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CasesDatabase – one year, 30,000 case reports and a whole mine of valuable clinical data

CasesDatabase – one year, 30,000 case reports and a whole mine of valuable clinical data | Databases & Softwares | Scoop.it
EPFL Library (SV)'s insight:

"Case reports describe in detail an individual patient’s diagnosis and treatment; they can provide first evidence of new medical conditions or emergent diseases, and can help in understanding the mechanisms of disease and in the identification of adverse drug reactions"

 

"CasesDatabase: the only database of peer-reviewed, full-text searchable medical case reports."

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The database of Genotypes and Phenotypes (dbGaP) - NCBI

EPFL Library (SV)'s insight:

"A repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype."

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#Article "An online database for plant image analysis software tools" - Plant Methods

Recent years have seen an increase in methods for plant phenotyping using image analyses. These methods require new software solutions for data extraction and treatment.
EPFL Library (SV)'s insight:

"The plant-image-analysis.org database provides an overview of existing plant image analysis software. The aim of such a toolbox is to help users to find solutions, and to provide developers a way to exchange and communicate about their work. "

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#Article "Browsing (Epi)genomes: A Guide to Data Resources and Epigenome Browsers for Stem Cell Researchers" - Cell Stem Cell

EPFL Library (SV)'s insight:

"The goal of this review is to provide the reader with information on where to find many of the data sets and how to utilize the various (epi)genome browsers for display and initial analysis. We provide selected examples to highlight key features and demonstrate the application of these browsers to stem cell biology."

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#Article "Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein..." - Molecular & Cellular Proteomics

Europe PubMed Central (Europe PMC) is an archive of life sciences journal literature.
EPFL Library (SV)'s insight:

"The Proteomics Standards Initiative has recently released the mzIdentML data standard for representing peptide and protein identification results, for example, created by a search engine. When a new standard format is produced, it is important that software tools are available that make it straightforward for laboratory scientists to use it routinely and for bioinformaticians to embed support in their own tools. Here we report the release of several open-source Java-based software packages based on mzIdentML: ProteoIDViewer, mzidLibrary, and mzidValidator."

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JCB DataViewer

JCB DataViewer | Databases & Softwares | Scoop.it
JCB DataViewer is the world's first web-based publication system for viewing original image data.
EPFL Library (SV)'s insight:

"The JCB DataViewer is an image hosting and visualization platform for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the "scores" from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard."

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Cool Season Food Legume Genome Database

Cool Season Food Legume Genome Database | Databases & Softwares | Scoop.it
EPFL Library (SV)'s insight:

"This database is being developed to serve as a resource to facilitate cool season food legume plant breeding and research by providing centralized, integrated access to relevant genetic and genomic information"

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iPfam: a database of protein family and domain interactions found in the Protein Data Bank

EPFL Library (SV)'s insight:

"It catalogues Pfam domain interactions based on known 3D structures that are found in the Protein Data Bank, providing interaction data at the molecular level"

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NECTAR intro

NECTAR intro | Databases & Softwares | Scoop.it
EPFL Library (SV)'s insight:

""A database and web application to annotate disease-related and functionally important amino acids in human proteins"

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#Article "Ribosomal Database Project: data and tools for high throughput rRNA analysis" - Nucleic Acids Research

#Article "Ribosomal Database Project: data and tools for high throughput rRNA analysis" - Nucleic Acids Research | Databases & Softwares | Scoop.it
EPFL Library (SV)'s insight:

"Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines"

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#Article "Comparison of software packages for detecting differential expression in RNA-seq studies" - Briefings in Bioinformatics

Europe PubMed Central (Europe PMC) is an archive of life sciences journal literature.
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#Article "Chemical annotation of small and peptide-like molecules at the Protein Data Bank" - Database

#Article "Chemical annotation of small and peptide-like molecules at the Protein Data Bank" - Database | Databases & Softwares | Scoop.it
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Bio-Formats: software tool for reading microscopy image data files

Bio-Formats: software tool for reading microscopy image data files | Databases & Softwares | Scoop.it
EPFL Library (SV)'s insight:

"Bio-Formats is a software tool for reading microscopy image data files in any format and writing image data using standardized, open formats"

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