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

A 18-months Postdoc position is available in the Laboratoire de Mathématiques de Besançon (LMB), at the University of Bourgogne Franche-Comté, France, to work on the project “Parameter estimation for nonlocal PDEs with applications in cell biology”.

We are looking for candidates with a strong research background in either one of the 2 research directions of this project: (a) parameter identification and uncertainty quantification for time-evolving PDEs, and/or (b) numerical analysis (a posteriori error estimates and adaptive mesh refinement) for time-evolving PDEs.

Applications will be accepted on a rolling basis, and their review will continue until the position is filled. The contract will start as soon as possible.

For more information, please contact Raluca Eftimie (raluca.eftimie@univ-fcomte.fr). Applicants are requested to send their expression of interest electronically in a single PDF file. Applications should include (1) a cover letter, (2) a CV, (3) contact details of up to three referees. 

I am looking for motivated master interns, PhD students, and postdocs in theoretical physics or applied mathematics to work on the interactions between mechanics, biochemistry, and genetics in stem cell aggregates.

The positions are fully funded by the ERC Synergy Grant project BREAKDANCE. Our theory work will be carried out in close collaboration with the experimental labs of Pierre-François Lenne (Marseille), Vikas Trivedi (Barcelona), and Verena Rupprecht (Barcelona).

For more details on the positions, please see https://www.merkellab.net/open-positions

A recent preprint from our consortium can be found here: https://www.biorxiv.org/content/10.1101/2023.09.22.559003

The start date is flexible.

Please do not hesitate to contact me for any informal inquiries: matthias.merkel@posteo.de

A call is open for an 18 month postdoc at Inria Saclay center, entitled "Post-doctoral position in mathematical and/or computational biology: Multiscale modeling of single cell-based dynamics of ovarian development" :
https://recrutement.inria.fr/public/classic/fr/offres/2024-07738

The postdoc position is open in the framework of the AI4scMED ("MultiScale AI for SingleCell-Based Precision Medicine") consortium (https://ai4scmed.github.io) of PEPR Santé Numérique (project no. 22-PESN-0002). The postdoc will be supervised by Frédérique Clément (Inria), Chloe Audebert (Sorbonne Université) and Fabien Crauste (CNRS & Université Paris Cité).

The contract is expected to start between October, 1st and December, 1st 2024.

For any additional information, you can contact Frédérique Clément (frederique.clement@inria.fr), Chloe Audebert (chloe.audebert@sorbonne-universite.fr) and Fabien Crauste (fabien.crauste@math.cnrs.fr).

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.

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

We are looking for a two years postdoctoral to investigate the genome annotations in non-model plants by means of machine learning approaches.

Genome annotations is one of the major bottlenecks to obtain high quality genomes, especially in non-model species. Efficient tools to evaluate the quality of a genome annotation are needed. The goal for this position is to develop a toolkit with several applications to evaluate genome annotations using K-mers and AI. This is a project developed in collaboration with Dr. Ian Morilla (UMA, Spain).

Qualifications
Applicants should have demonstrated experience in the field of bioinformatics and/or computational biology. They should be proficient in at least one programming language (preferably Python). The candidate should have proficiency on data science, with focus machine learning. Deep learning apsproaches will be a plus. Good English communication skills are essential. The applicants should have a PhD degree in the fields of Biology or Computational Science.

The applicant should meet the requirements needed to apply to CSIC work system (https://sede.csic.gob.es/servicios/formacion-y-empleo/bolsa-de-trabajo).

If you are interested in this position or have any questions, please contact Prof. Aureliano Bombarely or Prof. Ian Morilla
(abombarely@ibmcp.upv.es, ian.morilla@ihsm.uma-csic.es)

The Department of Computational and Quantitative Biology (LCQB) at the
prestigious Sorbonne University, located in the heart of Paris, France, is on the
lookout for a new director set to start January 1, 2025. This position is for a five-
year term, with the possibility of renewal.

