Hierarchical Modeling for Computational Biology

Maus, Carsten; John, Mathias; Röhl, Mathias; Uhrmacher, Adelinde M.

doi:10.1007/978-3-540-68894-5_4

Cited by 8 publications

(10 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An insect colony, roughly speaking, is a social system when observed at its top level, but has also an obvious "organism" layer, when observed at the "insectlevel, " along with some biochemical, chemical, and physical layers under them. More generally, "diverse hierarchies play a role in modelling and simulation for computational biology" [95], so hierarchical/layered models, where different layers obey to different sorts of laws, represent a functional example of how different metaphors and mechanism could be successfully mixed up and work together in a complex system.…”

Section: Blending Patterns Andmentioning

confidence: 99%

Nature-Inspired Coordination Models: Current Status and Future Trends

Omicini

2013

ISRN Software Engineering

View full text Add to dashboard Cite

Coordination models and languages are meant to provide abstractions and mechanisms to harness the space of interaction as one of the foremost sources of complexity in computational systems. Nature-inspired computing aims at understanding the mechanisms and patterns of complex natural systems in order to bring their most desirable features to computational systems. Thus, the promise of nature-inspired coordination models is to prove themselves fundamental in the design of complex computational systems|such as intelligent, knowledge-intensive, pervasive, adaptive, and self-organising ones. In this paper, we survey the most relevant nature-inspired coordination models in the literature, focussing in particular on tuple-based models, and foresee the most interesting research trends in the field.

show abstract

Section: Blending Patterns Andmentioning

confidence: 99%

Nature-Inspired Coordination Models: Current Status and Future Trends

Omicini

2013

ISRN Software Engineering

View full text Add to dashboard Cite

show abstract

“…Models of biological systems can be designed as hierarchies [8]. Nodes in a "hierarchical model" typically reflect real-world entities in the represented system.…”

Section: Resultsmentioning

confidence: 99%

“…The equation below indicates that the particle with ID 7 is tethered to those with IDs 2, 9, 8, and 5. V (7) ("tethered") = [2,9,8,5] The "loaded" attribute is a selector that maps particle IDs to momentum vectors. From the following equation we would infer that the particles identified by 7 and 2 are loaded with an associated restitution impulse of ppj], and that the particles with IDs 7 and 6 are loaded with P [7,6] We now define the first of the tether edjparticle system functions.…”

Section: Cmp([xy\) := Sgn(x-y)mentioning

confidence: 99%

See 1 more Smart Citation

DEVS-based dynamic simulation of deformable biological structures

Goldstein¹

View full text Add to dashboard Cite

The author has granted a nonexclusive license allowing Library and Archives Canada to reproduce, publish, archive, preserve, conserve, communicate to the public by telecommunication or on the Internet, loan, distribute and sell theses worldwide, for commercial or noncommercial purposes, in microform, paper, electronic and/or any other formats. AVIS: L'auteur a accorde une licence non exclusive permettant a la Bibliotheque et Archives Canada de reproduire, publier, archiver, sauvegarder, conserver, transmettre au public par telecommunication ou par I'lnternet, preter, distribuer et vendre des theses partout dans le monde, a des fins commerciales ou autres, sur support microforme, papier, electronique et/ou autres formats. Bien que ces formulaires aient inclus dans la pagination, il n'y aura aucun contenu manquant.

show abstract

“…Simulating biological systems poses many technical challenges that are often not present in other real systems. This is mainly due to the fact that biological systems are governed by the laws of physics as well as chemistry whose interactions by itself are not well understood and documented [7]. This difficulty mainly has two reasons behind it.…”

Section: Simulation Of Biological Systemsmentioning

confidence: 99%

Using Discrete EVent System Specification in Real-Time (DEVSRT) in Order to Model and Simulate Artificial Pancreas.

D'Souza¹

View full text Add to dashboard Cite

One of the key areas that are being paid special attention to is known as red biotechnology (i.e. biotechnology used in the medical field). An example of this is 'The Artificial Pancreas' specifically for diabetes mellitus. The device would be composed of a continuous glucose sensor that senses the user's sugar level, an insulin infusion pump that secretes insulin into the user's body when required; and an algorithm that regulates the insulin based on the glucose levels obtained from the sensor. In the past recent years, there have been significant developments in technology that are very specific to the artificial pancreas. Although these devices show promise of future device developments, it currently faces a lot of error and criticism. In order to minimize cost and time to build and verify such a complex system, one must first model and simulate the system. This methodology in turn provides risk-free testing environments and can also be tested with different scenarios. This thesis will focus on modelling and simulating the artificial pancreas using Discrete EVent System Specification in Real-Time (DEVSRT).This is accomplished by simulating both a meal model and a control algorithm to control the insulin pump based of the data provided by the continuous glucose monitor. The meal model simulation will validate the control algorithm model. The results indicate that the meal model was successfully modelled and validated via comparison to literature. While the control algorithm implemented is not effective when large meals are ingested. iii To my mother, Colette D'Souza, who is my rock and source of encouragement. If I have accomplished anything today it is because of you.iv There are a number of people without whose help this thesis might have not been written and to whom I am greatly indebted.First and foremost, I thank my thesis supervisor, Dr. Gabriel Wainer, for his support; guidance; and, encouragement throughout these past couple of years. It has been both a privilege and pleasure to work under your supervision.

show abstract

Hierarchical Modeling for Computational Biology

Cited by 8 publications

References 46 publications

Nature-Inspired Coordination Models: Current Status and Future Trends

Nature-Inspired Coordination Models: Current Status and Future Trends

DEVS-based dynamic simulation of deformable biological structures

Using Discrete EVent System Specification in Real-Time (DEVSRT) in Order to Model and Simulate Artificial Pancreas.

Contact Info

Product

Resources

About