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<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig3 BlagoderovZooKeys2012 209.jpg|240px]]</div>
<div style="float: left; margin: 0.5em 0.9em 0.4em 0em;">[[File:Fig1 Hernandez BMCSystemsBiology2014 8-Suppl2.jpg|240px]]</div>
'''"[[Journal:No specimen left behind: Industrial scale digitization of natural history collections|No specimen left behind: Industrial scale digitization of natural history collections]]"'''
'''"[[Journal:STATegra EMS: An experiment management system for complex next-generation omics experiments|STATegra EMS: An experiment management system for complex next-generation omics experiments]]"'''


Traditional approaches for digitizing natural history collections, which include both imaging and metadata capture, are both labour- and time-intensive. Mass-digitization can only be completed if the resource-intensive steps, such as specimen selection and databasing of associated [[information]], are minimized. Digitization of larger collections should employ an “industrial” approach, using the principles of automation and crowd sourcing, with minimal initial metadata collection including a mandatory persistent identifier. A new workflow for the mass-digitization of natural history museum collections based on these principles, and using SatScan® tray scanning system, is described. ('''[[Journal:No specimen left behind: Industrial scale digitization of natural history collections|Full article...]]''')<br />
High-throughput [[sequencing]] assays are now routinely used to study different aspects of genome organization. As decreasing costs and widespread availability of sequencing enable more [[Laboratory|laboratories]] to use sequencing assays in their research projects, the number of samples and replicates in these experiments can quickly grow to several dozens of samples and thus require standardized [[Genome informatics|annotation, storage and management]] of preprocessing steps. As a part of the STATegra project, we have developed an Experiment Management System (EMS) for high throughput omics data that supports different types of sequencing-based assays such as RNA-seq, ChIP-seq, Methyl-seq, etc, as well as proteomics and metabolomics data. The STATegra EMS provides metadata annotation of experimental design, samples and processing pipelines, as well as storage of different types of data files, from raw data to ready-to-use measurements. The system has been developed to provide research laboratories with a freely-available, integrated system that offers a simple and effective way for experiment annotation and tracking of analysis procedures. ('''[[Journal:STATegra EMS: An experiment management system for complex next-generation omics experiments|Full article...]]''')<br />
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''Recently featured'':  
''Recently featured'':  
: ▪ [[Journal:No specimen left behind: Industrial scale digitization of natural history collections|No specimen left behind: Industrial scale digitization of natural history collections]]
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Revision as of 14:48, 2 May 2016

Fig1 Hernandez BMCSystemsBiology2014 8-Suppl2.jpg

"STATegra EMS: An experiment management system for complex next-generation omics experiments"

High-throughput sequencing assays are now routinely used to study different aspects of genome organization. As decreasing costs and widespread availability of sequencing enable more laboratories to use sequencing assays in their research projects, the number of samples and replicates in these experiments can quickly grow to several dozens of samples and thus require standardized annotation, storage and management of preprocessing steps. As a part of the STATegra project, we have developed an Experiment Management System (EMS) for high throughput omics data that supports different types of sequencing-based assays such as RNA-seq, ChIP-seq, Methyl-seq, etc, as well as proteomics and metabolomics data. The STATegra EMS provides metadata annotation of experimental design, samples and processing pipelines, as well as storage of different types of data files, from raw data to ready-to-use measurements. The system has been developed to provide research laboratories with a freely-available, integrated system that offers a simple and effective way for experiment annotation and tracking of analysis procedures. (Full article...)

Recently featured:

No specimen left behind: Industrial scale digitization of natural history collections
MaPSeq, a service-oriented architecture for genomics research within an academic biomedical research institution
Grand challenges in environmental informatics