Relevant bibliographies by topics / Gene mapping – Computer simulation

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  2. Dissertations / Theses
  3. Books
  4. Book chapters
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Academic literature on the topic 'Gene mapping – Computer simulation'

Author: Grafiati
Published: 4 June 2021
Last updated: 19 February 2022

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Journal articles on the topic "Gene mapping – Computer simulation"

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Malakar, Preeti, Thomas George, Sameer Kumar, Rashmi Mittal, Vijay Natarajan, Yogish Sabharwal, Vaibhav Saxena, and Sathish S. Vadhiyar. "A Divide and Conquer Strategy for Scaling Weather Simulations with Multiple Regions of Interest." Scientific Programming 21, no. 3-4 (2013): 93–107. http://dx.doi.org/10.1155/2013/682356.

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Accurate and timely prediction of weather phenomena, such as hurricanes and flash floods, require high-fidelity compute intensive simulations of multiple finer regions of interest within a coarse simulation domain. Current weather applications execute these nested simulations sequentially using all the available processors, which is sub-optimal due to their sub-linear scalability. In this work, we present a strategy for parallel execution of multiple nested domain simulations based on partitioning the 2-D processor grid into disjoint rectangular regions associated with each domain. We propose a novel combination of performance prediction, processor allocation methods and topology-aware mapping of the regions on torus interconnects. Experiments on IBM Blue Gene systems using WRF show that the proposed strategies result in performance improvement of up to 33% with topology-oblivious mapping and up to additional 7% with topology-aware mapping over the default sequential strategy.
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Tyson, Adam L., Charly V. Rousseau, Christian J. Niedworok, Sepiedeh Keshavarzi, Chryssanthi Tsitoura, Lee Cossell, Molly Strom, and Troy W. Margrie. "A deep learning algorithm for 3D cell detection in whole mouse brain image datasets." PLOS Computational Biology 17, no. 5 (May 28, 2021): e1009074. http://dx.doi.org/10.1371/journal.pcbi.1009074.

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Understanding the function of the nervous system necessitates mapping the spatial distributions of its constituent cells defined by function, anatomy or gene expression. Recently, developments in tissue preparation and microscopy allow cellular populations to be imaged throughout the entire rodent brain. However, mapping these neurons manually is prone to bias and is often impractically time consuming. Here we present an open-source algorithm for fully automated 3D detection of neuronal somata in mouse whole-brain microscopy images using standard desktop computer hardware. We demonstrate the applicability and power of our approach by mapping the brain-wide locations of large populations of cells labeled with cytoplasmic fluorescent proteins expressed via retrograde trans-synaptic viral infection.
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Xu, Shizhong. "Mapping quantitative trait loci using four-way crosses." Genetical Research 68, no. 2 (October 1996): 175–81. http://dx.doi.org/10.1017/s0016672300034066.

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SummaryIn plant species, typical gene mapping strategies use populations initiated from crosses between two inbred lines. However, schemes including more than two parents could be used. In this paper, a new approach is introduced which uses a four-way cross population derived from four inbred lines. The four-way cross design for mapping quantitative trait loci (QTLs) provides tests for QTL segregation in four lines simultaneously in one experiment. Therefore, it is a more economical strategy than oneusing line crosses between only two lines. The new strategy also increases the probability of detecting QTLs if they segregate in one line cross but not in the other. A multiple linear regression analysis is used for QTL detection. It is proven that the expected residual variance from the regression analysis differs from the pure environmental variance. Correction for the bias is proposed and verified by computer simulations.
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Fortune, Mary D., and Chris Wallace. "simGWAS: a fast method for simulation of large scale case–control GWAS summary statistics." Bioinformatics 35, no. 11 (October 29, 2018): 1901–6. http://dx.doi.org/10.1093/bioinformatics/bty898.

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Abstract Motivation Methods for analysis of GWAS summary statistics have encouraged data sharing and democratized the analysis of different diseases. Ideal validation for such methods is application to simulated data, where some ‘truth’ is known. As GWAS increase in size, so does the computational complexity of such evaluations; standard practice repeatedly simulates and analyses genotype data for all individuals in an example study. Results We have developed a novel method based on an alternative approach, directly simulating GWAS summary data, without individual data as an intermediate step. We mathematically derive the expected statistics for any set of causal variants and their effect sizes, conditional upon control haplotype frequencies (available from public reference datasets). Simulation of GWAS summary output can be conducted independently of sample size by simulating random variates about these expected values. Across a range of scenarios, our method, produces very similar output to that from simulating individual genotypes with a substantial gain in speed even for modest sample sizes. Fast simulation of GWAS summary statistics will enable more complete and rapid evaluation of summary statistic methods as well as opening new potential avenues of research in fine mapping and gene set enrichment analysis. Availability and implementation Our method is available under a GPL license as an R package from http://github.com/chr1swallace/simGWAS. Supplementary information Supplementary data are available at Bioinformatics online.
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Millstein, Joshua, Francesca Battaglin, Malcolm Barrett, Shu Cao, Wu Zhang, Sebastian Stintzing, Volker Heinemann, and Heinz-Josef Lenz. "Partition: a surjective mapping approach for dimensionality reduction." Bioinformatics 36, no. 3 (August 26, 2019): 676–81. http://dx.doi.org/10.1093/bioinformatics/btz661.

