Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262477
Saori Iwanaga, A. Namatame
This paper deals with evacuation decision making of people in the disaster area. In previous papers, the cascade model is discussed contagion of evacuation decision making. The work finds that local neighborhood and their connection of the sub network are necessary to contagion. In this paper, we deal with effect of evacuee on contagion or propagation of evacuation. We found that if agents watch the agents who evacuate for shelter, many agents come to evacuate because evacuating agents for shelter comes in field of vision for many agents.
{"title":"Effect of evacuee on contagion of evacuation","authors":"Saori Iwanaga, A. Namatame","doi":"10.4108/EAI.3-12-2015.2262477","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262477","url":null,"abstract":"This paper deals with evacuation decision making of people in the disaster area. In previous papers, the cascade model is discussed contagion of evacuation decision making. The work finds that local neighborhood and their connection of the sub network are necessary to contagion. In this paper, we deal with effect of evacuee on contagion or propagation of evacuation. We found that if agents watch the agents who evacuate for shelter, many agents come to evacuate because evacuating agents for shelter comes in field of vision for many agents.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128832749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262470
L. Becchetti, V. Bonifaci, M. Dirnberger, A. Karrenbauer, K. Mehlhorn, G. Varma
We demonstrate that a simple model of P. polycephalum can be used to compute shortest paths between two points in a graph. Reminiscent of how the real organism behaves in a maze when presented with two distinct food sources s and t, the algorithm gradually identifies the shortest s-t path by retreating from everywhere else in the graph.
{"title":"P. polycephalum Can Compute Shortest Paths","authors":"L. Becchetti, V. Bonifaci, M. Dirnberger, A. Karrenbauer, K. Mehlhorn, G. Varma","doi":"10.4108/EAI.3-12-2015.2262470","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262470","url":null,"abstract":"We demonstrate that a simple model of P. polycephalum can be used to compute shortest paths between two points in a graph. Reminiscent of how the real organism behaves in a maze when presented with two distinct food sources s and t, the algorithm gradually identifies the shortest s-t path by retreating from everywhere else in the graph.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"41 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117241647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262418
Satyaki Roy, V. Shah, Sajal K. Das
The innate resilience of biological organisms have long inspired the design of robust systems. Gene regulatory network (GRN) is one such biological network which possesses a gamut of topological properties that contribute to its robustness. In this work, we study E. coli GRN as a three-tier topology to characterize such properties and explain why GRN is particularly vulnerable to failure of hub nodes. We also propose an edge rewiring mechanism on existing E. coli GRN topology to strengthen its robustness against hub failure. With extensive experiments on E. coli GRN, we show that its topological properties improve significantly after applying edge rewiring. Finally, we design wireless sensor networks using original and rewired E. coli GRN topologies. Simulation results indicate that rewired GRN has higher packet delivery and lower latency than original GRN.
{"title":"Characterization of E. coli Gene Regulatory Network and its Topological Enhancement by Edge Rewiring","authors":"Satyaki Roy, V. Shah, Sajal K. Das","doi":"10.4108/EAI.3-12-2015.2262418","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262418","url":null,"abstract":"The innate resilience of biological organisms have long inspired \u0000 \u0000the design of robust systems. Gene regulatory network \u0000 \u0000(GRN) is one such biological network which possesses \u0000 \u0000a gamut of topological properties that contribute to its robustness. \u0000 \u0000In this work, we study E. coli GRN as a three-tier \u0000 \u0000topology to characterize such properties and explain why \u0000 \u0000GRN is particularly vulnerable to failure of hub nodes. We \u0000 \u0000also propose an edge rewiring mechanism on existing E. coli \u0000 \u0000GRN topology to strengthen its robustness against hub failure. \u0000 \u0000With extensive experiments on E. coli GRN, we show \u0000 \u0000that its topological properties improve significantly after applying \u0000 \u0000edge rewiring. Finally, we design wireless sensor networks \u0000 \u0000using original and rewired E. coli GRN topologies. \u0000 \u0000Simulation results indicate that rewired GRN has higher \u0000 \u0000packet delivery and lower latency than original GRN.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"57 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129998843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262507
I. Riedel-Kruse
This extended abstract summarizes a contributed/invited presentation delivered at PhysNet 2015.