Full details are available here:
https://dropsu.sorbonne-universite.fr/s/iegn9ftgTb6EmbS

4-years position (75%) | E13 TV-L | Potsdam close to Berlin

Project Title: Modelling context-dependent shifts in the forms of symbioses

Project Description: Symbiotic interactions - representing prolonged physical associations of several species - are common in natural systems and can determine population dynamics, species persistence and ecosystem functioning, as demonstrated for example in coral reefs and plantpollinator networks. Symbiotic interactions can take different forms including parasitism, mutualism and competition.
Depending on the underlying costs and benefits of the symbiotic interaction, the form of symbiosis may shift between different types of species interactions, e.g. mutualism and predator-prey interaction (see figure). While recent work has shown that the costs and benefits of symbioses depend on the densities of the symbiosis partners, we currently lack an understanding of how the form of symbioses depends on species traits and the overall food web context. This is particularly important as individuals and populations may adapt their traits to altered environmental conditions and as the food web structure may strongly vary across time and space. Hence, we want to improve general theory in community ecology by accounting for context-dependent changes in the form of symbiosis including the species’ potential to adapt to altering conditions in a food web context.

The project is embedded into a network of experimental and theoretical working groups across Germany, conducting regular workshops and meetings promoting international networking. The prospective PhD student will join the working group of Prof. Dr. Ursula Gaedke, jointly supervised by Dr. Toni Klauschies. The prospective PhD candidate has the opportunity to closely interact with an experimental PhD student addressing the same overarching topic in our working group and related research groups on Campus. They can join the Potsdam Graduate School (PoGS) allowing for a broad interdisciplinary training of soft skills and early career development. The unique location of our campus in Park Sanssouci is part of a historical place in Potsdam
providing a fruitful scientific environment and good working atmosphere.

Your qualification: MSc degree in Ecology or other relevant subjects such as Physics, Mathematics or Environmental Science. We are seeking enthusiastic and committed candidates who enjoy ecology and applied mathematics with a solid background in ecology and ecological modelling. The successful candidate is expected to implement and analyze numerically differential equation models with a modern programming language such as Python, MatLab or Mathematica. Very good English writing and communication skills are expected, German is an asset but not essential.

Application: To apply, please send the following documents as a single PDF to gaedke@uni-potsdam.de (the position is open until it is filled)

· Cover letter, including a statement of motivation and from when on you would be available
· Detailed curriculum vitae including a description of your pre-knowledge in (theoretical) ecology,
programming and former research activities
· Certifications of education
· If possible, provide letters of recommendation from previous supervisors

 4-years position (75%) | E13 TV-L | Potsdam close to Berlin

Project Title: Context dependent effects on protective symbiosis driven by predation, competition and parasitism

Project Description:
Symbiosis is a biological interaction which refers to the physical association of individuals from different species that can be positive, negative or neutral to either species. In planktonic systems several symbiotic interactions can occur simultaneously and can interact with each other. We want to study the symbiosis between Daphnia and the rotifer Brachionus rubens within a multi-species interaction web. B. rubens can attach to Daphnia which reduces the fitness of Daphnia. At the same time both species compete for resources (algae). The
attachment becomes more relevant, when a predator of B. rubens, A. brighwelli (another rotifer) is present because attached B. rubens are protected from predation. The aim is to quantify the costs and benefits for Brachionus and Daphnia under varying conditions and to better understand symbioses in a community context. Thus, the present project will contribute to a new food web theory which includes density dependence of symbioses. In addition, video analyses will be performed to study the attachment process in more detail.

In the case of final approval, the project is embedded into a network of several experimental and theoretical working groups across Germany conducting regular workshops and meetings.

The prospective PhD student will join the working group of apl. Prof. Dr. Guntram Weithoff at the University of Potsdam. We provide an active research  environment covering a broad range in ecological research. Beyond that, the Potsdam Graduate School (PoGS) offers a broad program on interdisciplinary training in soft skills and early career development.

Your qualification: MSc degree in Ecology preferably in Aquatic Ecology or a related field. We are looking for a motivated candidate with good experimental skills. Further relevant skills are: sound knowledge in conceptional ecology, statistics and very good English in writing and communication.

Application: To apply, please send the following documents as a single PDF to weithoff@uni-potsdam.de (the position is open until it is filled):
• Cover letter, including a statement of motivation and from when on you would be available
• Curriculum vitae including information on relevant skills
• Certificates of education
• If possible, provide letters of recommendation from previous supervisors