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52
Grid-BGC: a Grid-enabled research platform for high-resolution surface weather interpolation and biogeochemical process modeling.
"... Abstract- Over the past three years we have developed a research-quality platform to support scientific users in the configuration, deployment, and analysis of high-resolution simulations of terrestrial biogeochemical processes. The platform consists of a web-based user interface (portal) that organ ..."
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Abstract- Over the past three years we have developed a research-quality platform to support scientific users in the configuration, deployment, and analysis of high-resolution simulations of terrestrial biogeochemical processes. The platform consists of a web-based user interface (portal
SYMPOSIUM SeaBase: A Multispecies Transcriptomic Resource and Platform for Gene Network Inference
"... Synopsis Marine and aquatic animals are extraordinarily useful as models for identifying mechanisms of development and evolution, regeneration, resistance to cancer, longevity and symbiosis, among many other areas of research. This is due to the great diversity of these organisms and their wide-rang ..."
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Synopsis Marine and aquatic animals are extraordinarily useful as models for identifying mechanisms of development and evolution, regeneration, resistance to cancer, longevity and symbiosis, among many other areas of research. This is due to the great diversity of these organisms and their wide
Original article Choosing a genome browser for a Model Organism Database: surveying the
"... As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resourc ..."
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GDB resource, personnel at MaizeGDB surveyed research-ers ’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers ’ needs. Here, we document the survey’s outcomes
RESEARCH ARTICLE Open Access A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus)
"... Background: Snakes provide a unique vertebrate system for studying a diversity of extreme adaptations, including those related to development, metabolism, physiology, and venom. Despite their importance as research models, genomic resources for snakes are few. Among snakes, the Burmese python is the ..."
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Background: Snakes provide a unique vertebrate system for studying a diversity of extreme adaptations, including those related to development, metabolism, physiology, and venom. Despite their importance as research models, genomic resources for snakes are few. Among snakes, the Burmese python
HelmCoP: an online resource for helminth functional genomics and drug and vaccine targets prioritization
- PLoS One
, 2011
"... A vast majority of the burden from neglected tropical diseases result from helminth infections (nematodes and platyhelminthes). Parasitic helminthes infect over 2 billion, exerting a high collective burden that rivals high-mortality conditions such as AIDS or malaria, and cause devastation to crops ..."
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genomic data from plant, animal and human helminthes, to enable researchers to develop strategies for drug, vaccine and pesticide prioritization, while also providing a useful comparative genomics platform. HelmCoP encompasses genomic data from several hosts, including model organisms, along with a
Using eXframe to build Semantic Web Genomics Repositories
"... Abstract. We would to like to present eXframe: a software platform for devel-oping Semantic Web genomics repositories. eXframe is implemented using Drupal 7, an open-source PHP/MySQL based content management system. eXframe provides a user-friendly interface for researchers to enter the infor-mation ..."
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to established biomedical ontologies, which enable extended search across useful parameters such as experiment type, technology platform, model organism, au-thors, genes, proteins, and so forth. Using these mappings and the Drupal RDF modules, eXframe genomics data can be automatically published as Resource
High-Resolution Linkage and Quantitative Trait Locus Mapping Aided by Genome Survey Sequencing: Building Up An Integrative Genomic Framework for a Bivalve Mollusc
, 2013
"... Genetic linkage maps are indispensable tools in genetic and genomic studies. Recent development of genotyping-by-sequencing (GBS) methods holds great promise for constructing high-resolution linkage maps inorganisms lackingextensivegenomicresources. In thepresent study, linkagemapping wasconducted f ..."
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serve as an important platform for improving genome assembly and unifying multiple genomic resources. Our study, therefore, ex-emplifies how to build up an integrative genomic framework in a non-model organism.
Original article CrisprGE: a central hub of CRISPR/Cas-based genome editing
"... CRISPR system is a powerful defense mechanism in bacteria and archaea to provide immunity against viruses. Recently, this process found a new application in intended targeting of the genomes. CRISPR-mediated genome editing is performed by two main components namely single guide RNA and Cas9 protein. ..."
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. Despite the enormous data generated in this area, there is a dearth of high throughput resource. Therefore, we have developed CrisprGE, a central hub of CRISPR/Cas-based genome editing. Presently, this database holds a total of 4680 entries of 223 unique genes from 32 model and other organisms
Conceptual Modeling of Genetic Studies and Pharmacogenetics
"... Abstract. Genetic Studies examine relationships between genetic variation and disease development. Pharmacogenetics studies the responses to drugs against genetic variation. These two lines of research evaluate relationships among genotype, phenotype, and environment regarding subjects. These studie ..."
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by incorporating genomics, experimental data, domain knowledge, research approaches, and interface data for other publicly available resources into one cohesive model. Our model can support diverse biomedical research activities that use both clinical and biomedical data to improve patient care through
The Disease Ontology: fostering interoperability between biological and clinical human disease-related data
"... main data integration through a common standard of human disease terms and their etiological descriptions. Standardized disease descriptors that are integrated across mammalian genomic resources provide a human-readable, machine-interpretable, community-driven disease corpus that unifies the represe ..."
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the representation of human common and rare diseases. The DO is populated by consensus-driven disease data descriptors that incorporate disease terms utilized by genomic and genetic projects and resources engaged in studies to understand the genetics of human disease through the study of model organisms. The DO
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