TY - GEN
T1 - VDNA-Lab
T2 - 11th International Conference on Simulation and Modeling Methodologies, Technologies and Applications, SIMULTECH 2021
AU - Spencer, Frankie
AU - Sanwal, Usman
AU - Czeizler, Eugen
N1 - Funding Information:
This work was partially supported by the Academy of Finland, project 311371/2017, and by the Romanian National Authority for Scientific Research and Innovation, PED grant 2391.
Publisher Copyright:
Copyright © 2021 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved.
PY - 2021
Y1 - 2021
N2 - The dynamics of nucleic-acids dynamical systems is intrinsically based on local interaction. The major acting mechanisms are that of Watson-Crick complementarity on one-hand, generating binding events, and thermal energy on the other, generating random motion and un-binding. It is thus predictable that such systems can be successfully captured by computational modeling paradigms based on local interactions, such as the rule-based modeling methodology. In this research we introduce the Virtual DNA Lab (VDNA-Lab) a simulation tool which provides an easy to use graphical interface for creating, running and visualizing synthetic simulations for DNA assembly systems, such as assembly of DNA nanostructures, strand displacement cascades systems, DNA-tile assembly etc. It employs a custom designed model, implemented in the BioNetGen Language (BNGL) formalism, to capture the DNA dynamics, as well as the NFsim computational modeling engine to run simulations and generate outputs. These outputs can be visualized using the VDNA-Lab’s own visualization tool, which allows also for further analysis and filtering. The software is freely available at https://github.com/Frankie-Spencer/virtual dna lab.
AB - The dynamics of nucleic-acids dynamical systems is intrinsically based on local interaction. The major acting mechanisms are that of Watson-Crick complementarity on one-hand, generating binding events, and thermal energy on the other, generating random motion and un-binding. It is thus predictable that such systems can be successfully captured by computational modeling paradigms based on local interactions, such as the rule-based modeling methodology. In this research we introduce the Virtual DNA Lab (VDNA-Lab) a simulation tool which provides an easy to use graphical interface for creating, running and visualizing synthetic simulations for DNA assembly systems, such as assembly of DNA nanostructures, strand displacement cascades systems, DNA-tile assembly etc. It employs a custom designed model, implemented in the BioNetGen Language (BNGL) formalism, to capture the DNA dynamics, as well as the NFsim computational modeling engine to run simulations and generate outputs. These outputs can be visualized using the VDNA-Lab’s own visualization tool, which allows also for further analysis and filtering. The software is freely available at https://github.com/Frankie-Spencer/virtual dna lab.
KW - Course-grained Modeling
KW - DNA Assembly Simulator
KW - Graphical User Interface
KW - Multi-strand Assembly
KW - Rule-based Modeling
UR - http://www.scopus.com/inward/record.url?scp=85111768619&partnerID=8YFLogxK
U2 - 10.5220/0010546302880294
DO - 10.5220/0010546302880294
M3 - Conference contribution
AN - SCOPUS:85111768619
T3 - Proceedings of the 11th International Conference on Simulation and Modeling Methodologies, Technologies and Applications, SIMULTECH 2021
SP - 288
EP - 294
BT - Proceedings of the 11th International Conference on Simulation and Modeling Methodologies, Technologies and Applications, SIMULTECH 2021
A2 - Wagner, Gerd
A2 - Werner, Frank
A2 - Oren, Tuncer
A2 - De Rango, Floriano
PB - SCITEPRESS Digital Library
Y2 - 7 July 2021 through 9 July 2021
ER -