-level toxicology. No specific programming or mathematical experience is required.

    An Introductory Python and Principles of Modeling Tutorial will take place on July 28th, 2024. If you already know Python or have modeling experience, you may skip this tutorial (or take it as a review).

    Multicell Virtual-Tissue Modeling Summer School: Basic Course (July 29th – August 4th, 2024)
    Mechanistic agent-based modeling is an integral part of contemporary bioscience, used for hypothesis generation and testing, experiment design and interpretation, and the design of therapeutic interventions. The CompuCell3D modeling environment allows researchers to rapidly build and execute complex Virtual Tissue simulations with minimal programming experience. CompuCell3D enables biological simulations from subcellular to tissue scales, supporting explicit cell shapes, cell migration, contact-mediated cell interactions, soluble signals, and complex cell state dynamics (gene regulatory, signaling, and metabolic networks). By the end of the course, participants will have had practice in using all the standard features of CompuCell3D needed to run a variety of multicellular simulations. Post-course support and collaboration will be available to continue simulation development of your biological problem(s) of interest.

    Multicell Model-Building Hackathon (August 9th - August 11th, 2024):
    By the end of the workshop, participants will have implemented a variety of simulations using many advanced features of CompuCell3D, including biochemical network modeling with CC3D, cell compartments and links, tissue folding, collective migration, and cell shape manipulation. Participants in the Hackathon will spend two days implementing a simulation of their biological problem of interest with support from the instructional team. Post-course support and collaboration will be available to continue simulation development.

    Principles of modeling biological and biomedical problems
    Python and Antimony scripting
    Multicellular Virtual-Tissue simulations with CompuCell3D
    Combining network models with virtual-tissue models in multiscale models

    Prof. James A. Glazier (Indiana University), Prof. T.J. Sego (University of Florida, CompuCell3D lead developer), Dr. James Sluka (Indiana University), Prof. Julio Belmonte (North Carolina State University), Prof. Gilberto Thomas (Federal University of Rio Grande do Sul, Brazil), Pedro Cenci Dal Castel (Federal University of Rio Grande do Sul, Brazil), Dr. Priyom Adhyapok (Duke), Dr. Maciek Swat (CompuCell3D lead developer), Dr. Lorenzo Veschini (King’s College London).

    Because the number of attendees is limited, admission is by application only. To apply for admission, please visit the school website at https://compucell3d.org/Workshop24
    and to register, please visit: http://www.tinyurl.com/CC3D2024.

    June 1st, 2023. Applications will be processed as received.
    The workshop is partially supported by grants from the US National Institutes of Health. and the National Science Foundation: NIH U24 EB028887, NSF 2120200, NSF 2000281, NSF 1720625

    Enrollment is free.

    We look forward to welcoming you online this August!
    James A. Glazier
    Department of Intelligent Systems Engineering
    Indiana University, Bloomington

    • 14 Oct 2024
    • 18 Oct 2024
    • Udine, Italy

    I wanted to draw your attention to the workshop that Tamas Insperger and I organized for Udine, Italy for Oct 14-18, 2024. 

    It will have distinctly DDE and modeling perspective and likely will be near the last times that many of the speakers will give live teaching-style lectures (e.g.me, Stepan and Morasso). I suspect it may be expensive to travel to the meeting; however, it is possible to attend online. I think that the lectures given by Insperger and Stepan plus others would be of interest to mathematical biology students working on DDEs as well as those interested in falls in the elderly, etc.

    • 21 Oct 2024
    • 23 Oct 2024
    • Amsterdam

    We are pleased to announce the workshop "The Numerical Brain: forward and inverse problems in neuroscience applications", which will be held on the 21st-23rd of October 2024, organised within the Amsterdam Centre for Dynamics and Computation, at VU Amsterdam.

    The workshop is at the intersection between numerical analysis, computational and experimental neuroscience. It aims to form a community working on numerical methods for simulating brain processes and inferring parameters or states. The workshop will bring together scientists who specialize in data assimilation and uncertainty quantification methods, both within and outside the field of neuroscience.

    A list of participants can be found on our website

    The event is supported by funding from our Centre, NWO, the NDNS+ and STAR clusters. Registration will be open in due course: we anticipate attendance will be free, with an optional fee for a social dinner.

