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• 19th Annual Multicell Virtual-Tissue Modeling Online Summer School and Hackathon

  • Start
    28 Jul 2024
  • End
    11 Aug 2024
  • Location
    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.
  
  AIM AND FOCUS:
  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.

  CORE TOPICS:
  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

  INSTRUCTORS:
  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).

  PARTICIPATION:
  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.

  DEADLINE for APPLICATIONS:
  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
  jaglazier@gmail.com

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• Dynamics of Human Balancing

  • Start
    14 Oct 2024
  • End
    18 Oct 2024
  • Location
    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.

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• Workshop on forward and inverse problems in neuroscience applications

  • Start
    21 Oct 2024
  • End
    23 Oct 2024
  • Location
    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
  amsterdam-dynamics.nl/the-numerical-brain

  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

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