这篇扩展摘要总结了在2015年PhysNet上发表的一个贡献/邀请演讲。
{"title":"Interactive cloud experimentation for biology: Systems architecture and educational use case","authors":"I. Riedel-Kruse","doi":"10.4108/EAI.3-12-2015.2262507","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262507","url":null,"abstract":"This extended abstract summarizes a contributed/invited presentation delivered at PhysNet 2015.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"52 9","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132899110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262452
Adrian Fessel, H. Döbereiner
Physarum polycephalum, grown from fragments on an agar surface, forms a planar transportation network with exclusively low node degrees in a percolation transition. The dynamics of such a process can be captured by a rate equation reflecting basic events, such as growth and fusion of fragments.
{"title":"Motifs of Growth and Fusion Govern Physarum polycephalum Network Formation","authors":"Adrian Fessel, H. Döbereiner","doi":"10.4108/EAI.3-12-2015.2262452","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262452","url":null,"abstract":"Physarum polycephalum, grown from fragments on an agar \u0000 \u0000surface, forms a planar transportation network with exclusively low node degrees in a percolation transition. The \u0000 \u0000dynamics of such a process can be captured by a rate equation \u0000 \u0000reflecting basic events, such as growth and fusion of \u0000 \u0000fragments.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133450946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262459
B. Meyer, A. Weidenmüller, R. Chen, Julián García
One of the main factors behind the amazing ecological success of social insects is their ability to flexibly allocate the colony's workforce to all the different tasks it has to address. Insights into the self-organised task allocation methods used for this have given rise to the design of an important class of bio-inspired algorithms for network control, industrial optimisation, and other applications. The most widely used class of models for self-organised task allocation, which also forms the core of these algorithms, are response threshold models. We revisit response threshold models with new experiments using temperature regulation in bumblebee colonies as the model system. We show that standard response threshold models do not fit our experiments and present an alternative behavioural model. This captures a fine-grained, time resolved picture of task engagement, which enables us to investigate task allocation with a different set of statistical methods. Using these we show that our model fits the experiment well and explains its salient aspects. We compare the effectiveness of our model behaviour with that of response threshold models and demonstrate that it can lead to more efficient task management when demands fluctuate. Our results have the potential to provide a basis for the design of more efficient task allocation algorithms for dynamic environments and to elucidate important biological questions, such as the functional role of inter-individual variation.
{"title":"Collective Homeostasis and Time-resolved Models of Self-organised Task Allocation","authors":"B. Meyer, A. Weidenmüller, R. Chen, Julián García","doi":"10.4108/EAI.3-12-2015.2262459","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262459","url":null,"abstract":"One of the main factors behind the amazing ecological success of social insects is their ability to flexibly allocate the colony's workforce to all the different tasks it has to address. Insights into the self-organised task allocation methods used for this have given rise to the design of an important class of bio-inspired algorithms for network control, industrial optimisation, and other applications. The most widely used class of models for self-organised task allocation, which also forms the core of these algorithms, are response threshold models. \u0000 \u0000We revisit response threshold models with new experiments using temperature regulation in bumblebee colonies as the model system. We show that standard response threshold models do not fit our experiments and present an alternative behavioural model. This captures a fine-grained, time resolved picture of task engagement, which enables us to investigate task allocation with a different set of statistical methods. Using these we show that our model fits the experiment well and explains its salient aspects. \u0000 \u0000We compare the effectiveness of our model behaviour with that of response threshold models and demonstrate that it can lead to more efficient task management when demands fluctuate. Our results have the potential to provide a basis for the design of more efficient task allocation algorithms for dynamic environments and to elucidate important biological questions, such as the functional role of inter-individual variation.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134598428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262552
C. Barrett, F. Huang, C. Reidys
This contribution is a short version of a full paper submitted to Bioinformatics. DNA data transcribe into single stranded RNA, which folds into specific configurations. On the level of contact structures these are described by RNA secondary structures. Here we stipulate that RNA structures provide semantics for sequential DNA data. Accordingly we study the correlation between RNA sequences and RNA structures. We compute the partition function of sequences with respect to a fixed structure. We present a Boltzmann sampler and obtain the a priori probability of specific sequence patterns in such samples. We present a detailed analysis for the two PDB-structures, 2JXV (hairpin) and 2N3R (3-branch multi-loop). We localize where specific sequence patterns occur, contrast the energy spectrum of Boltzmann sampled sequences versus those sequences that refold into the same structure and derive a criterion to identify native structures.
