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| Registros recuperados: 1.312 | |
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| Michael Hucka. |
| SBML is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations.

The evolution of SBML continues. The latest iteration is SBML Level 3, a modular language consisting of a Core and optional "packages" that add topic-specific features to the Core to support more specialized models and application areas. In this presentation, I provide a very brief overview of SBML Level 3 activity areas. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5011/version/2 |
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| Kirtan P. Dave. |
| High-throughput genomic technology has rapidly become a major tool for the study of breast cancer. The recent development gene expression microarray and related technology provide to an opportunity to perform more detail profiling of the disease However, whole-genome approaches are still relatively new and critics have been quick to highlight, non-overlapping results from groups testing similar hypotheses. In this canopy, cluster analysis helps to reduce complex multivariate data and may be used to devise in the development of classification systems or taxonomies by gene ontology. |
| Tipo: Poster |
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4936/version/1 |
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| Antti Niemi; Andrey Krokhotin. |
| Alzheimer's disease has a devastating impact on its victims by causing severe neurodegeneration in the brain that leads to a certain death. Only in a small number of cases can the origin be traced to a variety of genetic mutations, for the greater part the reasons for its onset are unclear.The defining factor is the formation of extracellular senile amyloid plaques in the brain, but therapeutic approaches to remove them remain to be shown effective in humans. Here we investigate physical processes that are involved in the release of the extracellular amyloid, by scrutinizing the intracellular domain of its precursor protein. We identify a phenomenon that has never before been discussed in the context of protein research: Like ice and water... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Neuroscience; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6030/version/1 |
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| Adrian Paschke; Zhili Zhao. |
| Virtual e-Science infrastructures supporting Web-based scientific workflows are an example for knowledge-intensive collaborative and weakly-structured processes where the interaction with the human scientists during process execution plays a central role. In this paper we propose the lightweight dynamic user-friendly interaction with humans during execution of scientific workflows via the low-barrier approach of Semantic Wikis as an intuitive interface for non-technical scientists. Our Process Makna Semantic Wiki system is a novel combination of a business process management system adapted for scientific workflows with a Corporate Semantic Web Wiki user interface supporting knowledge intensive human interaction tasks during scientific workflow execution. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5633/version/1 |
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| Sk. Sarif Hassan; Pabitra Pal Choudhury; Arunava Goswami. |
| As per conservative estimate, approximately (51-105) Olfactory Receptors (ORs) loci are present in human genome occurring in clusters. These clusters are apparently unevenly spread as mosaics over 21 pair of human chromosomes. Olfactory Receptor (OR) gene families which are thought to have expanded for the need to provide recognition capability for huge number of pure and complex odorants. ORs form the largest known multi-gene family in the human genome. Recent studies have shown that 388 full length and 414 OR pseudo-genes are present in these OR genomic clusters. In this paper, the authors report a classification method for all human ORs based on their sequential quantitative information like presence of poly strings of nucleotides bases, long range... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5475/version/1 |
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| Anne-Lise Veuthey; Violaine Pillet; Yum Lina Yip; Patrick Ruch. |
| A text mining group has been set up at the Swiss Institute of Bioinformatics, with objective to develop and adapt information retrieval and extraction tools to help Swiss-Prot curators in their daily annotation work. After over 7 year activities, this group has gathered a significant amount of experience about the need in text mining for biocuration.

The first observation we made is that there is no “in-a-box” solution which can satisfy every needs. Each curator has his/her own strategy to find information from the literature and none of the existing information retrieval systems is able to compete with it, more for reason of habits than for reason of performance. Second observation: to be... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3166/version/1 |
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| Roderic D. M. Page. |
| Although the Web has transformed science publishing, scientific papers themselves are still essentially "black boxes", with much of their content intended for human readers only. Typically, computer-readable metadata associated with an article is limited to bibliographic details. By expanding article metadata to include taxonomic names, identifiers for cited material (e.g., publications, sequences, specimens, and other data), and geographical coordinates, publishers could greatly increase the scientific value of their digital content. At the same time this will provide novel ways for users to discover and navigate through this content, beyond the relatively limited linkage provided by bibliographic... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3173/version/1 |
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| M. S. Jeevitesh; Narayan Behera; Justin Jose; Krishna Kant; Alpana Dey. |
| Multiple Sequence Alignment gives insight into evolutionary, structural and functional relationships among the proteins. Here, a novel Protein Alignment by Stochastic Algorithm (PASA) is developed. Evolutionary operators of a genetic algorithm, namely, mutation and selection are utilized in combining the output of two most important sequence alignment programs and then developing an optimized new algorithm. Efficiency of protein alignments is evaluated in terms of Total Column score which is equal to the number of correctly aligned columns between a test alignment and the reference alignment divided by the total number of columns in the reference alignment. The PASA optimizer achieves, on an average, significant better alignment over the well known... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4258/version/1 |
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| Martin Gräßlin. |
| In computational biology there is a strong need to exchange quantitative models of biological processes in a standardized way. For storing and retrieving peer-reviewed models the BioModels Database has been available for several years. But at the moment there is no tool available to bring a model from development in the lab directly to the peer-reviewed online resource.

