3 citations · 7 across the 16 of their papers we have counts for
7 papers · 1 filter
Automating Observable Closure Analysis for Graph Transformation Models with MolFoundry
Marcel Friedrichs, Addie Jordon, Juri Kolčák +1
Graph transformations model changing systems, with applications in software, biology and chemistry, among others. We introduce MolFoundry, a graph transformation framework, and pre…
Enumerating Chemical Structures, Stereoisomers, and Stereogenic Units with Analytic Combinatorics
Casper Asbjørn Eriksen, Daniel Merkle
The enumeration of chemical structures traditionally relies on graph- and group-theoretic techniques, including Pólya theory, in order to account for stereochemical symmetries. The…
Systematic pathway comparison on the powerset of rule-based biochemical systems
Anne-Susann Abel, Sissel Banke, Erika M. Herrera Machado +4
Computational pathway design often focuses on evaluating selected pathways or optimizing fluxes in a fixed network, but gives less direct access to the combinatorial question of wh…
On the realizability of abstract reaction networks with real molecules and reactions
Tuyet-Minh Phan, Daniel Merkle, Tieu-Long Phan +2
Abstract reaction networks appear not only as models of chemical reactions but also as models of complex systems, with applications in areas such as ecology and epidemiology, and a…
A Collision-based strategy for Network-free Exploration of Complex Molecular Networks
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +2
This work presents a stochastic exploration framework for large, implicitly defined chemical reaction spaces that are too large to be generated and stored as explicit molecular net…
CombOL: a Library for Practical Enumeration and Boltzmann Sampling of Combinatorial Classes
Casper Asbjørn Eriksen, Daniel Merkle
We present CombOL (Combinatorial Objects Library), an open-source library for the enumeration and Boltzmann sampling of combinatorial classes. Classes can be specified by a concise…
ChemRecon: a Consolidated Meta-Database Platform for Biochemical Data Integration
Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg +1
In this paper, we present ChemRecon, a meta-database and Python interface for integrating and exploring biochemical data across multiple heterogeneous resources by consolidating co…