세미나 안내
2014년 9월 2일 세미나 일정
일시: 2014. 9. 2.(화) 11:00
연사: GUSTAVO SANTOS GARCÍA (University of Salamanca)
장소: 25동 411호
Title: Pathway Logic: Rewriting Logic and Symbolic Systems Biology
The idea of symbolic biological experiments opens up an exciting new world of challenging applications for formal methods. Pathway Logic is a step towards a vision of symbolic systems biology. I will describe the Pathway Logic approach to the modeling and analysis of signal transduction, and the use of the Pathway Logic Assistant tool to browse and query these models. The epidermal growth factor signaling pathway is used to illustrate the concepts. In particular, formal executable models of processes such as signal transduction, metabolic pathways, and immune system cell-cell signaling are developed using the rewriting logic language Maude and a variety of formal tools are used to query these models.
Pathway Logic is an approach to the modeling and analysis of molecular and cellular processes based on rewriting logic. Pathway Logic models of biological processes are developed using the Maude system. A Pathway Logic knowledge base includes data types representing cellular components such as proteins, small molecules, or complexes; compartments/locations; and post- translational modifications. Rewrite rules describe the behavior of proteins and other components depending on modification state and biological context.
The Pathway Logic Assistant provides an interactive visual representation of Pathway Logic models and facilitates the following tasks: display the network of signaling reactions for a given dish; formulate and submit queries to find pathways; visualize gene expression data in the context of a network; or compute and display the downstream subnet of one or more proteins.
Rewriting logic is a logic of concurrent change that can naturally deal with states and with highly nondeterministic concurrent computations. It has good properties as a flexible and general semantic framework for giving semantics to a wide range of languages and models of concurrency. Maude is a high performance language and system supporting both equational and rewriting logic computation.
Bio
Education. I studied Mathematics studies at the University of Salamanca (1986). I developed my doctoral thesis at CSIC under the direction of prof. R. Villar. I developed several techniques of pattern recognition and Artificial Intelligence for automatic speech recognition. I defended my doctoral thesis at the University of Valladolid (1993). In 1995 I was appointed as International Research Fellow at the legendary Computer Science Laboratory, the Stanford Research Institute International (Menlo Park, California, USA).
Research. The main lines of research in which I have worked are: Automatic Speech Recognition, Differential Geometry, Artificial Intelligence Applied to Medicine and Mathematical Logic.
In the field of Mathematical Logic I have worked in the definition of ITP automatic theorem prover, implementation of neural network models and logical definition of rewriting systems for biological models. Since 1995 I have participated as a researcher continuously in research projects. Currently I work in “Software Development High Quality, Reliable, and Secure Distributed” project (DESAFIOS10) of the Spanish Ministry of Science and Innovation with prof. Martí-Oliet (UCM, Spain).
I highlight research visits I have made in the United States (1993, 1994, 1995 and 2010) in the prestigious SRI International, Stanford University and University of Illinois at Urbana-Champaign. There I worked with the group led by profs. Meseguer and Talcott. I've also made other long stays in Bucharest and Iasi (Romania) and Università degli Studi di Firenze (Italy). I emphasize lectures I gave at different universities in Romania (1994 and 1996), SRI International and Stanford University (1993, 1994 and 1995).
Teaching. I am currently professor at the School of Economics and Business in the University of Salamanca. In 1987 got a tenure position as computer analyst in the Computer Center of the University of Salamanca. From 1990 to 1994, I was professor at the School of Sciences in the Univ. of Salamanca.
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