Pub Date : 2000-11-08DOI: 10.1109/BIBE.2000.889612
F. Erzen, G. Birol, A. Çinar
Glucose-insulin interaction in an insulin-dependent diabetic patient has been simulated using an overall and a detailed model based on pharmacokinetic diagrams of insulin and glucose. Both models are capable of predicting the blood glucose and insulin levels, total glucose uptake and the renal glucose excretion. The simulator is integrated with a graphical user interface to provide a user-friendly environment. The package may be used to perform virtual experiments with various characteristics, diet and exercise conditions.
{"title":"Simulation studies on the dynamics of diabetes mellitus","authors":"F. Erzen, G. Birol, A. Çinar","doi":"10.1109/BIBE.2000.889612","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889612","url":null,"abstract":"Glucose-insulin interaction in an insulin-dependent diabetic patient has been simulated using an overall and a detailed model based on pharmacokinetic diagrams of insulin and glucose. Both models are capable of predicting the blood glucose and insulin levels, total glucose uptake and the renal glucose excretion. The simulator is integrated with a graphical user interface to provide a user-friendly environment. The package may be used to perform virtual experiments with various characteristics, diet and exercise conditions.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116565324","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 : 2000-11-08DOI: 10.1109/BIBE.2000.889620
R. Chbeir, Franck Favetta
Medical Imaging suffers from different problems. This paper explores the authors' solution that aims to provide efficient retrieval of medical imaging. Depending on the user, the same image can be described through different views. In essence, an image can be described on the basis of either low-level properties, such as texture or color; context, such as date of acquisition or author; or semantic content, such as real-world objects and relations. The authors' approach consists of providing a global description solution capable of integrating different dimensions (or views) of a medical image. The description problem of medical images during both storage and retrieval processes is studied. Few proposed solutions take into consideration the heterogeneity of user competence (physician, researcher, student, etc.) and the necessity of a high expressive power for medical imaging description. For example, spatial content in terms of relationships in surgical or radiation therapy of brain tumors is very decisive because the location of a tumor has profound implications on a therapeutic decision. Visual solutions are recommended and are the most appropriated for non computer-scientist users. However, current visual languages suffer from several problems, especially ambiguities generated by the user and/or the system at different levels of image description, imprecision and no respect of the integrity of spatial relations. This framework exposes the authors' solution showing how this problematic can be resolved. An implementation has been realized to prove their proposition.
{"title":"A global description of medical image with high precision","authors":"R. Chbeir, Franck Favetta","doi":"10.1109/BIBE.2000.889620","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889620","url":null,"abstract":"Medical Imaging suffers from different problems. This paper explores the authors' solution that aims to provide efficient retrieval of medical imaging. Depending on the user, the same image can be described through different views. In essence, an image can be described on the basis of either low-level properties, such as texture or color; context, such as date of acquisition or author; or semantic content, such as real-world objects and relations. The authors' approach consists of providing a global description solution capable of integrating different dimensions (or views) of a medical image. The description problem of medical images during both storage and retrieval processes is studied. Few proposed solutions take into consideration the heterogeneity of user competence (physician, researcher, student, etc.) and the necessity of a high expressive power for medical imaging description. For example, spatial content in terms of relationships in surgical or radiation therapy of brain tumors is very decisive because the location of a tumor has profound implications on a therapeutic decision. Visual solutions are recommended and are the most appropriated for non computer-scientist users. However, current visual languages suffer from several problems, especially ambiguities generated by the user and/or the system at different levels of image description, imprecision and no respect of the integrity of spatial relations. This framework exposes the authors' solution showing how this problematic can be resolved. An implementation has been realized to prove their proposition.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"41 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123876964","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 : 2000-11-08DOI: 10.1109/BIBE.2000.889593
J. Reich
While I was investigating methods to construct 'controlled vocabularies' and 'ontologies', I created a set of 'ontological design patterns'. These engineering design patterns and terminologies specific to some protein families were represented within the object-oriented programming language CLOS (Common Lisp Object System). Within bioinformatics, 'ontologies' are represented on the World Wide Web (WWW) in terminology files that are tagged and marked up by the syntax and keywords of HTML or XML. Therefore, I specified, designed and partially implemented a compiler to translate specified 'controlled vocabularies' and 'ontologies' represented in CLOS and structured by 'ontological design patterns' into the language called 'Simple Hypertext Ontology Extension' (SHOE). First results show that a 'one-step-look-ahead' parser can automatically print the original CLOS version of the 'ontologies' into a file reorganised according to the SHOE syntax.