The JUMMP (JUst a Model Management Platform) project aims at providing a generic model management platform for any standardized model file. Through a well-elaborated security layer models can be developed and shared privately and later on be made available to the curation process and the broader community. Each change to a model is recorded in a version... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6371/version/1 |
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| Kentaro Onizuka. |
| The Entropic Landscape Analysis was applied to the prion protein sequences of various mammals in order to detect potential sites of variants that would be responsible for the susceptibility of prion disease infection. Among familiar mammals, canines including dogs have been demonstrating strong resistance to prion diseases. Among the canine specifc substitutions the entropic landscape analysis pinpoints the substitutions Asn104Gly and Ser107Asn having the biggest impact to the conformational transition and stability. Although they must be further corroborated by experiments in vivo et vitro, the results are demonstrating that the entropic landscape analysis is useful enough to screen substitutions and polymorphisms potentially relevant to conformational... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Neuroscience; Bioinformatics; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3043/version/1 |
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| Chisato Yamasaki; Jun-ichi Takeda; Takuya Habara; Makoto Ogawa; Akiko Noda; Ryuichi Sakate; Katsuhiko Murakami; Tadashi Imanishi; Takashi Gojobori. |
| H-Invitational Database (H-InvDB: "http://www.h-invitational.jp/":http://www.h-invitational.jp/) is a comprehensive annotation resource for human transcriptome. By extensive analyses of all human transcripts, we provide curated annotations of human genes, transcripts and proteins that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. The latest release of H-InvDB (release 7.0) provides annotation for 296,912 human transcripts in... |
| Tipo: Presentation |
Palavras-chave: Genetics & Genomics; Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5272/version/1 |
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| Pinar Wennerberg; Manuel Möller; Sonja Zillner. |
| To realize applications such as semantic medical image search different domain ontologies are necessary that provide complementary knowledge about human anatomy and radiology. Consequently, integration of these different but nevertheless related types of medical knowledge from disparate domain ontologies becomes necessary. Ontology alignment is one way to achieve this objective. Our approach for aligning medical ontologies has three aspects: (a) linguistic-based, (b) corpus-based, and (c) dialogue-based. We briefly report on the linguistic alignment (i.e. the first aspect) using an ontology on human anatomy and a terminology on radiology. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3521/version/2 |
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| Mary Shimoyama; Melinda Dwinell; Howard Jacob. |
| There has been an emergence of multiple large scale phenotyping projects in the rat model organism community as well as renewed interest in the ongoing phenotype data generated by thousands of researchers using hundreds of rat strains worldwide. Unfortunately, this data is scattered and is neither described nor formatted in a standardized manner. A system to integrate complex phenotype data from multiple sources and facilitate data mining and analysis is being developed using multiple ontologies.

*Introduction*
The potential value of integrating phenotype data from multiple sources (different laboratories, varying techniques to measure similar phenotypes, multiple strains) is enormous. Presented here is... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3554/version/2 |
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| David Nickerson; Dongxue Amy You. |
| libSedML is a collection of libraries and tools developed in support of the Simulation Experiment Markup Language ("SED-ML":http://sed-ml.org/). "libSedML":http://libsedml.sourceforge.net/ is implemented in C# and provides libraries for processing SED-ML documents and for running the numerical simulations required for the encoded simulation experiment(s). SED-ML supports models encoded in any encoding format, although predominantly expected to be an XML based encoding. To date, however, libSedML has only supported performing simulations using models encoded in the Systems Biology Markup Language ("SBML":http://sbml.org/). The presented project looked at using the "CellML... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5897/version/1 |
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| Nicolas Le Novere. |
| The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all the aspects of modeling in biology.

Building on the experience of mature projects, which already have stable specifications, software support, user-base and community governance, COMBINE will help foster or support fledging efforts aimed at filling gaps or new needs. As those efforts mature, they may become part of the core set of COMBINE... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6332/version/1 |
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| Andras Gelencser; Themistoklis Prodromakis; Christofer Toumazou; Tamas Roska. |
| In this paper we present a biorealistic model for the first part of the early vision processing by incorporating memristive nanodevices. The architecture of the proposed network is based on the organisation and functioning of the outer plexiform layer (OPL) in the vertebrate retina. We demonstrate that memristive devices are indeed a valuable building block for neuromorphic architectures, as their highly non-linear and adaptive response could be exploited for establishing ultra-dense networks with similar dynamics to their biological counterparts. We particularly show that hexagonal memristive grids can be employed for faithfully emulating the smoothing-effect occurring at the OPL for enhancing the dynamic range of the system. In addition, we employ a... |
| Tipo: Manuscript |
Palavras-chave: Neuroscience; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6664/version/1 |
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| Marco Cosentino Lagomarsino; Alessandro Sellerio; Philip Heijning; Bruno Bassetti. |
| The availability of many genome sequences gives us abundant information, which is, however, very difficult to decode. As a consequence, in order to advance our understanding of biological processes at the whole-cell scale, it becomes very important to develop higher-level, synthetic descriptions of the contents of a genome. At the protein level, an effective scale of description is provided by protein domains. Domains are independent unit-shapes (or "folds") forming proteins. They are structurally stable and have thermodynamic origin. A domain determines a set of potential functions and interactions for the protein that carries it, for example DNA- or protein-binding capability or catalytic sites. Protein domains are found on genomes with... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Genetics & Genomics; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1376/version/1 |
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| Registros recuperados: 1.312 | |
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