Dataset Information

Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models.

ABSTRACT:

Background

Hybrid simulation of (computational) biochemical reaction networks, which combines stochastic and deterministic dynamics, is an important direction to tackle future challenges due to complex and multi-scale models. Inherently hybrid computational models of biochemical networks entail two time scales: fast and slow. Therefore, it is intricate to efficiently and accurately analyse them using only either deterministic or stochastic simulation. However, there are only a few software tools that support such an approach. These tools are often limited with respect to the number as well as the functionalities of the provided hybrid simulation algorithms.

Results

We present Snoopy's hybrid simulator, an efficient hybrid simulation software which builds on Snoopy, a tool to construct and simulate Petri nets. Snoopy's hybrid simulator provides a wide range of state-of-the-art hybrid simulation algorithms. Using this tool, a computational model of biochemical networks can be constructed using a (coloured) hybrid Petri net's graphical notations, or imported from other compatible formats (e.g. SBML), and afterwards executed via dynamic or static hybrid simulation.

Conclusion

Snoopy's hybrid simulator is a platform-independent tool providing an accurate and efficient simulation of hybrid (biological) models. It can be downloaded free of charge as part of Snoopy from http://www-dssz.informatik.tu-cottbus.de/DSSZ/Software/Snoopy .

SUBMITTER: Herajy M

PROVIDER: S-EPMC5534078 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models.

Herajy Mostafa M Liu Fei F Rohr Christian C Heiner Monika M

BMC systems biology 20170728 1

<h4>Background</h4>Hybrid simulation of (computational) biochemical reaction networks, which combines stochastic and deterministic dynamics, is an important direction to tackle future challenges due to complex and multi-scale models. Inherently hybrid computational models of biochemical networks entail two time scales: fast and slow. Therefore, it is intricate to efficiently and accurately analyse them using only either deterministic or stochastic simulation. However, there are only a few softwa ...[more]

PMID: 28754122

Similar Datasets

Project description:OBJECTIVES: The main objectives of this study were to establish expert validity (a convincing realistic representation of colonoscopy according to experts) and construct validity (the ability to discriminate between different levels of expertise) of the Simbionix GI Mentor II virtual reality (VR) simulator for colonoscopy tasks, and to assess the didactic value of the simulator, as judged by experts. METHODS: Four groups were selected to perform one hand-eye coordination task (EndoBubble level 1) and two virtual colonoscopy simulations on the simulator; the levels were: novices (no endoscopy experience), intermediate experienced (<200 colonoscopies performed before), experienced (200-1,000 colonoscopies performed before), and experts (>1,000 colonoscopies performed before). All participants filled out a questionnaire about previous experience in flexible endoscopy and appreciation of the realism of the colonoscopy simulations. The average time to reach the cecum was defined as one of the main test parameters as well as the number of times view of the lumen was lost. RESULTS: Novices (N = 35) reached the cecum in an average time of 29:57 (min:sec), intermediate experienced (N = 15) in 5:45, experienced (N = 20) in 4:19 and experts (N = 35) in 4:56. Novices lost view of the lumen significantly more often compared to the other groups, and the EndoBubble task was also completed significantly faster with increasing experience (Kruskal Wallis Test, p < 0.001). The group of expert endoscopists rated the colonoscopy simulation as 2.95 on a four-point scale for overall realism. Expert opinion was that the GI Mentor II simulator should be included in the training of novice endoscopists (3.51). CONCLUSION: In this study we have demonstrated that the GI Mentor II simulator offers a convincing realistic representation of colonoscopy according to experts (expert validity) and that the simulator can discriminate between different levels of expertise (construct validity) in colonoscopy. According to experts the simulator should be implemented in the training programme of novice endoscopists.

Project description:PurposeWe evaluate the face, content, and construct validity of a portable hip arthroscopy module in a regional orthopaedic unit.MethodsParticipants were recruited from a regional orthopaedic centre, and categorized into novice (0 arthroscopies), intermediate (1-29 arthroscopies), and expert (>50 arthroscopies) groups based on reported experience in arthroscopy. Face and content validity was evaluated by feedback from users immediately following completion of modules. Objective measurements, including time taken and subjective measurements consisting of simulation software metrics including, cam lesion locations attempts, scope strikes on bone, healthy bone burred, and cam lesion burred. Scores achieved by experts were recorded, and the median score was set at the level at which proficiency was demonstrated. Participant feedback on perceived educational use was collected following completion.ResultsIn total, 20 participant results were included for analysis. Good face and content validity was expressed by participants with previous arthroscopic experience. Number of scope strikes within the simulator-derived metrics accurately discerned between levels of experience. Novices had a mean of 5 strikes per attempt (SD ±5), intermediates a mean of 5.8 strikes (SD ± 4.1). There was a significant difference between expert and novice groups (P = .01), and expert and intermediate groups (P = .002). No significant difference between overall performance scores achieved by participants in expert, intermediate, and novice groups (62% ±19 vs 55% ±22 vs 50% ±23, P = .15). This demonstrates incomplete construct validity of the simulator software-derived metrics.ConclusionsThis hip arthroscopy simulator demonstrated acceptable face and content validity, with incomplete construct validity of simulator software metrics. Participants reported high levels of satisfaction with the module, highlighting that the addition of haptic feedback would be beneficial to improve procedural steps. Incorporation of tactile feedback to the modulator components would likely enable the software to accurately delineate between levels of experience.Clinical relevanceThis study demonstrates good face and content validity. The addition of haptic feedback in a hip arthroscopy simulator may improve learning.

Dataset Information

Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models.

Background

Results

Conclusion

Publications

Snoopy's hybrid simulator: a tool to construct and simulate hybrid biological models.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets