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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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| Simon A. Mathias; Paul E. Hardisty; Mark R. Trudell; Robert W. Zimmerman. |
| If geo-sequestration of CO2 is to be employed as a key emissions reduction method in the global effort to mitigate climate change, simple yet robust screening of the risks of disposal in brine aquifers will be needed. There has been significant development of simple analytical and semi-analytical techniques to support screening analysis and performance assessment for potential carbon sequestration sites. These techniques have generally been used to estimate the size of CO2 plumes for the purpose of leakage rate estimation. A common assumption has been that both the fluids and the geological formation are incompressible. Consequently, calculation of pressure distribution requires the specification of an arbitrary radius of influence. In this talk, a new... |
| Tipo: Presentation |
Palavras-chave: Earth & Environment. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2634/version/1 |
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| Raf Aerts; Eva November; Martin Hermy; Jozef Deckers; Mitiku Haile; Bart Muys. |
| Management strategies aimed at rehabilitating degraded and cleared forests often rely on temporary or permanent exclusion of herbivores (wild animals, livestock or both). But in many cases, this simple management technique is not sufficient to induce ecosystem restoration: many negative effects keep the ecosystem in a suboptimal, low biomass state. The presence of such stable states requires restoration measures to act on multiple stress factors simultaneously.

Compensating for all limiting factors is neither practically nor economically feasible. But detailed knowledge about the autoecology of tree species – i.e. their site requirements, regeneration strategies and recruitment dynamics – may be... |
| Tipo: Presentation |
Palavras-chave: Earth & Environment; Plant Biology. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2437/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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| Dominique Bachelet; James Strittholt; Tosha Comendant. |
| Monitoring datasets is essential to detect changes that are occurring and identify thresholds that cause them, but scientists around the world are now generating large volumes of data that vary in quality, format, supporting documentation, and accessibility. Moreover, diverse models are being run at various spatial and temporal scales to try and understand past climate variability and its impacts, generate future climate and land use scenarios, and project potential future impacts to the planet. Conservation practitioners and land managers are struggling to synthesize this wealth of information, identify relevant and usable datasets, and translate evolving science results into on-the-ground climate-aware strategies.
In partnership with... |
| Tipo: Presentation |
Palavras-chave: Earth & Environment. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5256/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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| Robert Ribe; Rebecca Ford; Kath Williams. |
| Major controversies have erupted in recent years about extensive and intensive timber harvesting programs in Tasmania and the U.S. Pacific Northwest. These conflicts have centered on ecological impacts and both regions have responded by adopting similar programs of “ecological forestry.” Both programs emphasize the retention of varying amounts of trees in aggregated or dispersed patterns within harvests, and seek to “life boat” mature-forest habitat functions across some harvest prescriptions. Are these programs garnering similar public acceptance? Do people with similar ideologies judge the acceptability of forests similarly in both regions? Do perceptions differ between regions due to differences in... |
| Tipo: Presentation |
Palavras-chave: Earth & Environment. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3744/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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| 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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| 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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| Trish Whetzel. |
| In order to effectively search, retrieve, and analyze data oftentimes it is curated and tagged with ontology terms. However, the amount of effort to curate the existing set of data resources is beyond the limits of purely manual curation. We present three ontology-based tools developed by the National Center for Biomedical Ontology to enhance the curation workflow: Ontology Widgets, Notes, and the Annotator. The Ontology Widgets provide a mechanism to use ontologies in Web-based forms without the need to locally parse and store the ontology. The widgets provide a variety of functionality including term autocompletion and ontology visualization. The Ontology Widgets are implemented for all BioPortal ontologies, including those from the OBO Foundry and... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5213/version/1 |
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| Asif Husain Naqvi; Hardik H. Sheth; Vijay Kumar; Suchindran H S; Vivek Gupta. |
| The tumor suppressor protein p53 is a transcription factor that plays a key role in the prevention of cancer development. The p53 cancer mutation Y220C induces formation of a cavity on the protein's surface that can accommodate stabilizing small molecules. We have attempted with the help of virtual screening and molecular docking approach using Lamarckian Genetic Algorithm to elucidate the extent of specificity of p53 cancer mutation Y220C towards different class of Phenothiazines (an anti-cancer agent). 

The 393 residue p53 tumor suppressor protein exists in a dynamic equilibrium to form homotetramers. Each chain comprises several functional domains. The N terminal part of the protein consists of the... |
| Tipo: Presentation |
Palavras-chave: Cancer; Pharmacology; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6135/version/1 |
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| Bart Vandenbossche; Björn Niere; Stefan Vidal. |
| _Heterodera schachtii_, the white beet cyst nematode, is considered as one of the most important nematode pests on sugar beet and is present in most sugar-beet growing areas. The yellow beet cyst nematode, _Heterodera betae_, is less prevalent but has also been found damaging beet crops. However, knowledge about the damage potential and population dynamics of the yellow beet cyst nematode is limited. The amount of damage inflicted by nematodes is dependent on different factors. An important factor influencing the sugar beet yield decline by beet cyst nematodes is the soil temperature. Relationships between soil temperature, _H. schachtii_ population densities and sugar beet yields have been reported previously. Until present, most studies have been... |
| Tipo: Presentation |
Palavras-chave: Plant Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5744/version/1 |
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| Peter Ralph; Graham Coop; Carl Boettiger. |
| Phylogenetic comparative methods have become all but ubiquitous in only a few decades, forcing us to reconsider if information from a phylogenetic tree can justify the results. Existing approaches to this question have been inadequate and do not scale with tree size or the ability to resolve branches. For instance, selection between phylogenetic models typically based on information criteria fails to adequately reflect this uncertainty, and can lead to preference for arbitrarily complicated models. Common measures of phylogenetic signal tend to characterize the goodness-of-fit of a Brownian motion model to the data, rather than indicate whether the data is sufficient to confidently distinguish between different hypotheses. We present a Monte Carlo based... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6453/version/1 |
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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. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5011/version/1 |
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| Registros recuperados: 1.470 | |
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