Tag Archives: JSPS

The National Institute of Informatics (NII) possess this gorgeous seminar house in Karuizawa. It was built on land donated by Dr. Hiroshi Inose, the first director general of NII. According to the website of NII, Dr Inose's idea was to create an ideal place for interdisciplinary and international discussions.

Invited Talk at Systems Resilience Workshop in Karuizawa: Resilience in the mammalian circadian clock

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I have been invited to give a talk at a workshop of the Transdisciplinary Research Integration Center Systems Resilience project at the International Seminar House for Advanced Studies in Karuizawa (in the Nagano prefecture).

Since the 2011 Tōhoku earthquake and tsunami, resilience is a key research topic in Japan. What lies behind this notion? Without going into the details that the community addresses in the papers on this topic, this is roughly the capacity of a system to absorb sudden changes in the (social, environmental, medical, …) environment while maintaining its key features. This concept is of interest in a wide range of sectors: in the societal domain (ensure the proper functioning of a city or a country when the devastating earthquake), in psychology (to recover from a traumatic event), etc.

I took the opportunity of this workshop to present some thoughts of a joint project with researchers from University of Nice about the circadian rhythm, that appears to be a very resilient biological system that discrete approaches can help to analyze.

This talk was part of my activity as JSPS invited researcher at Inoue Lab, National Institute of Informatics (Tokyo).

Thanks to Asama Shinkansen, one can reach Karuizawa from Tōkyō in just one hour.
The National Institute of Informatics (NII) possess this gorgeous seminar house in Karuizawa. It was built on land donated by Dr. Hiroshi Inose, the first director general of NII. According to the website of NII, Dr Inose’s idea was to create an ideal place for interdisciplinary and international discussions.
The National Institute of Informatics (NII) possess this gorgeous seminar house in Karuizawa. It was built on land donated by Dr. Hiroshi Inose, the first director general of NII. According to the website of NII, Dr Inose’s idea was to create an ideal place for interdisciplinary and international discussions.
All the researchers who attended the 2014 workshop of Systems Resilience Project
Systems Resilience Workshop in Karuizawa
Invited Talk at Systems Resilience Workshop in Karuizawa
The National Institute of Informatics (NII) possess this gorgeous seminar house in Karuizawa. It was built on land donated by Dr. Hiroshi Inose, the first director general of NII. According to the website of NII, Dr Inose’s idea was to create an ideal place for interdisciplinary and international discussions.
Global view on Karuizawa, which is a small city in the mountains in the center of Japan. Karuizawa currently bids for hosting G8 meeting in Japan in 2016.
Invited Talk at Systems Resilience Workshop in Karuizawa
The National Institute of Informatics (NII) possess this gorgeous seminar house in Karuizawa. It was built on land donated by Dr. Hiroshi Inose, the first director general of NII. According to the website of NII, Dr Inose’s idea was to create an ideal place for interdisciplinary and international discussions.
Global view on Karuizawa, which is a small city in the mountains in the center of Japan. It seems much appreciated by rich people, who have some second home there.
Global view on Karuizawa, which is a small city in the mountains in the center of Japan. Karuizawa currently bids for hosting G8 meeting in Japan in 2016.

Details

  • Title: Resilience in the mammalian circadian clock
  • Place: Karuizawa, International Seminar House for Advanced Studies
  • Date: 2014/09/01
  • Duration: 20 minutes
  • Attendance: 20+ persons (researchers, PhD students)
View on Kobe from the Rokkodai campus of Kobe University

Invited Talk at 5th CSPSAT2 meeting in Kobe University: Challenges of model-checking of hybrid systems

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I have been invited to give a talk at the 5th CSPSAT2 meeting in Kobe University on the challenges of model-checking and its connection with Constraint Satisfaction Problem and Boolean satisfiability. This was really enriching to give such a presentation to an audience expert with CSP and SAT approaches. This raised many interesting questions, especially with regard to the applicability of these methods to large-scale industrial cases studies.

This talk was part of my activity as JSPS invited researcher at Inoue Lab, National Institute of Informatics (Tokyo).

Details

  • Place: Kobe, Kobe University, Rokko campus
  • Date: 2014/08/21
  • Duration: 1 hour
  • Attendance: 20+ persons (researchers, PhD students)

Invited Talk at Yamanashi University: Analyzing the Dynamics of Large Biological Regulatory Networks with Process Hitting

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I have been invited to give a talk at Yamanashi University on the contribution of Computer Science to biological modeling (especially when it comes to gene regulatory networks). It was both challenging to introduce my research to a brand new audience and exciting to discover a (beautiful) place like Yamanashi.

This talk was part of my activity as JSPS invited researcher at Inoue Lab, National Institute of Informatics (Tokyo).

Invited talk at Yamanashi University
Invited talk at Yamanashi University
Hidetomo Nabeshima was chairing my Invited talk at Yamanashi University. Thanks to him!
Yamanashi University
One of the announcement of my talk at Yamanashi University
View from the 8th floor of some building at Yamanashi University
Yamanashi countryside
Sengataki Falls in the area of Yamanshi

 

Details

  • Place: Kofu, Yamanashi University
  • Date: 2014/06/18
  • Duration: 1 hour and 30 minutes
  • Attendance: 30+ persons (researchers, PhD students)

Abstract

Analyzing the Dynamics of Large Biological Regulatory Networks with Process Hitting
(joint work with Maxime Folschette, Loïc Paulevé and Olivier Roux)

Regulation is a key aspect of biological systems, all the way from the molecular scale to the ecological scale. In order to make relevant analyzes of such systems, it is then crucial to get a precise understanding of this phenomenon. This is precisely one of the main goals of systems biology.

The modeling of biological regulation can be divided into two main trends. The first is based on ordinary differential equations involving the quantitative expression of the interacting components. However, as data in a biological context are often more qualitative than quantitative, it is meaningful that another trend, based on qualitative modeling, emerged in the late 1960s. The principle of this modeling framework, introduced as synchronous Boolean networks by Kauffman and asynchronous Thomas’ networks, is to represent genes as Boolean variables. These Boolean paradigms may appear to be simplified models, but they led to significant results about the behavior of networks, such as cyclicity or steady states. Moreover, these models have been extended over the years, for example, to consider additional levels of expressions.

Nevertheless, classical analysis approaches generally rely on the exploration of the state space and parameter identification requires some indirect reasoning. This becomes tricky when the model grows beyond 10 interacting components; because of the combinatorial explosion, it is extremely difficult to handle large, realistic regulatory networks.

In order to address this scalability issue, we recently introduced a new framework, called Process Hitting. Establishing relationships between the components at the most atomic level possible, the Process Hitting opens the way to many static analysis and abstract interpretation methods to study complex dynamic properties.

In this talk, we will present the Process Hitting modeling approach and the methods we designed to analyze its dynamics. We will illustrate its benefits on a case study and give some benchmarks.