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Automating the Development of Metabolic Network Models

Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Robert Rozanski
  • Stefano Bragaglia
  • Oliver Ray
  • Ross King
Original languageEnglish
Title of host publicationComputational Methods in Systems Biology
Subtitle of host publication13th International Conference, CMSB 2015, Nantes, France, September 16-18, 2015, Proceedings
EditorsOlivier Roux, Jérémie Bourdon
Publisher or commissioning bodySpringer
Pages145-156
Number of pages12
ISBN (Electronic)9783319234014
ISBN (Print)9783319234007
DOIs
DateAccepted/In press - 12 Jun 2015
DatePublished (current) - 2 Sep 2015
Event13th Conference on Computational Methods for Systems Biology, 16-18 September 2015, Nantes, France - Nantes, France
Duration: 16 Sep 201518 Sep 2015

Publication series

NameLecture Notes in Computer Science
PublisherSpringer Verlag
Volume9308
ISSN (Print)0302-9743
ISSN (Electronic)0302-9743

Conference

Conference13th Conference on Computational Methods for Systems Biology, 16-18 September 2015, Nantes, France
CountryFrance
CityNantes
Period16/09/1518/09/15

Abstract

Although substantial progress has been made in the automa-tion of many areas of systems biology, from data processing and model building to experimentation, comparatively little work has been done on more encompassing systems that combine all of these aspects. This paper presents an active learning system called Huginn that integrates experiment design and model revision in order to automate scientific reasoning about Metabolic Network Models. We validate our approach in a simulated environment using test cases derived from a state-of-the-art model of yeast metabolism. We show that Huginn can not only improve metabolic models but that it is able to solve a wider range of biochemical problems than previous methods and use a wider range of experiment types. Also, we show how design of extended crucial experiments can be automated using Abductive Logic Programming for the first time.

Event

13th Conference on Computational Methods for Systems Biology, 16-18 September 2015, Nantes, France

Duration16 Sep 201518 Sep 2015
CityNantes
CountryFrance
Degree of recognitionInternational event

Event: Conference

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