{"title":"A compiler to transfer controlled vocabularies and ontologies represented in an object-oriented programming language into text mark-up languages","authors":"J. Reich","doi":"10.1109/BIBE.2000.889593","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889593","url":null,"abstract":"While I was investigating methods to construct 'controlled vocabularies' and 'ontologies', I created a set of 'ontological design patterns'. These engineering design patterns and terminologies specific to some protein families were represented within the object-oriented programming language CLOS (Common Lisp Object System). Within bioinformatics, 'ontologies' are represented on the World Wide Web (WWW) in terminology files that are tagged and marked up by the syntax and keywords of HTML or XML. Therefore, I specified, designed and partially implemented a compiler to translate specified 'controlled vocabularies' and 'ontologies' represented in CLOS and structured by 'ontological design patterns' into the language called 'Simple Hypertext Ontology Extension' (SHOE). First results show that a 'one-step-look-ahead' parser can automatically print the original CLOS version of the 'ontologies' into a file reorganised according to the SHOE syntax.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130055871","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 : 2000-11-08DOI: 10.1109/BIBE.2000.889585
L. Wong
We describe the Pizzkell/Kleisli suite of software for bioinformatics data integration. We also present a protein interaction extraction system to illustrate the power of this software in the rapid construction of bioinformatics applications.
{"title":"Kleisli: its exchange format, supporting tools, and an application in protein interaction extraction","authors":"L. Wong","doi":"10.1109/BIBE.2000.889585","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889585","url":null,"abstract":"We describe the Pizzkell/Kleisli suite of software for bioinformatics data integration. We also present a protein interaction extraction system to illustrate the power of this software in the rapid construction of bioinformatics applications.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"55 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130226207","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 : 2000-11-08DOI: 10.1109/BIBE.2000.889606
A. Bansal
Describes a framework for the automated reconstruction of metabolic pathways using information about orthologous and homologous gene groups derived by the automated comparison of whole genomes archived in GenBank. The method integrates automatically derived orthologs, orthologous and homologous gene groups (), the biochemical pathway template available in the Kegg database (), and enzyme information derived from the SwissProt enzyme database () and the Ligand database (). The technique is useful to identify refined metabolic pathways based on operons, and to derive the non-enzymatic genes within a group of enzymes. The technique has been illustrated by a comparison between the E. coli and B. subtilis genomes.
{"title":"A framework of automated reconstruction of microbial metabolic pathways","authors":"A. Bansal","doi":"10.1109/BIBE.2000.889606","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889606","url":null,"abstract":"Describes a framework for the automated reconstruction of metabolic pathways using information about orthologous and homologous gene groups derived by the automated comparison of whole genomes archived in GenBank. The method integrates automatically derived orthologs, orthologous and homologous gene groups (<http:www.mcs.kent.edu//spl sim/arvind/orthos.html>), the biochemical pathway template available in the Kegg database (<http://www.genome.ad.jp/>), and enzyme information derived from the SwissProt enzyme database (<http://expasy.hcuge.ch/>) and the Ligand database (<http://www.genome.ad.jp/>). The technique is useful to identify refined metabolic pathways based on operons, and to derive the non-enzymatic genes within a group of enzymes. The technique has been illustrated by a comparison between the E. coli and B. subtilis genomes.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"134 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127409391","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 : 2000-11-08DOI: 10.1109/BIBE.2000.889611
T. Jiang, Xiaodong Li, F. Kruggel
The authors compare the performance of three typical and widely used optimization techniques for a specific MEG source localization problem. Firstly, they introduce a hybrid algorithm by combining genetic and local search strategies to overcome disadvantages of conventional genetic algorithms. Secondly, they apply the tabu search: a widely used optimization methods in combinational optimization and discrete mathematics, to source localization. To the best of the authors' knowledge, this is the first attempt in the literature to apply tabu search to MEG/EEG source localization. Thirdly, in order to further comparison of the performance of above algorithms, simulated annealing is also applied to MEG source localization problem. The computer simulation results show that the authors' local genetic algorithm is the most effective approach to dipole location.
{"title":"Global optimization approaches to MEG source localization","authors":"T. Jiang, Xiaodong Li, F. Kruggel","doi":"10.1109/BIBE.2000.889611","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889611","url":null,"abstract":"The authors compare the performance of three typical and widely used optimization techniques for a specific MEG source localization problem. Firstly, they introduce a hybrid algorithm by combining genetic and local search strategies to overcome disadvantages of conventional genetic algorithms. Secondly, they apply the tabu search: a widely used optimization methods in combinational optimization and discrete mathematics, to source localization. To the best of the authors' knowledge, this is the first attempt in the literature to apply tabu search to MEG/EEG source localization. Thirdly, in order to further comparison of the performance of above algorithms, simulated annealing is also applied to MEG source localization problem. The computer simulation results show that the authors' local genetic algorithm is the most effective approach to dipole location.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122145787","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 : 2000-11-08DOI: 10.1109/BIBE.2000.889590
C. Raguenaud, J. Kennedy, P. Barclay
M.R. Pullen et al. (2000) have designed a new model of plant taxonomy (called Prometheus); it supports multiple overlapping classifications, and distinguishes the process of naming from classifying. The concepts identified in this taxonomic model necessitated the design of a new database model - the Prometheus Object-Oriented Model (POOM) - to represent and manipulate the data. POOM is an extended object-oriented model which emphasises relationships, thereby providing graph behaviour in an object-oriented database and providing an expressive means of defining relationships between objects. Additionally, the Object Query Language (OQL) is extended to the Prometheus Object-Oriented Language (POOL) in order to provide unified querying of object-oriented graph structures. This paper presents a taxonomic database system designed in terms of the concepts offered by POOM. Through examples we show how the representation of the semantics and processes of taxonomy, not possible using existing data models, can be supported. Example POOL queries highlight the need for the extended features for manipulating relationships, graph structures and complex objects such as are found in taxonomies.
{"title":"The Prometheus taxonomic database","authors":"C. Raguenaud, J. Kennedy, P. Barclay","doi":"10.1109/BIBE.2000.889590","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889590","url":null,"abstract":"M.R. Pullen et al. (2000) have designed a new model of plant taxonomy (called Prometheus); it supports multiple overlapping classifications, and distinguishes the process of naming from classifying. The concepts identified in this taxonomic model necessitated the design of a new database model - the Prometheus Object-Oriented Model (POOM) - to represent and manipulate the data. POOM is an extended object-oriented model which emphasises relationships, thereby providing graph behaviour in an object-oriented database and providing an expressive means of defining relationships between objects. Additionally, the Object Query Language (OQL) is extended to the Prometheus Object-Oriented Language (POOL) in order to provide unified querying of object-oriented graph structures. This paper presents a taxonomic database system designed in terms of the concepts offered by POOM. Through examples we show how the representation of the semantics and processes of taxonomy, not possible using existing data models, can be supported. Example POOL queries highlight the need for the extended features for manipulating relationships, graph structures and complex objects such as are found in taxonomies.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124830417","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 : 2000-11-08DOI: 10.1109/BIBE.2000.889588
Alexander Hinneburg, D. Keim, W. Brandt
In the past, a good number of rotamer libraries have been published, which allow a deeper understanding of the conformational behavior of amino acid residues in proteins. Since the number of available high-resolution X-ray protein structures has grown significantly over the last years, a more comprehensive analysis of the conformational behavior is possible today. In this paper, we present a method to compile a new class of rotamer libraries for detecting interesting relationships between residue conformations and their sequential context in proteins. The method is based on a new algorithm for clustering residue conformations. To demonstrate the effectiveness of our method, we apply our algorithm to a library consisting of all 8000 tripeptide fragments formed by the 20 native amino acids. The analysis shows some very interesting new results, namely that some specific tripeptide fragments show some unexpected conformation of residues instead of the highly preferred conformation. In the neighborhood of two asparagine residues, for example, threonine avoids the conformation which is most likely to occur otherwise. The new insights obtained by the analysis are important in understanding the formation and prediction of secondary structure elements and will consequently be crucial for improving the state-of-the-art of protein folding.
{"title":"Clustering 3D-structures of small amino acid chains for detecting dependences from their sequential context in proteins","authors":"Alexander Hinneburg, D. Keim, W. Brandt","doi":"10.1109/BIBE.2000.889588","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889588","url":null,"abstract":"In the past, a good number of rotamer libraries have been published, which allow a deeper understanding of the conformational behavior of amino acid residues in proteins. Since the number of available high-resolution X-ray protein structures has grown significantly over the last years, a more comprehensive analysis of the conformational behavior is possible today. In this paper, we present a method to compile a new class of rotamer libraries for detecting interesting relationships between residue conformations and their sequential context in proteins. The method is based on a new algorithm for clustering residue conformations. To demonstrate the effectiveness of our method, we apply our algorithm to a library consisting of all 8000 tripeptide fragments formed by the 20 native amino acids. The analysis shows some very interesting new results, namely that some specific tripeptide fragments show some unexpected conformation of residues instead of the highly preferred conformation. In the neighborhood of two asparagine residues, for example, threonine avoids the conformation which is most likely to occur otherwise. The new insights obtained by the analysis are important in understanding the formation and prediction of secondary structure elements and will consequently be crucial for improving the state-of-the-art of protein folding.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129577827","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 : 2000-11-08DOI: 10.1109/BIBE.2000.889613
J. C. D. Conway, C. Coelho, D. Silva, A. O. Fernandes, L. C. G. Andrade, H. Carvalho
Describes the design of a wearable multiparametric physiological signal monitor, a continuously running internetworking system for monitoring multiple physiological parameters of individuals during daily tasks. A prototype, measuring parameters such as electrocardiogram, oximetry and non-invasive blood pressure is now in test. The system performs real-time processing on the signals and can send these parameters to a central monitoring station over a computer network. The relevant points of the control operating system and applications are described, along with future directions for research.
{"title":"Wearable computer as a multi-parametric monitor for physiological signals","authors":"J. C. D. Conway, C. Coelho, D. Silva, A. O. Fernandes, L. C. G. Andrade, H. Carvalho","doi":"10.1109/BIBE.2000.889613","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889613","url":null,"abstract":"Describes the design of a wearable multiparametric physiological signal monitor, a continuously running internetworking system for monitoring multiple physiological parameters of individuals during daily tasks. A prototype, measuring parameters such as electrocardiogram, oximetry and non-invasive blood pressure is now in test. The system performs real-time processing on the signals and can send these parameters to a central monitoring station over a computer network. The relevant points of the control operating system and applications are described, along with future directions for research.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"77 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126686867","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 : 2000-11-08DOI: 10.1109/BIBE.2000.889603
P. Deschavanne, A. Giron, Joseph Vilain, Christine Dufraigne, B. Fertil
The "chaos game representation" (CGR) paradigm has been implemented to display the use of short oligonucleotides in genomes in the form of fractal images. These images can be considered as a genomic signature. Using an unsupervised classification approach, it is shown that short fragments of genomic sequences retain most of the characteristics of the species they come from. It thus appears possible to perform a global comparison of species by means of genome fragments found in databases. The efficiency of this approach is evaluated as a function of the size of the fragments and the length of the oligonucleotides.
采用混沌博弈表示(chaos game representation, CGR)范式，以分形图像的形式展示短寡核苷酸在基因组中的应用。这些图像可以被认为是基因组的特征。使用非监督分类方法，研究表明基因组序列的短片段保留了它们来自的物种的大部分特征。因此，通过在数据库中找到的基因组片段，似乎有可能对物种进行全球比较。这种方法的效率被评价为片段大小和寡核苷酸长度的函数。
{"title":"Genomic signature is preserved in short DNA fragments","authors":"P. Deschavanne, A. Giron, Joseph Vilain, Christine Dufraigne, B. Fertil","doi":"10.1109/BIBE.2000.889603","DOIUrl":"https://doi.org/10.1109/BIBE.2000.889603","url":null,"abstract":"The \"chaos game representation\" (CGR) paradigm has been implemented to display the use of short oligonucleotides in genomes in the form of fractal images. These images can be considered as a genomic signature. Using an unsupervised classification approach, it is shown that short fragments of genomic sequences retain most of the characteristics of the species they come from. It thus appears possible to perform a global comparison of species by means of genome fragments found in databases. The efficiency of this approach is evaluated as a function of the size of the fragments and the length of the oligonucleotides.","PeriodicalId":196846,"journal":{"name":"Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2000-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114941061","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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