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RCR Semantics and Efficient Simulation Algorithms of An Expressive Multilevel Modeling Language

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RCR Semantics and Efficient Simulation Algorithms of An Expressive Multilevel Modeling Language

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Replicated Computations Results (RCR) Report for “Semantics

and Efficient Simulation Algorithms for an Expressive


Multi-Level Modeling Language”
JANE HILLSTON, University of Edinburgh

“Semantics and Efficient Simulation Algorithms on an Expressive Multi-Level Modeling Language,” by


Helms et al. presents new work on the domain-specific modelling and simulation language ML-Rules [Maus
et al. 2011]. For the first time, the language is given a formal semantics that establishes the relationship be- 9
tween the language and its underlying mathematical model, continuous time Markov chains. Furthermore,
subclasses of the language are identified for which it is possible to specify and implement more efficient ap-
proaches to simulation. These new algorithms are demonstrated on substantial case studies. This replicated
computation report focuses on the ML-Rules modelling tool, specifically, the new algorithms as demonstrated
in the case studies in the paper [Helms et al. 2017]. The software was straightforward to install and use,
and all experimental results from the paper could be reproduced.
CCS Concepts: r
Computer systems organization → Embedded systems; Redundancy; Robotics; r
Networks → Network reliability
Additional Key Words and Phrases: RCR report, formal semantics, efficient simulation algorithms, systems
biology
ACM Reference Format:
Jane Hillston. 2017. Replicated computations results (RCR) report for ‘Semantics and Efficient Simulation
Algorithms for an Expressive Multi-Level Modeling Language.” ACM Trans. Model. Comput. Simul. 27, 2,
Article 9 (April 2017), 3 pages.
DOI: http://dx.doi.org/10.1145/3055539

1. INTRODUCTION
The ML-Rules modelling and simulation language is well established and supported
by a fairly mature software toolkit from the University of Rostock [2017]. Never-
theless, the replication of the results of this paper took place in two stages. First,
the ML-Rules tool was downloaded and installed and its functionality was investi-
gated in a general sense. In the second stage, the focus was explicitly on the results
presented in the paper by Helms et al. [2017], “Semantics and Efficient Simulation
Algorithms of an Expressive Multi-Level Modeling Language.” This work was sup-
ported by the authors as, in addition to running the models through the ML-Rules
software, it was necessary to also run the results through R scripts in order to cre-
ate plots that could be compared to the results in the paper. The authors provided
appropriate scripts, allowing the evaluator to conduct the experiments in ML-Rules
and the R processing; these scripts were made available in the ML-Rules repository
(https://git.informatik.uni-rostock.de/mosi/mlrules2). This approach to result replica-
tion is similar to the approach taken in the previous RCR report by Lück [2016].

Author’s address: J. Hillston, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, Scotland,
UK; email: [email protected].
Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted
without fee provided that copies are not made or distributed for profit or commercial advantage and that
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components of this work owned by others than ACM must be honored. Abstracting with credit is permitted.
To copy otherwise, to republish, to post on servers, to redistribute to lists, or to use any component of this
work in other works requires prior specific permission and/or a fee. Permissions may be requested from
Publications Dept., ACM, Inc., 2 Penn Plaza, Suite 701, New York, NY 10121-0701 USA, fax +1 (212)
869-0481, or [email protected].
c 2017 ACM 1049-3301/2017/04-ART9 $15.00
DOI: http://dx.doi.org/10.1145/3055539

ACM Transactions on Modeling and Computer Simulation, Vol. 27, No. 2, Article 9, Publication date: April 2017.
9:2 J. Hillston

2. REPLICATION OF COMPUTATION RESULTS


2.1. Installation of ML-Rules Tool
The ML-Rules software suite is already well developed and is supported by a compre-
hensive and clear website. This repository contains not only the source code for the tool
and instructions for its installation but also a sizeable collection of example models,
grouped around the publications in which they appear. Downloading the software and
installing it was straightforward and proceeded without any problems. Several simple
example models were then explored to check that the functionality of the tool is as
represented in the paper. This proved to be the case and the tool was intuitive to use
both for editing and running models.