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Abstract Motivation Large amounts of information generated by genomic technologies are accompanied by statistical and computational challenges due to redundancy, badly behaved data and noise. Dimensionality reduction (DR) methods have been developed to mitigate these challenges. However, many approaches are not scalable to large dimensions or result in excessive information loss. Results The proposed approach partitions data into subsets of related features and summarizes each into one and only one new feature, thus defining a surjective mapping. A constraint on information loss determines the size of the reduced dataset. Simulation studies demonstrate that when multiple related features are associated with a response, this approach can substantially increase the number of true associations detected as compared to principal components analysis, non-negative matrix factorization or no DR. This increase in true discoveries is explained both by a reduced multiple-testing challenge and a reduction in extraneous noise. In an application to real data collected from metastatic colorectal cancer tumors, more associations between gene expression features and progression free survival and response to treatment were detected in the reduced than in the full untransformed dataset. Availability and implementation Freely available R package from CRAN, https://cran.r-project.org/package=partition. Supplementary information Supplementary data are available at Bioinformatics online.
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Drusbosky, Leylah, Neeraj Kumar Singh, Pranav Tiwari, Shireen Vali, Taher Abbasi, Sarbjit Sarkaria, Adam Lorant, Satin Burns, Rafael Bejar, and Christopher R. Cogle. "A Genomic Rule Predicting HMA Treatment Response in MDS Identified By Protein Network Mapping and Validated By Clinical Trial Simulation." Blood 128, no. 22 (December 2, 2016): 3151. http://dx.doi.org/10.1182/blood.v128.22.3151.3151.

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Abstract Background: Hypomethyating agents (HMAs) for the treatment of the myelodysplastic syndromes (MDS) fail to achieve clinical improvement in nearly 60% of patients. We previously reported a genomics-informed computational method that had >80% accuracy in predicting HMA treatment response in higher risk MDS patients. Aim: To define novel genomic signature rules to predict MDS response to HMA therapy and validate the rules in a clinical trial simulation. Methods: We analyzed a cohort of 213 high-risk MDS patients treated with an HMA and assessed for disease response by IWG criteria (Bejar, et al. Blood 2014). Bone marrow cells from these MDS patients were examined by conventional cytogenetics and next generation sequencing of target myeloid genes. For each patient, every available genomic abnormality was entered into a computational biology program (Cellworks Group) that uses PubMed and other online resources to generate patient-specific protein network maps of activated and inactivated protein pathways. Digital drug simulations with HMAs were conducted by quantitatively measuring drug effect on a composite MDS disease inhibition score (i.e., cell proliferation, viability, and apoptosis). This information was then used to create virtual Kaplan Meier-type estimates plotting the percent of responders (Y axis) to their disease inhibition score (X axis). A database was developed to house the clinical, genomic, and demographic information for each patient, and used to run clinical trial simulations. Results: A training cohort of 80 MDS patients was used to identify genomic signature rules capable of predicting clinical response to HMA treatment. The 3 rules identified were (1) null hypothesis, no rule for selection of MDS patients for HMA response; (2) TET2 mutation alone, which is known to influence response to HMA in MDS; and (3) TET2 function exclusion, defined as TET2 mutation without the presence of ASXL1 mutation, harboring wild-type SRSF2, and wild-type EZH2. Next, we used these rules in a clinical trial simulation involving 109 different patients in the test dataset. 14 of 203 patients lacked adequate genomic or clinical data for the virtual trial. The 3 rules identified in the training set served as inclusion criteria for 3 HMA treatment arms. The data enabled us to generate the predictive equivalent to a Kaplan-Meier estimate for each arm. Using rule (1) as a control treatment arm, we used rule (2) as an inclusion criterion for a second treatment arm and found a non-significant probability that a randomly selected patient obtained a better MDS disease inhibition score using the rule (2) inclusion criterion (P=0.08) (Figure 1). When rule (3) was used as inclusion criteria, the probability that a randomly selected patient obtained a better MDS disease inhibition score was significantly increased (P=0.0023) (Figure 1). Conclusions: In this study we identified a new four-gene rule predicting MDS response to HMA treatment. We also present a novel method of clinical trial simulation to validate biomarker rules. This unique computer-based approach is intended to inform the design of phase 2 and 3 clinical trials with the ultimate goal of improving drug development time and expense by establishing and validating inclusion criteria for precision enrollment. Figure 1 Clinical Trial Simulation of HMA Treatment in MDS Patients Based on Gene Signature Rules. A genomically-informed computational method identified 3 MDS genomic signatures with potential to predict HMA treatment response based on a training set of patient data (N=80). A separate validation cohort of 109 patients was then virtually recruited into one of 3 HMA treatment arms based on genomic signature rules. In this study, patients with TET2 mutation alone (red line) showed a trend toward greater clinical response than the unselected control cohort (black line) (P=0.08). However, patients harboring TET2 mutation without mutations of ASXL1, SRSF2, and EZH2 (green line) showed significantly greater response to HMA treatment than the unselected control cohort (black line) (p=0.0023). Figure 1. Clinical Trial Simulation of HMA Treatment in MDS Patients Based on Gene Signature Rules. A genomically-informed computational method identified 3 MDS genomic signatures with potential to predict HMA treatment response based on a training set of patient data (N=80). A separate validation cohort of 109 patients was then virtually recruited into one of 3 HMA treatment arms based on genomic signature rules. In this study, patients with TET2 mutation alone (red line) showed a trend toward greater clinical response than the unselected control cohort (black line) (P=0.08). However, patients harboring TET2 mutation without mutations of ASXL1, SRSF2, and EZH2 (green line) showed significantly greater response to HMA treatment than the unselected control cohort (black line) (p=0.0023). Disclosures Kumar Singh: Cellworks: Employment. Tiwari:Cellworks: Employment. Vali:Cellworks Group: Employment. Abbasi:Cellworks: Employment. Bejar:Celgene: Consultancy, Honoraria; Genoptix: Consultancy, Honoraria, Patents & Royalties: No royalties; Foundation Medicine: Consultancy.
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Zhang, Lei, Chenxing Zheng, Yu Zheng, Haihong Huang, and Qingdi Ke. "Product evolutionary design driven by environmental performance." Concurrent Engineering 27, no. 1 (October 15, 2018): 40–56. http://dx.doi.org/10.1177/1063293x18805200.

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This article is in terms of product environmental performance demand and proposes four structure evolutionary operation modes which include combined evolutionary method, decomposition evolutionary method, replacement evolutionary method, and material-changing evolutionary method to express the structure evolutionary process of products. Through the quotient space theory and proposed method combined with probability statistics, probability mapping from environmental performance to product structure is established and the evolutionary individuals with outstanding environmental performance are listed. Through the analysis to the specific conditions of the evolutionary individuals, the design constraints are extracted, and the objective function of environmental performance is established. This article presents an interactive genetic algorithm as evolutionary algorithm and combines it with four structure evolutionary operation modes to conduct corresponding gene manipulation and generates evolutionary product. Finally, the proposed methodology is successfully applied to engine gear chamber and the environmental impact is found to be better than before evolution.
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Hori, Atsushi, Kazumi Yoshinaga, Thomas Herault, Aurélien Bouteiller, George Bosilca, and Yutaka Ishikawa. "Overhead of using spare nodes." International Journal of High Performance Computing Applications 34, no. 2 (February 4, 2020): 208–26. http://dx.doi.org/10.1177/1094342020901885.

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With the increasing fault rate on high-end supercomputers, the topic of fault tolerance has been gathering attention. To cope with this situation, various fault-tolerance techniques are under investigation; these include user-level, algorithm-based fault-tolerance techniques and parallel execution environments that enable jobs to continue following node failure. Even with these techniques, some programs with static load balancing, such as stencil computation, may underperform after a failure recovery. Even when spare nodes are present, they are not always substituted for failed nodes in an effective way. This article considers the questions of how spare nodes should be allocated, how to substitute them for faulty nodes, and how much the communication performance is affected by such a substitution. The third question stems from the modification of the rank mapping by node substitutions, which can incur additional message collisions. In a stencil computation, rank mapping is done in a straightforward way on a Cartesian network without incurring any message collisions. However, once a substitution has occurred, the optimal node-rank mapping may be destroyed. Therefore, these questions must be answered in a way that minimizes the degradation of communication performance. In this article, several spare node allocation and failed node substitution methods will be proposed, analyzed, and compared in terms of communication performance following the substitution. The proposed substitution methods are named sliding methods. The sliding methods are analyzed by using our developed simulation program and evaluated by using the K computer, Blue Gene/Q (BG/Q), and TSUBAME 2.5. It will be shown that when failures occur, the stencil communication performance on the K and BG/Q can be slowed around 10 times depending on the number of node failures. The barrier performance on the K can be cut in half. On BG/Q, barrier performance can be slowed by a factor of 10. Further, it will also be shown that almost no such communication performance degradation can be seen on TSUBAME 2.5. This is because TSUBAME 2.5 has an Infiniband network connected with a FatTree topology, while the K computer and BG/Q have dedicated Cartesian networks. Thus, the communication performance degradation depends on network characteristics.
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Destiarani, Wanda, Rahmaniar Mulyani, Muhammad Yusuf, and Iman Permana Maksum. "Molecular Dynamics Simulation of T10609C and C10676G Mutations of Mitochondrial ND4L Gene Associated With Proton Translocation in Type 2 Diabetes Mellitus and Cataract Patients." Bioinformatics and Biology Insights 14 (January 2020): 117793222097867. http://dx.doi.org/10.1177/1177932220978672.

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The mutation rate of mitochondrial DNA (mtDNA) is 17 times higher than nuclear DNA, and these mutations can cause mitochondrial disease in 1 of 10.000 people. The T10609C mutation was identified in type 2 diabetes mellitus (T2DM) patients and the C10676G mutation in cataract patients, with both mutations occurring in the ND4L gene of mtDNA that encodes ND4L protein. ND4L protein, a subunit of complex I in the respiratory complex, has been shown to play a role in the proton translocation process. The purpose of this study was to investigate the effect of both mutations on the proton translocation mechanism. Mutation mapping showed changes in amino acids M47T (T10609C) and C69W (C10676G). The 100 ns molecular dynamics (MD) simulations performed on native and mutants of ND4L-ND6 subunits. It is revealed that the native model had a similar proton translocation pathway to that of complex I from other organisms. Interestingly, the mutant M47T and C69W showed the interruption of the translocation pathway by a hydrogen bond formation between Glu34 and Tyr157. It is observed that the mutations were restricting the passage of water molecules through the transmembrane region. These results could help to develop the computational assay for the validation of a specific genetic biomarker for T2DM and cataracts.
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Yang, Chin Jian, Rajiv Sharma, Gregor Gorjanc, Sarah Hearne, Wayne Powell, and Ian Mackay. "Origin Specific Genomic Selection: A Simple Process To Optimize the Favorable Contribution of Parents to Progeny." G3: Genes|Genomes|Genetics 10, no. 7 (May 19, 2020): 2445–55. http://dx.doi.org/10.1534/g3.120.401132.

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Modern crop breeding is in constant demand for new genetic diversity as part of the arms race with genetic gain. The elite gene pool has limited genetic variation and breeders are trying to introduce novelty from unadapted germplasm, landraces and wild relatives. For polygenic traits, currently available approaches to introgression are not ideal, as there is a demonstrable bias against exotic alleles during selection. Here, we propose a partitioned form of genomic selection, called Origin Specific Genomic Selection (OSGS), where we identify and target selection on favorable exotic alleles. Briefly, within a population derived from a bi-parental cross, we isolate alleles originating from the elite and exotic parents, which then allows us to separate out the predicted marker effects based on the allele origins. We validated the usefulness of OSGS using two nested association mapping (NAM) datasets: barley NAM (elite-exotic) and maize NAM (elite-elite), as well as by computer simulation. Our results suggest that OSGS works well in its goal to increase the contribution of favorable exotic alleles in bi-parental crosses, and it is possible to extend the approach to broader multi-parental populations.
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Dissertations / Theses on the topic "Gene mapping – Computer simulation"

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Kruczkiewicz, Peter. "A comparative genomic framework for the in silico design and assessment of molecular typing methods using whole-genome sequence data with application to Listeria monocytogenes." Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Biological Sciences, c2013, 2013. http://hdl.handle.net/10133/3391.

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Although increased genome sequencing e orts have increased our understanding of genomic variability within many bacterial species, there has been limited application of this knowledge towards assessing current molecular typing methods and developing novel molecular typing methods. This thesis reports a novel in silico comparative genomic framework where the performance of typing methods is assessed on the basis of the discriminatory power of the method as well as the concordance of the method with a whole-genome phylogeny. Using this framework, we designed a comparative genomic ngerprinting (CGF) assay for Listeria monocytogenes through optimized molecular marker selection. In silico validation and assessment of the CGF assay against two other molecular typing methods for L. monocytogenes (multilocus sequence typing (MLST) and multiple virulence locus sequence typing (MVLST)) revealed that the CGF assay had better performance than these typing methods. Hence, optimized molecular marker selection can be used to produce highly discriminatory assays with high concordance to whole-genome phylogenies. The framework described in this thesis can be used to assess current molecular typing methods against whole-genome phylogenies and design the next generation of high-performance molecular typing methods from whole-genome sequence data.
xiii, 100 leaves : ill. ; 29 cm
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Akhtar, Mahmood Electrical Engineering &amp Telecommunications Faculty of Engineering UNSW. "Genomic sequence processing: gene finding in eukaryotes." Publisher:University of New South Wales. Electrical Engineering & Telecommunications, 2008. http://handle.unsw.edu.au/1959.4/40912.

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Of the many existing eukaryotic gene finding software programs, none are able to guarantee accurate identification of genomic protein coding regions and other biological signals central to pathway from DNA to the protein. Eukaryotic gene finding is difficult mainly due to noncontiguous and non-continuous nature of genes. Existing approaches are heavily dependent on the compositional statistics of the sequences they learn from and are not equally suitable for all types of sequences. This thesis firstly develops efficient digital signal processing-based methods for the identification of genomic protein coding regions, and then combines the optimum signal processing-based non-data-driven technique with an existing data-driven statistical method in a novel system demonstrating improved identification of acceptor splice sites. Most existing well-known DNA symbolic-to-numeric representations map the DNA information into three or four numerical sequences, potentially increasing the computational requirement of the sequence analyzer. Proposed mapping schemes, to be used for signal processing-based gene and exon prediction, incorporate DNA structural properties in the representation, in addition to reducing complexity in subsequent processing. A detailed comparison of all DNA representations, in terms of computational complexity and relative accuracy for the gene and exon prediction problem, reveals the newly proposed ?paired numeric? to be the best DNA representation. Existing signal processing-based techniques rely mostly on the period-3 behaviour of exons to obtain one dimensional gene and exon prediction features, and are not well equipped to capture the complementary properties of exonic / intronic regions and deal with the background noise in detection of exons at their nucleotide levels. These issues have been addressed in this thesis, by proposing six one-dimensional and three multi-dimensional signal processing-based gene and exon prediction features. All one-dimensional and multi-dimensional features have been evaluated using standard datasets such as Burset/Guigo1996, HMR195, and the GENSCAN test set. This is the first time that different gene and exon prediction features have been compared using substantial databases and using nucleotide-level metrics. Furthermore, the first investigation of the suitability of different window sizes for period-3 exon detection is performed. Finally, the optimum signal processing-based gene and exon prediction scheme from our evaluations is combined with a data-driven statistical technique for the recognition of acceptor splice sites. The proposed DSP-statistical hybrid is shown to achieve 43% reduction in false positives over WWAM, as used in GENSCAN.
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Hon, Wing-hong, and 韓永康. "Analysis of DNA shuffling by computer simulation." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B27771027.

