Software Development to Enhance Echinobase
Software Development to Enhance Echinobase
批准号:
10715581
负责人:
PETER D VIZE
金额:
$17.52万
依托单位国家:
美国
项目类别:
财政年份:
2023
资助国家:
美国
项目状态:
未结题
起止时间:
2023-09-22 至 2028-06-30
关键词:
ATAC-seqArchitectureAtlasesAwardBioinformaticsCellsCodeCollaborationsCommunitiesComputer softwareConsultationsConsumptionCustomDataData SetDatabasesDevelopmentEchinoBaseEchinodermataEducational workshopFundingFutureGene ExpressionGenesGenomeGenomic SegmentGenomicsGenus MenthaGoalsGrantHeadHigh-Throughput Nucleotide SequencingIntuitionLinkLiteratureMachine LearningMapsMethodsOrthologous GenePhasePhenotypePhylogenetic AnalysisProcessRegulatory ElementResearchResourcesSiteSpecific qualifier valueSurveysSyntenySystemTechnologyTestingUpdateVariantVisualizationVisualization softwareWritingXenBasebasebiomedical scientistdata accessdata exchangedata modelingdata resourcedata reusedatabase querydatabase schemadesignempowermentflexibilitygenome browsergenome resourcegenome-wideimprovedknowledgebasemembermiddlewaremigrationnew technologynovelparalogous genesingle cell technologysingle-cell RNA sequencingsoftware developmentsymposiumtechnology developmenttooltranscriptome sequencingusabilityweb appweb interfaceweb portal
中文摘要
技术发展总结
英文摘要
SUMMARY TECHNICAL DEVELOPMENT
Software Development to Enhance Echinobase
The Technical Development component describes software development for Echinobase. This includes code in
the database, web applications, user and curator interfaces. New data types and new curation efforts require
new systems, tools and software interfaces to be built. Importantly, interfaces must be designed to allow our
community members to browse and interrogate the data via our web portal. We have recently added many new
content types and features to Echinobase, including multi-species support, Gene, Literature and Community
pages; and there are many additional types of content that will require support from the technical development
team, including the GEO pipeline, single-cell omics, ortholog GO terms, tools to integrate paralog gene data
and more. As many of the biologists generating and accessing these data are not bioinformaticians, we need
to develop tools and interfaces that are intuitive and easy to use. An excellent example of how we plan to
achieve this goal is the Xenbase GEO module that we will implement in Echinobase, that allows non-experts to
view, interact with, and understand RNA-seq data through a simple, intuitive and interactive web interface.
Over the next five years, we will proceed through numerous steps for each new type of data we aim to support:
assessing data requirements, data modeling, middleware software development, testing and optimization of
trial releases, developing curator, user and data browsing interfaces. Prioritization of projects is done in
consultation with the echinoderm research community via annual surveys and workshops at conferences, input
from our scientific advisory board and collaborators, and, in the future, in consultation with the Alliance of
Genome Resources (AGR) workgroups and other external resources such as the NCBI and UCSC. Planned
new projects include ATAC-seq data from GEO, paralog data from DIOPT, single-cell RNA-seq, support for
genome wide CRE predictions, and computed expression phenotypes. Technical Development will also
support our increased use of machine learning as applied to Echinobase literature and content curation.
Aim 1. Support expanded and novel content.
Aim 2. Generate custom content and support variants and single-cell datasets.
Aim 3. Interface with external resources.
期刊论文(0)
专著(0)
科研奖励(0)
会议论文
Computational Support for All Echinobase Objectives
-
批准号:10715582
-
项目类别:
-
资助金额:$15.79万
-
财政年份:2023
-
负责人:PETER D VIZE
-
依托单位:
Computational Support for All Echinobase Objectives
-
批准号:10442597
-
项目类别:
-
资助金额:$16.77万
-
财政年份:2018
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负责人:PETER D VIZE
-
依托单位:
Computational Support for All Echinobase Objectives
-
批准号:10241293
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项目类别:
-
资助金额:$15.43万
-
财政年份:2018
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负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Knowledgebase
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批准号:10404996
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项目类别:
-
资助金额:$159.63万
-
财政年份:2010
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Knowledgebase
-
批准号:10674802
-
项目类别:
-
资助金额:$164.68万
-
财政年份:2010
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Database
-
批准号:8471740
-
项目类别:
-
资助金额:$82.17万
-
财政年份:2010
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Database
-
批准号:8678968
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项目类别:
-
资助金额:$85.96万
-
财政年份:2010
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Database
-
批准号:7869674
-
项目类别:
-
资助金额:$90.57万
-
财政年份:2010
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Database
-
批准号:8292203
-
项目类别:
-
资助金额:$84.35万
-
财政年份:2010
-
负责人:PETER D VIZE
-
依托单位:
Cloud implementation of Xenbase the Xenopus model organism knowledgebase
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批准号:10824813
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项目类别:
-
资助金额:$23.83万
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财政年份:2010
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Database
-
批准号:8076838
-
项目类别:
-
资助金额:$85.5万
-
财政年份:2010
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: The Xenopus model organism database
-
批准号:9000309
-
项目类别:
-
资助金额:$172.54万
-
财政年份:2010
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Database
-
批准号:7066028
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项目类别:
-
资助金额:$40.11万
-
财政年份:2005
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Database
-
批准号:7487445
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项目类别:
-
资助金额:$38.17万
-
财政年份:2005
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Database
-
批准号:7204198
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项目类别:
-
资助金额:$38.95万
-
财政年份:2005
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Database
-
批准号:7635907
-
项目类别:
-
资助金额:$36.18万
-
财政年份:2005
-
负责人:PETER D VIZE
-
依托单位:
Xenbase: a Xenopus Model Organism Database
-
批准号:6925743
-
项目类别:
-
资助金额:$41.08万
-
财政年份:2005
-
负责人:PETER D VIZE
-
依托单位:
Technical
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批准号:9193646
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项目类别:
-
资助金额:$18.35万
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财政年份:--
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负责人:PETER D VIZE
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依托单位:
Computation
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批准号:9000314
-
项目类别:
-
资助金额:$33.12万
-
财政年份:--
-
负责人:PETER D VIZE
-
依托单位:
Computational Support for All Echinobase Objectives
-
批准号:9789704
-
项目类别:
-
资助金额:$16.77万
-
财政年份:--
-
负责人:PETER D VIZE
-
依托单位:
海外基金