    We would be grateful if you helped us spreading the word, and we look forward to hosting you in Amsterdam in October.
    The organisers
    Daniele Avitabile and Svetlana Dubinkina

Past workshops

12 Jun 2024 3nd Perturbations in Epilepsy Workshop
9 Jun 2024 Workshop on Chemical Reaction Networks
22 May 2024 Mathematics in Life Sciences workshop
13 May 2024 3-Day International Workshop on Mathematical Models and Methods in Life Sciences (M³LS 2024)
15 Apr 2024 Workshop on Models and Inference in Population Genetics: Fragmentation-coalescence and related models
25 Mar 2024 Grant development sandpit in environmental determinants of lung health
23 Nov 2023 2023 AUA Academic Workshop on Delay Differential Equations: Applications to Immunology and Infectious Diseases
20 Nov 2023 Workshop Modeling of Tumor Invasion
31 Oct 2023 Workshop Data-driven mechanistic models of complex biomedical systems, 11-12th December
11 Oct 2023 MC2D: Mathematical Challenges in Modelling Cancer Dynamics
2 Oct 2023 Workshop on Quantitative Principles in Microbial Physiology
21 Sep 2023 A Challenge led sandpit on structure and function in airways disease - hosted by the BIOREME network
11 Sep 2023 Workshop on Mathematical Perspectives on Immunobiology
11 Sep 2023 MoDiS 2023: Modelling Diffusive Systems
31 Jul 2023 2023 Virtual Summer Workshop and Hackathon on Multi-Cell Modeling with CompuCell3D (July 31-August 13)
3 Jul 2023 Topics on Neuroscience, Collective Migration and Parameter Estimation
26 Jun 2023 Workshop on ‘Perturbations in Epilepsy - Quantifying the impact of seizure triggers'
19 Jun 2023 Workshop on Epidemic Modelling: Current challenges
22 May 2023 Lorentz Workshop on wound care technology
24 Mar 2023 A Study Group in Mathematical Modelling: Developing the next generation of lung function measurement
12 Jan 2023 3rd International Workshop on Stochastic Processes and Their Applications (IWSPA 2023)
31 Dec 2022 ‘Model of the year’ 2023 competition
27 Nov 2022 BIRS Workshop "Topics in Multiple Time Scale Dynamics"
14 Nov 2022 Mathematical Methods for the Study of Self-Organisation in the Biological Sciences
12 Aug 2022 Midwest workshop of women in experimental biology: towards an integration of modern machine learning methods to the biological sciences
6 Jul 2022 Workshop on Chemical Reaction Networks
13 Jun 2022 Models in Population Dynamics, Ecology and Evolution – MPDEE-22 (2nd announcement)
9 Jun 2022 Workshop in Mathematical and Computational Biology (WMCB 2022)
2 May 2022 Junior Trimester Program "Stochastic modelling in the life science: From evolution to medicine“
20 Dec 2021 Mini-symposium on emerging frontiers in application to understand complex phenomena in biology and ecology. SciCADE 2022
23 Nov 2021 2nd International Workshop on Stochastic Processes and their Applications, IWSPA 2021
1 Oct 2021 Workshop "Waiting for the BioToMath Conference - Mathematics Challenges in Biology and Medicine"
28 Sep 2021 Mathematical modelling and control for Healthcare and Biomedical Systems (MCHBS 2021)
26 Sep 2021 Modeling and Computational Approaches to Individual and Collective Cell Movement in Complex Environments
6 Sep 2021 ICMS Workshop on “Modelling Diffusive Systems: Theory & Biological Applications”
10 Jun 2021 Workshop in Mathematical and Computational Biology (WMCB2021)
24 Nov 2020 International Workshop on Stochastic Processes and their Applications, IWSPA 2020
21 Sep 2020 Stochastic Models and Experiments in Ecology and Biology. European Center of Living Technology. Venice.
20 Apr 2020 Mathematical Models in Biology: PDE & Stochastic Approaches
2 Mar 2020 ICTP-SAIFR Workshop on Modelling of Infectious Diseases Dynamics
10 Oct 2019 The very first Day of Mathematical Biology 1010 at the Royal Swedish Academy of Sciences
29 May 2019 Transients in Biological Systems
1 May 2019 Mathematics of Gun Violence
23 Apr 2019 Social Norms: Emergence, Persistence, and Effects
11 Feb 2019 Stochastic Models in Systems and Synthetic Biology
6 Dec 2018 Viral Infections from an Evolutionary Perspective
5 Dec 2018 Extending the Theory of Sustainability
8 Oct 2018 Multidisciplinary workshop on Mathematics for BioMedicine
5 Sep 2018 Evolutionary Models of Structured Populations: Integrating Methods
3 Sep 2018 Mittag-Leffler semester in Mathematical Biology
5 Aug 2018 13th Annual CompuCell3D Training Workshop

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