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Luotsinen, Linus Jan. "AUTONOMOUS ENVIRONMENTAL MAPPING IN MULTI-AGENT UAV SYSTEMS." Master's thesis, University of Central Florida, 2004. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4421.

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UAV units are by many researchers and aviation specialists considered the future and cutting edge of modern flight technology. This thesis discusses methods for efficient autonomous environmental mapping in a multi-agent domain. An algorithm that emphasizes on team work by sharing the agents local map information and exploration intentions is presented as a solution to the mapping problem. General theories on how to model and implement rational autonomous behaviour for UAV agents are presented. Three different human and tactical behaviour modeling techniques are evaluated. The author found the CxBR paradigm to be the most interesting approach. Also, in order to test and quantify the theories presented in this thesis a simulation environment was developed. This simulation software allows for UAV agents to operate in a visual 3-D environment with mountains, other various terrain types, danger points and enemies to model unexpected events.
M.S.
Department of Electrical and Computer Engineering
Engineering and Computer Science;
Electrical and Computer Engineering
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Ayar, Yusuf Yavuz. "Design And Simulation Of A Flash Translation Layer Algorithm." Master's thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/12611995/index.pdf.

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Flash Memories have been widely used as a storage media in electronic devices such as USB flash drives, mobile phones and cameras. Flash Memory offers a portable and non-volatile de- sign, which can be carried to everywhere without data loss. It is durable against temperature and humidity. With all these advantages, Flash Memory gets popular day by day. However, Flash Memory has also some disadvantages, such as erase-before restriction and erase limi- tation of each individual block. Erase-before restriction pushes every single writable unit to be erased before an update operation. Another limitation is that every block can be erased up to a fixed number. Flash Translation Layer - FTL is the solution for these disadvantages. Flash Translation Layer is a software module inside the Flash Memory working between the operating system and the memory. FTL tries to reduce these disadvantages of Flash Memory via implementing garbage collector, address mapping scheme, error correcting and many oth- ers. There are various Flash Translation Layer software. Some of them have been reviewed in terms of their advantages and disadvantages. The study aims at designing, implementing and simulating a NAND type FTL algorithm.
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Hao, Guoliang. "Imaging of the atria and cardiac conduction system : from experiment to computer modelling." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/imaging-of-the-atria-and-cardiac-conduction-system--from-experiment-to-computer-modelling(3e5dba52-70f3-4fa8-890d-adfe2380086c).html.

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Background: Experimental mapping and computer modelling provide important platforms to study the fundamental mechanisms underlying normal and abnormal activation of the heart. However, accurate computer modelling requires detailed anatomical models and needs support and validation from experimental data. Aims: 1) Construction of detailed anatomical heart models with the cardiac conduction system (CCS). 2) Mapping of the electrical activation sequence in rabbit atria to support and validate computer simulation. 3) Mapping of the spontaneous activity in the atrioventricular ring tissues (AV rings), which consist of nodal-like myocytes and can be a source of atrial tachycardia. Methods: High-resolution magnetic resonance imaging (MRI) and computed tomography (CT) were used to provide two-dimensional (2D) images for the construction of the detailed anatomical heart models. Immunohistochemistry and Masson’s trichrome staining were used to distinguish the CCS in the heart. LabVIEW was used in the development of a multi-electrode mapping system. The multi-electrode mapping technique was employed to map the electrical activation sequence of the rabbit atria. The cellular automaton model was used to simulate electrical activation of the rabbit atria. Results: 1) Three detailed anatomical models were constructed, including a detailed three dimensional (3D) anatomical model of the rabbit heart (whole of the atria and part of the ventricles), a 3D anatomical model of the rat heart with the CCS and AV rings, and a 3D anatomical model of the human atrioventricular node. 2) A multi-electrode mapping system was developed. 3) The electrical activation sequence of the rabbit atria was mapped in detail using the multi-electrode mapping system. The conduction velocity in the rabbit atria was measured. The mapping data showed the coronary sinus and the left superior vena cava do not provide an interatrial conduction route during sinus rhythm in the rabbit heart. 4) Electrical activation of the rabbit atria was simulated with the support of the 3D anatomical model of the rabbit atria and the experimental mapping data. 5) The spontaneous activity in the rat AV rings was mapped using the multi-electrode mapping system. Conclusions: The detailed anatomical models developed in this study can be used to support accurate computer simulation and can also be used in anatomical teaching and research. The experimental mapping data from the rabbit atria can be used to support and validate computer simulation. The computer simulation study demonstrated the importance of anatomical structure and electrophysiological heterogeneity. This study also demonstrated that the AV rings could potentially act as ectopic pacemakers.
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Walter, Matthew R. "Sparse Bayesian information filters for localization and mapping." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/46498.