2.2. Repeating the Results from the Paper


For the purposes of this replication report, the focus was on the version of the ML-
Rules tool corresponding to the paper [Helms et al. 2017]. The corresponding entry in
the repository University of Rostock [2017] provides the models that are used in the
three presented case studies, the R scripts needed to create the plots, and results as
shown in the paper, as well as all the necessary software. Each experiment has been
packaged as a .jar file.
In the paper, three case studies are presented; all three cases were scrutinized for this
replication report. The first study considers the Wnt/β-catenin pathway, which has been
shown to play an important role in cell differentiation and the development of cancer.
The ML-Rules model developed in this case is shown to satisfy the characterization of
the Mstatic subclass identified in the paper (its spatial compartmental structure does not
change over the course of an execution of the model), allowing it to take advantage of
the corresponding Static Simulator. The replication followed the same experimental
settings as described in the paper—100 replications of each parameter setting until
simulation time 300. The results reported in Section 7.1 of the paper were reproduced
without any problems.
The second case study in the paper considers a less restrictive class of models, for
which only some rules can be considered as static with respect to compartmentaliza-
tion. This scheme is termed hybrid and the example considered in the paper relates to
a unicellular organism, the Dictyostelium discoideum amoeba, commonly referred to as
“slime mold.” This model captures both the intracellular chemical reactions and physi-
cal movement (in a grid) of the amoebae, investigating the formation of a multicellular
“slug,” which occurs in some circumstances. This uses the Hybrid Simulator. Again,
the replication followed the same experimental settings as described in the paper—20
simulation replications, each until simulation time 5000. The number of amoeba cells
present was varied across the experiments and the objective was to investigate the for-
mation of slugs. Considerable computational effort was needed but the results reported
in Section 7.3 of the paper were replicated.
The final case study of the paper presents a model in which the dynamic formation
and dissolution of networks of mitochondria is investigated. In particular, the model
probes the influence of fission protein on mitochondrial structure and health. This
model falls into the subclass Mbind, and the execution of the model takes advantage of
the corresponding algorithm. The replication followed the same experimental settings
as described in the paper—20 replications of each experiment setting until simulation
time 100. The results obtained were indistinguishable to those presented in the paper.

ACKNOWLEDGMENTS
The author would like to thank Dr. Tobias Helms of the University of Rostock for providing access to the
appropriate scripts in the ML-Rules repository.

ACM Transactions on Modeling and Computer Simulation, Vol. 27, No. 2, Article 9, Publication date: April 2017.
Replicated Computations Results (RCR) Report 9:3

REFERENCES
Tobias Helms, Tom Warnke, Carsten Maus, and Adelinde M. Uhrmacher. 2017. Semantics and efficient
simulation algorithms of an expressive multi-level modeling language. Transactions on Modeling and
Computer Simulation to appear (2017).
Alexander Lück. 2016. Replicated computational results (RCR) report for “automatic moment-closure approx-
imation of spatially distributed collective adaptive systems.” Transactions on Modeling and Computer
Simulation 26, 4, 27:1–27:3.
Carsten Maus, Stefan Rybacki, and Adelinde M. Uhrmacher. 2011. Rule-based multi-level modeling of cell
biological systems. BMC Systems Biology 5, 166. DOI:http://dx.doi.org/10.1186/1752-0509-5-166
University of Rostock. 2017. ML-Rules Repository. Retrieved March 28, 2017 from https://git.informatik.uni-
rostock.de/mosi/mlrules2.

Received February 2017; accepted February 2017

ACM Transactions on Modeling and Computer Simulation, Vol. 27, No. 2, Article 9, Publication date: April 2017.

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