TOP
Search the Dagstuhl Website
Looking for information on the websites of the individual seminars? - Then please:
Not found what you are looking for? - Some of our services have separate websites, each with its own search option. Please check the following list:
Schloss Dagstuhl - LZI - Logo
Schloss Dagstuhl Services
Seminars
Within this website:
External resources:
  • DOOR (for registering your stay at Dagstuhl)
  • DOSA (for proposing future Dagstuhl Seminars or Dagstuhl Perspectives Workshops)
Publishing
Within this website:
External resources:
dblp
Within this website:
External resources:
  • the dblp Computer Science Bibliography


Dagstuhl Seminar 17452

Algorithmic Cheminformatics

( Nov 05 – Nov 10, 2017 )

(Click in the middle of the image to enlarge)

Permalink
Please use the following short url to reference this page: https://www.dagstuhl.de/17452

Organizers

Contact


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.

Copyright Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler

Summary

Cheminformatics is the application of algorithms, combinatorial approaches, and formal methods from Computer Science to problems in Chemistry. While being formally a very old research field, building the theoretical foundations for Cheminformatics seen from the perspective of state-of-the-art theoretical Computer Science is not at all established research. The second edition of the seminar on ``Algorithmic Cheminformatics'' brought together researchers working in Chemistry, Cheminformatics, and most importantly the relevant fields in Computer Science related to it. In contrast to the first Dagstuhl meeting in 2014, we specifically focused on the analysis of the behaviour 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 integrated 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. Most current modeling approaches in chemistry are either very abstract and aimed at formal algebraic properties of reaction networks, or use precise modeling on a very fine grained level such as the quantum mechanical one where computational costs prevent handling of more than a few molecules. In this seminar we therefore seeked to advance discrete modeling approaches for Systems Chemistry. In addition to bringing together the experts in the respective fields from Computer Science, we also invited wet-lab chemists in order to cross-fertilize the fields and generate mutually beneficial activities.

Copyright Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler

Participants
  • Jakob Lykke Andersen (Tokyo Institute of Technology, JP) [dblp]
  • Sarah Berkemer (MPI für Mathematik in den Naturwissenschaften, DE) [dblp]
  • Mary Ann Blätke (IPK Gatersleben, DE) [dblp]
  • Erick Chastain (Rutgers University - Piscataway, US) [dblp]
  • Cinzia Di Giusto (Laboratoire I3S - Sophia Antipolis, FR) [dblp]
  • Peter Dittrich (Universität Jena, DE) [dblp]
  • Mark Dörr (Universität Greifswald, DE) [dblp]
  • Rolf Fagerberg (University of Southern Denmark - Odense, DK) [dblp]
  • Harold Fellermann (University of Newcastle, GB) [dblp]
  • Jérôme Feret (ENS - Paris, FR) [dblp]
  • Christoph Flamm (Universität Wien, AT) [dblp]
  • Walter Fontana (Harvard Medical School - Boston, US) [dblp]
  • David Gilbert (Brunel University - Uxbridge, GB) [dblp]
  • Monika Heiner (BTU Cottbus, DE) [dblp]
  • Marc Hellmuth (Universität Greifswald, DE) [dblp]
  • Wim Hordijk (Konrad Lorenz Institut - Klosterneuburg, AT) [dblp]
  • Rojin Kianian (University of Southern Denmark - Odense, DK)
  • Daniel Merkle (University of Southern Denmark - Odense, DK) [dblp]
  • Markus E. Nebel (Universität Bielefeld, DE) [dblp]
  • Nikolai Nøjgaard (Universität Greifswald, DE) [dblp]
  • Marco Peressotti (University of Southern Denmark - Odense, DK) [dblp]
  • Guillermo Restrepo (Universität Leipzig, DE) [dblp]
  • Heinz W. Schmidt (RMIT University - Melbourne, AU) [dblp]
  • D. Eric Smith (Santa Fe Institute, US) [dblp]
  • Peter F. Stadler (Universität Leipzig, DE) [dblp]
  • Mirco Tribastone (IMT - Lucca, IT) [dblp]
  • Klaus-Peter Zauner (University of Southampton, GB) [dblp]

Related Seminars
  • Dagstuhl Seminar 14452: Algorithmic Cheminformatics (2014-11-02 - 2014-11-07) (Details)

Classification
  • networks
  • semantics / formal methods

Keywords
  • process algebras
  • petri nets
  • concurrency theory
  • graph transformation
  • reaction networks