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Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2008.
Includes bibliographical references (p. 159-170).
This thesis formulates an estimation framework for Simultaneous Localization and Mapping (SLAM) that addresses the problem of scalability in large environments. We describe an estimation-theoretic algorithm that achieves significant gains in computational efficiency while maintaining consistent estimates for the vehicle pose and the map of the environment.We specifically address the feature-based SLAM problem in which the robot represents the environment as a collection of landmarks. The thesis takes a Bayesian approach whereby we maintain a joint posterior over the vehicle pose and feature states, conditioned upon measurement data. We model the distribution as Gaussian and parametrize the posterior in the canonical form, in terms of the information (inverse covariance) matrix. When sparse, this representation is amenable to computationally efficient Bayesian SLAM filtering. However, while a large majority of the elements within the normalized information matrix are very small in magnitude, it is fully populated nonetheless. Recent feature-based SLAM filters achieve the scalability benefits of a sparse parametrization by explicitly pruning these weak links in an effort to enforce sparsity. We analyze one such algorithm, the Sparse Extended Information Filter (SEIF), which has laid much of the groundwork concerning the computational benefits of the sparse canonical form. The thesis performs a detailed analysis of the process by which the SEIF approximates the sparsity of the information matrix and reveals key insights into the consequences of different sparsification strategies. We demonstrate that the SEIF yields a sparse approximation to the posterior that is inconsistent, suffering from exaggerated confidence estimates.
(cont) This overconfidence has detrimental effects on important aspects of the SLAM process and affects the higher level goal of producing accurate maps for subsequent localization and path planning. This thesis proposes an alternative scalable filter that maintains sparsity while preserving the consistency of the distribution. We leverage insights into the natural structure of the feature-based canonical parametrization and derive a method that actively maintains an exactly sparse posterior. Our algorithm exploits the structure of the parametrization to achieve gains in efficiency, with a computational cost that scales linearly with the size of the map. Unlike similar techniques that sacrifice consistency for improved scalability, our algorithm performs inference over a posterior that is conservative relative to the nominal Gaussian distribution. Consequently, we preserve the consistency of the pose and map estimates and avoid the effects of an overconfident posterior. We demonstrate our filter alongside the SEIF and the standard EKEF both in simulation as well as on two real-world datasets. While we maintain the computational advantages of an exactly sparse representation, the results show convincingly that our method yields conservative estimates for the robot pose and map that are nearly identical to those of the original Gaussian distribution as produced by the EKF, but at much less computational expense. The thesis concludes with an extension of our SLAM filter to a complex underwater environment. We describe a systems-level framework for localization and mapping relative to a ship hull with an Autonomous Underwater Vehicle (AUV) equipped with a forward-looking sonar. The approach utilizes our filter to fuse measurements of vehicle attitude and motion from onboard sensors with data from sonar images of the hull. We employ the system to perform three-dimensional, 6-DOF SLAM on a ship hull.
by Matthew R. Walter.
S.M.
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Barran, Brian Arthur. "View dependent fluid dynamics." Texas A&M University, 2006. http://hdl.handle.net/1969.1/3827.

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This thesis presents a method for simulating fluids on a view dependent grid structure to exploit level-of-detail with distance to the viewer. Current computer graphics techniques, such as the Stable Fluid and Particle Level Set methods, are modified to support a nonuniform simulation grid. In addition, infinite fluid boundary conditions are introduced that allow fluid to flow freely into or out of the simulation domain to achieve the effect of large, boundary free bodies of fluid. Finally, a physically based rendering method known as photon mapping is used in conjunction with ray tracing to generate realistic images of water with caustics. These methods were implemented as a C++ application framework capable of simulating and rendering fluid in a variety of user-defined coordinate systems.
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Cai, Xinye. "A multi-objective GP-PSO hybrid algorithm for gene regulatory network modeling." Diss., Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1492.

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Agyapong-Kodua, Kwabena. "Multi-product cost and value stream modelling in support of business process analysis." Thesis, Loughborough University, 2009. https://dspace.lboro.ac.uk/2134/5585.

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Books on the topic "Gene mapping – Computer simulation"

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1942-, Cantor Charles R., and Lim Hwa A, eds. The First International Conference on Electrophoresis, Supercomputing, and the Human Genome: Proceedings of the April 10-13 conference at Florida State University, Tallahassee, Florida. Singapore: World Scientific, 1991.

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Kinetic modeling of gene expression. Austin, Tex: R.G. Landes Co., 1994.

