http://www.dagstuhl.de/17452

November 5 – 10 , 2017, Dagstuhl Seminar 17452

Algorithmic Cheminformatics

Organizers

Jakob Lykke Andersen (Tokyo Institute of Technology, JP)
Christoph Flamm (Universität Wien, AT)
Daniel Merkle (University of Southern Denmark – Odense, DK)
Peter F. Stadler (Universität Leipzig, DE)

For support, please contact

Annette Beyer for administrative matters

Marc Herbstritt for scientific matters

Documents

List of Participants
Shared Documents
Dagstuhl Seminar Wiki
Dagstuhl Seminar Schedule (Upload here)

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Motivation

Cheminformatics is the application of algorithms, combinatorial approaches, and formal methods from computer science to problems in chemistry. Although cheminformatics is an old research field and has thrived with the advances e.g. in machine learning techniques, it has drawn little from the rapid development of state-of-the-art theoretical computer science. The advance of the theoretical foundations of many aspects of cheminformatics on the basis of theoretical computer science is a sorely needed research endeavor that will serve to integrate ad hoc approaches motivated by chemical insight into coherent computational and algorithmic frameworks.

At the first Dagstuhl Seminar "Algorithmic Cheminformatics" in 2014 a wide range of topics were discussed in order to underline the significance of computer science for chemistry. Aiming at a triennial seminar series, we bring together researchers working in chemistry, cheminformatics, and most importantly the relevant fields in computer science related to it.

At this event, we specifically focus on the analysis of the behavior of chemical systems in terms of reaction networks. This includes both networks inferred from experimental data, as well as networks implicitly specified by for example formal grammars. We aim at integrating experts in concurrency theory, in particular using process calculi, Petri nets, and related formal approaches. State-of-the-art results in these fields are hardly used to infer qualitative and/or quantitative properties of chemical reaction systems, which are highly concurrent systems by nature. The majority of current modeling approaches in chemistry are either very abstract and aimed at formal algebraic properties of reaction networks, or use very fine grained modeling on the level of quantum mechanics where computational costs prevent handling of reaction systems larger than a few molecules. We therefore seek to advance discrete modeling approaches for Systems Chemistry including the notion of causality and concurrency. In addition to bringing together the experts in the respective fields from computer science, we will intentionally also invite wet-lab chemists in order to cross-fertilize the fields and generate mutually beneficial activities.

License
  Creative Commons BY 3.0 DE
  Jakob Lykke Andersen and Christoph Flamm and Daniel Merkle and Peter F. Stadler

Related Dagstuhl Seminar

Classification

  • Networks
  • Semantics / Formal Methods

Keywords

  • Process algebras
  • Petri nets
  • Concurrency theory
  • Graph transformation
  • Reaction networks

Book exhibition

Books from the participants of the current Seminar 

Book exhibition in the library, ground floor, during the seminar week.

Documentation

In the series Dagstuhl Reports each Dagstuhl Seminar and Dagstuhl Perspectives Workshop is documented. The seminar organizers, in cooperation with the collector, prepare a report that includes contributions from the participants' talks together with a summary of the seminar.

 

Download overview leaflet (PDF).

Publications

Furthermore, a comprehensive peer-reviewed collection of research papers can be published in the series Dagstuhl Follow-Ups.

Dagstuhl's Impact

Please inform us when a publication was published as a result from your seminar. These publications are listed in the category Dagstuhl's Impact and are presented on a special shelf on the ground floor of the library.

NSF young researcher support