Tutorial and Workshop on Formal Methods for BioMedicine

October 8, 2019, Porto, Portugal

Affiliated with the 3rd World Congress on Formal Methods.

Organisers

Background

Biomedicine is undergoing a transformation toward a data-driven, quantitative science, propelled in part by major technological breakthroughs: high throughput sequencing and assaying technologies have made it possible to generate comprehensive genomic insights, and advances in bioimaging enable imaging live organisms at the single-cell resolution. On the other hand, mathematical modeling techniques and computational approaches that enable numerical simulations, model analysis, and predictions are increasingly becoming a part of systems biomedicine. A major effort in systems biomedicine goes into understanding the biological behavior of the whole based on the function of its parts. The aim is to formalize and analyze the ever-changing inter-connections between components (often on different time and space scales), their influence on one another, regulatory patterns, aberrations responsible for disease states, and compensatory pathways. This is a typical example of a branch of biomedicine where formal reasoning rather than empirical observations is a major driving force. On the other hand, the importance of biology as a new application area for applied mathematics and computer science is becoming increasingly apparent.

Computer scientist entering this field often lack a background in biological sciences and may even lack training in the mathematical and computational techniques most often used in this field. Through this one-day (6 hours) tutorial and workshop, we aim to give an introduction to computational systems biomedicine, starting with a crash course on molecular biology for computer scientists, and continuing with an introduction to continuous and discrete modeling techniques, including formal methods-based modeling approaches. We also plan to give an overview of several systems biology/biomedicine projects (including applications to oncology and a formal methods-based modeling of the heat-shock protein biological pathway) that we have been working on recently. We believe that this combination of foundational concepts and techniques on both the computational and the biomedical sides, combined with the description of several well-defined research projects would give our audience a valuable insight into the beauty and the challenges of systems biomedicine. We also hope to show how computer science tools and techniques they are already familiar with can be applied to the biological setting.

The event will take the form of a tutorial (4h) followed by a student-focused workshop. The tutorial will consist of lectures and demos by the 3 organisers. The workshop part will be centered on students, with poster presentations + mentoring by senior researchers (selected from formal methods seniors active in computational biomedicine), and a roundtable discussion on the opportunities, challenges, and perspectives on the field for junior researchers. 

Program

  • Part 1: Genes, diseases, and rational therapeutics
    • Hour 1 (Orieta Celiku): The flow of genetic information within biological systems — A crash course on the genetics of cells and organisms
    • Hour 2 (Orieta Celiku): Rational diagnostics and therapeutics — Challenges and opportunities for the formal computer scientist
  • Part 2: Network modeling in biomedicine
    • Hour 3 (Luigia Petre): Reaction network modeling with Event B
    • Hour 4 (Ion Petre): Network controllability for precision medicine
  • Part 3: Poster session
  • Part 4: Round-table discussion on current challenges for formal methods in biomedicine
    • Moderators: Orieta Celiku, Ion Petre, Luigia Petre.

Call for posters

We welcome poster submissions on all aspects of formal methods for biomedicine: theoretical investigations, software tools, case studies, experimental studies, data analyses, etc.

To submit a poster proposal, send a max. 1-page description of your results to ion.petre@utu.fi. We accept submissions on a continuous basis until October 1, 2019, with an acceptance response aimed shortly after the submission. Unpublished work, recently published work, and mature enough preliminary results are all welcome.

Useful information

  • FM Week: The event is part of a week-full of scientific events on Formal Methods. The full info on the programme can be found on the FM Week page. The list of the invited speakers at event throughout the week can be found here.
  • Getting to Porto: information can be found from the FM Week page.
  • Accommodation: suggestions can be found here.

Registration: TBA

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