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Groundwater, Vulnerability Assessment and Mapping International Conference (2004 Ustroń Poland). Groundwater vulnerability assessment and mapping. London: Taylor & Francis, 2007.

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Dikau, Richard. Landform classification of New Mexico by computer. [Menlo Park, CA]: U.S. Dept. of the Interior, U.S. Geological Survey, 1991.

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Groundwater Vulnerability Assessment and Mapping International Conference (2004 Ustroń, Poland). Groundwater vulnerability assessment and mapping: Selected papers from the Groundwater Vulnerability Assessment and Mapping International Conference : Ustron, Poland, 2004. Boca Raton: Taylor & Francis, 2007.

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Kumler, Mark P. An intensive comparison of triangulated irregular networks (TINs) and digital elevation models (DEMs). [Ontario]: University of Toronto Press, 1994.

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Shmulevich, Ilya. Probabilistic boolean networks: The modeling and control of gene regulatory networks. Philadelphia: Society for Industrial and Applied Mathematics, 2010.

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Sansom, Roger. Ingenious genes: How gene regulation networks evolve to control development. Cambridge, Mass: MIT Press, 2011.

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Roth, Michelle L. Sample analysis and modeling to determine GPR capability for mapping fluvial mine tailings in the Coeur d'Alene River channel. [Denver, CO]: U.S. Geological Survey, 1996.

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International Conference on Bioinformatics, Supercomputing, and Complex Genome Analysis (2nd 1992 Saint Petersburg Beach, Dla.). The Second International Conference on Bioinformatics, Supercomputing, and Complex Genome Analysis: Proceedings of the June 4-7, 1992 Conference at St. Petersburg Beach, Florida, USA. Edited by Lim Hwa A. Singapore: World Scientific, 1993.

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Book chapters on the topic "Gene mapping – Computer simulation"

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Wu, Shiquan, and Xun Gu. "Gene Network: Model, Dynamics and Simulation." In Lecture Notes in Computer Science, 12–21. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11533719_4.

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Lee, Eunsung. "Evaluation of E-government Systems with Cognitive Mapping Simulation." In Communications in Computer and Information Science, 369–76. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-35594-3_50.

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Serpa, Matheus S., Eduardo H. M. Cruz, Jairo Panetta, Antônio Azambuja, Alexandre S. Carissimi, and Philippe O. A. Navaux. "Improving Oil and Gas Simulation Performance Using Thread and Data Mapping." In Communications in Computer and Information Science, 55–68. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-41050-6_4.

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Gao, Yuan, and HongYi Yu. "An Enhanced System Level to Link Level Mapping Method for 3GPP LTE System Level Simulation." In Communications in Computer and Information Science, 371–77. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21411-0_61.

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Eulenstein, Oliver, Boris Mirkin, and Martin Vingron. "Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees." In DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 71–94. Providence, Rhode Island: American Mathematical Society, 1997. http://dx.doi.org/10.1090/dimacs/037/05.

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Brandstetter, Andrea, Najoua Bolakhrif, Christian Schiffer, Timo Dickscheid, Hartmut Mohlberg, and Katrin Amunts. "Deep Learning-Supported Cytoarchitectonic Mapping of the Human Lateral Geniculate Body in the BigBrain." In Lecture Notes in Computer Science, 22–32. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-82427-3_2.

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AbstractThe human lateral geniculate body (LGB) with its six sickle shaped layers (lam) represents the principal thalamic relay nucleus for the visual system. Cytoarchitectonic analysis serves as the groundtruth for multimodal approaches and studies exploring its function. This technique, however, requires experienced knowledge about human neuroanatomy and is costly in terms of time. Here we mapped the six layers of the LGB manually in serial, histological sections of the BigBrain, a high-resolution model of the human brain, whereby their extent was manually labeled in every 30th section in both hemispheres. These maps were then used to train a deep learning algorithm in order to predict the borders on sections in-between these sections. These delineations needed to be performed in 1 µm scans of the tissue sections, for which no exact cross-section alignment is available. Due to the size and number of analyzed sections, this requires to employ high-performance computing. Based on the serial section delineations, high-resolution 3D reconstruction was performed at 20 µm isotropic resolution of the BigBrain model. The 3D reconstruction shows the shape of the human LGB and its sublayers for the first time at cellular precision. It represents a use case to study other complex structures, to visualize their shape and relationship to neighboring structures. Finally, our results could provide reference data of the LGB for modeling and simulation to investigate the dynamics of signal transduction in the visual system.
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"Toward Computer Simulation of the Whole Cell." In Gene Regulation and Metabolism. The MIT Press, 2002. http://dx.doi.org/10.7551/mitpress/3215.003.0015.

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Slomp, Marcos, Michihiro Mikamo, and Kazufumi Kane. "Fast Local Tone Mapping, Summed-Area Tables and Mesopic Vision Simulation." In Computer Graphics. InTech, 2012. http://dx.doi.org/10.5772/37288.

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Esfahanipour, Akbar, and Ali Reza Montazemi. "Cognitive Mapping in Support of Intelligent Information Systems." In Advanced Methodologies and Technologies in Artificial Intelligence, Computer Simulation, and Human-Computer Interaction, 678–91. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-7368-5.ch051.