{"title":"Evidence of higher order patterns in information transmission between nucleotide sequences and folded molecular shapes of RNA","authors":"C. Barrett, F. Huang, C. Reidys","doi":"10.4108/EAI.3-12-2015.2262552","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262552","url":null,"abstract":"This contribution is a short version of a full paper submitted to Bioinformatics. \u0000 \u0000DNA data transcribe into single stranded RNA, which folds into \u0000 \u0000specific configurations. On the level of contact structures these are described by \u0000 \u0000RNA secondary structures. Here we stipulate that RNA structures provide semantics \u0000 \u0000for sequential DNA data. Accordingly we study the correlation between RNA sequences \u0000 \u0000and RNA structures. \u0000 \u0000We compute the partition function of sequences with respect to a fixed structure. \u0000 \u0000We present a Boltzmann sampler and obtain the a priori probability of specific \u0000 \u0000sequence patterns in such samples. We present a detailed analysis for the two \u0000 \u0000PDB-structures, 2JXV (hairpin) and 2N3R (3-branch multi-loop). We localize \u0000 \u0000where specific sequence patterns occur, contrast the energy spectrum of Boltzmann sampled sequences \u0000 \u0000versus those sequences that refold into the same structure and derive a criterion to identify \u0000 \u0000native structures.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114833995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262543
A. Mamuye, M. Rucco
In this ongoing work, we employ persistent homology to analyze the RNA suboptimal structure space and secondary structure space of 5s rRNA. Our basic idea is to measure the topological similarity of the suboptimal structures by sliding the minimum free energy window. The preliminary result shows that the more the energy window slides from the lowest minimum energy structure the more dissimilar the structures with the lowest one. In addition, persistent homology is also used to classify 5s rRNA of Archaea species into different family of classes. Our preliminary result shows that structural dissimilarity can be observed even for species that are grouped under the same genus.
{"title":"Persistent Homology on RNA Secondary Structure Space","authors":"A. Mamuye, M. Rucco","doi":"10.4108/EAI.3-12-2015.2262543","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262543","url":null,"abstract":"In this ongoing work, we employ persistent homology to analyze the RNA suboptimal structure space and secondary structure space of 5s rRNA. Our basic idea is to measure the topological similarity of the suboptimal structures by sliding the minimum free energy window. The preliminary result shows that the more the energy window slides from the lowest minimum energy structure the more dissimilar the structures with the lowest one. In addition, persistent homology is also used to classify 5s rRNA of Archaea species into different family of classes. Our preliminary result shows that structural dissimilarity can be observed even for species that are grouped under the same genus.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"402 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123469586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262491
Christina Oettmeier, H. Döbereiner
Physarum polycephalum, cultivated on a glucose-deficient agar surface, forms disconnected foraging units (satellites). Our aim is to shed light onto the amoeboid locomotion of the slime mould, using satellites as reproducible and well-defined models and employing a wide range of techniques. This work was presented at PhysNet 2015.
{"title":"A close look at amoeboid locomotion: An integrated picture of a migrating, starvation-induced foraging unit of Physarum polycephalum","authors":"Christina Oettmeier, H. Döbereiner","doi":"10.4108/EAI.3-12-2015.2262491","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262491","url":null,"abstract":"Physarum polycephalum, cultivated on a glucose-deficient agar surface, forms disconnected foraging units (satellites). Our aim is to shed light onto the amoeboid locomotion of the slime mould, using satellites as reproducible and well-defined models and employing a wide range of techniques. This work was presented at PhysNet 2015.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"239 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122987447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2016-05-24DOI: 10.4108/EAI.3-12-2015.2262479
H. Barnett
The slime mold Physarum polycephalum is a well-established model organism within fields of biology, physics and computing. It is also increasingly employed within art and design disciplines, pedagogic practices and public engagement activities as a vehicle for exploring questions of intelligence, agency and emergence. This work was presented at PhysNet 2015.
{"title":"A Malleable Metaphor: Physarum polycephalum as artistic and educational medium","authors":"H. Barnett","doi":"10.4108/EAI.3-12-2015.2262479","DOIUrl":"https://doi.org/10.4108/EAI.3-12-2015.2262479","url":null,"abstract":"The slime mold Physarum polycephalum is a well-established model organism within fields of biology, physics and computing. It is also increasingly employed within art and design disciplines, pedagogic practices and public engagement activities as a vehicle for exploring questions of intelligence, agency and emergence. This work was presented at PhysNet 2015.","PeriodicalId":415083,"journal":{"name":"International Conference on Bio-inspired Information and Communications Technologies","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128697333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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