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This chapter provides a review of the recent applications and trends on cognitive mapping techniques in support of the design and development of intelligent information systems. Cognitive maps are inference networks, using cyclic directed graphs for knowledge representation and reasoning. Cognitive mapping techniques are widely used to analyze causal systems such as industrial marketing planning, risk management, and product planning. Four knowledge management categories are adopted in this chapter to portray different applications of cognitive mapping techniques in the design and development of intelligent information systems. These four categories are knowledge creation, knowledge storage/retrieval, knowledge transfer, and knowledge application.
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Rojo, Lorenzo Fernández, Luis Paya, Francisco Amoros, and Oscar Reinoso. "Using Global Appearance Descriptors to Solve Topological Visual SLAM." In Advanced Methodologies and Technologies in Artificial Intelligence, Computer Simulation, and Human-Computer Interaction, 1127–40. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-7368-5.ch082.

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Mobile robots have extended to many different environments, where they have to move autonomously to fulfill an assigned task. With this aim, it is necessary that the robot builds a model of the environment and estimates its position using this model. These two problems are often faced simultaneously. This process is known as SLAM (simultaneous localization and mapping) and is very common since when a robot begins moving in a previously unknown environment it must start generating a model from the scratch while it estimates its position simultaneously. This chapter is focused on the use of computer vision to solve this problem. The main objective is to develop and test an algorithm to solve the SLAM problem using two sources of information: (1) the global appearance of omnidirectional images captured by a camera mounted on the mobile robot and (2) the robot internal odometry. A hybrid metric-topological approach is proposed to solve the SLAM problem.
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Conference papers on the topic "Gene mapping – Computer simulation"

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"Rule-Based Modeling and Simulation of Gene Expression Process." In 2020 the 10th International Workshop on Computer Science and Engineering. WCSE, 2020. http://dx.doi.org/10.18178/wcse.2020.06.054.

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Guevara, Mauricio, and Edgar E. Vallejo. "A computer simulation model of gene replacement in vector populations." In 2008 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE). IEEE, 2008. http://dx.doi.org/10.1109/bibe.2008.4696743.

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Davis, Lloyd M., John G. Williams, and Don T. Lamb. "Computer simulation of gene detection without PCR by single molecule detection." In BiOS Europe '98, edited by Francesco Baldini, Nathan I. Croitoru, Martin Frenz, Ingemar Lundstroem, Mitsunobu Miyagi, Riccardo Pratesi, and Otto S. Wolfbeis. SPIE, 1999. http://dx.doi.org/10.1117/12.336943.

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Chen, Zhiguang, Nong Xiao, Fang Liu, and Yimo Du. "PBFTL: The Page to Block Mapping FTL with Low Response Time." In Simulation of Computer and Telecommunication Systems (MASCOTS). IEEE, 2011. http://dx.doi.org/10.1109/mascots.2011.31.

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Lv, Gang, Kunlun Wang, and Dengsheng Liu. "An Improved Method of Multi-strategy Ontology Mapping." In 2010 Second International Conference on Computer Modeling and Simulation (ICCMS). IEEE, 2010. http://dx.doi.org/10.1109/iccms.2010.59.

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Westermann, Peter, Ludwig Schwoerer, and Andre Kaufmann. "Applying Data Mapping Techniques to Vector DSPs." In 2007 International Conference on Embedded Computer Systems: Architectures, Modeling and Simulation. IEEE, 2007. http://dx.doi.org/10.1109/icsamos.2007.4285727.

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Kumar, P., and M. P. Desai. "Learning based address mapping for improving the performance of memory subsystems." In amp; Simulation of Computer and Telecommunication Systems (MASCOTS). IEEE, 2009. http://dx.doi.org/10.1109/mascot.2009.5366234.

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Cao, Bu-Qing, and Jian-Xun Liu. "Currency Recognition Modeling Research Based on BP Neural Network Improved by Gene Algorithm." In 2010 Second International Conference on Computer Modeling and Simulation (ICCMS). IEEE, 2010. http://dx.doi.org/10.1109/iccms.2010.270.

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Bountas, Dimitris, Georgios Stamoulis, and Nestoras Evmorfopoulos. "A macromodel technique for VLSI dynamic simulation by mapping pre-characterized transitions." In 2008 IEEE International Conference on Computer Design (ICCD). IEEE, 2008. http://dx.doi.org/10.1109/iccd.2008.4751900.

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Mohamed, Syazilawati, and Wahyudi Martono. "Design of Post-Mapping Fusion Classifiers for Voice-Based Access Control System." In 2010 12th International Conference on Computer Modelling and Simulation. IEEE, 2010. http://dx.doi.org/10.1109/uksim.2010.55.

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Reports on the topic "Gene mapping – Computer simulation"

1

Pratt, L. R., A. E. Garcia, and G. Hummer. Computer simulation of protein solvation, hydrophobic mapping, and the oxygen effect in radiation biology. Office of Scientific and Technical Information (OSTI), August 1997. http://dx.doi.org/10.2172/524859.

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