High-Throughput Computing for Genomics and Bioinformatics Research
High-Throughput Computing for Genomics and Bioinformatics Research
批准号:
10176848
负责人:
Adrian V Lee
金额:
$57.36万
依托单位国家:
美国
项目类别:
财政年份:
2021
资助国家:
美国
项目状态:
已结题
起止时间:
2021-07-01 至 2022-06-30
关键词:
AreaBioinformaticsBiomedical ComputingCLC GeneCellular biologyCollaborationsComputer softwareDataData ScienceData SetDevelopmentDiseaseEducationEducation and OutreachEducational workshopEnsureFundingGenomicsHealth Science LibraryHealth SciencesHigh Performance ComputingHourInfrastructureInstitutesInstitutionLicensingLinkLongevityMalignant Childhood NeoplasmMedicineMemoryModelingMolecular BiologyMonitorResearchResearch PersonnelResearch SupportRunningScienceSecureSupport SystemSystemTaxonomyTechniquesUnited States National Institutes of HealthUniversitiescluster computingcomputing resourcescost effectiveimage reconstructionnext generation sequencingoperationprecision medicineprogramstooltumor immunology
中文摘要
生物医学研究人员在全面研究细胞和分子生物学方面的能力越来越强,
英文摘要
Biomedical researchers have an increasing ability to comprehensively interrogate cell and molecular biology,
for example with advanced imaging and next-generation sequencing. These techniques are producing
datasets of increasing size and complexity and necessitate high-performance computing for biomedical
researchers. Results from these studies are rapidly changing our understanding of normal development, our
taxonomy of disease, and ultimately will enable precision medicine.
Recognizing the importance of data science in precision medicine, the Institute for Precision Medicine (IPM)
and the University of Pittsburgh invested in a high-throughput computing cluster (HTC), with infrastructure
suited for memory-intensive and IO-intensive genomic and bioinformatic operations, and an education program
dedicated to enabling computing for health science researchers. The HTC is located in the Center for
Research Computing (CRC), a secure and centralized enterprise facility providing computing resources to the
whole of the University. The CRC provides a scalable model for research computing with expertise in use and
monitoring of advanced computing. In 2015, the HTC was installed with 16 nodes (256 cores). Usage of the
HTC grew rapidly (2016 - 0.5M core-hours to 2019 – 3.1M core-hours), and despite the addition of computing
nodes in 2017 (4 nodes), 2018 (4 nodes) and 2019 (16 nodes) the system often runs at capacity. Furthermore,
the nodes have reached their useable lifespan. In this application, we are requesting funds to replace the HTC
cluster and increase computing availability with a new cluster of 20 CPU nodes (960 cores) and 8 GPU cards,
2 CPU nodes as application servers, and 1.2 PB of BeeGFS storage, all linked by Infiniband HDR networking.
The new HTC cluster is dedicated to NIH-funded research in biomedical science including medicine, pediatrics,
cancer, immunology, and other areas. To assist health science researchers, the IPM, CRC and the health
science library system (HSLS) support institution-wide licenses from numerous analysis and bioinformatics
software suites, several of which are installed on the HTC server. Importantly, HSLS and CRC provide
education outreach through workshops for command line tools, R for genomics and software suites.
Researchers using software suites such as CLC Genomics, Open OnDemand, or command line can
transparently migrate data and perform analysis on the multi-core HTC. IPM collaboration with the CRC
ensures that the new HTC cluster will be operated in the most cost-effective and efficient manner and will be of
high value to health sciences researcher performing NIH-supported research. This collaborative effort
significantly reduces barriers for biomedical researchers needing to perform computational research.
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ESR1 fusion proteins invoke breast cancer subtype-dependent enrichment of ligand independent pro-oncogenic signatures and phenotypes.
ESR1融合蛋白引起乳腺癌亚型依赖性配体独立的促癌特征和表型的富集。
DOI:
10.1101/2023.09.18.558175
发表时间:
2023
期刊:
bioRxiv : the preprint server for biology
影响因子:
--
作者:
[Yates,MeganE, Li,Zheqi, Li,Yiting, Guzolik,Hannah, Wang,Xiaosong, Liu,Tiantong, Hooda,Jagmohan, Atkinson,JenniferM, Lee,AdrianV, Oesterreich,Steffi]
通讯作者:
Oesterreich,Steffi
DOI:
10.1097/hc9.0000000000000289
发表时间:
2023-11-01
期刊:
Hepatology communications
影响因子:
5.1
作者:
[]
通讯作者:
DOI:
10.3389/fcell.2023.1197109
发表时间:
2023
期刊:
Frontiers in cell and developmental biology
影响因子:
5.5
作者:
[]
通讯作者:
DOI:
10.3389/fphys.2023.1195001
发表时间:
2023
期刊:
Frontiers in physiology
影响因子:
4
作者:
[]
通讯作者:
DOI:
10.1097/hc9.0000000000000220
发表时间:
2023-09-01
期刊:
Hepatology communications
影响因子:
5.1
作者:
[]
通讯作者:
共 12 条
Credentialing Models of Invasive Lobular Breast Cancer for Translational Research
-
批准号:10219509
-
项目类别:
-
资助金额:$57.3万
-
财政年份:2021
-
负责人:Adrian V Lee
-
依托单位:
Credentialing Models of Invasive Lobular Breast Cancer for Translational Research
-
批准号:10589777
-
项目类别:
-
资助金额:$57.03万
-
财政年份:2021
-
负责人:Adrian V Lee
-
依托单位:
Estrogen receptor fusions genes as drivers of endocrine resistance in breast cancer
-
批准号:10219505
-
项目类别:
-
资助金额:$58.63万
-
财政年份:2021
-
负责人:Adrian V Lee
-
依托单位:
Estrogen receptor fusions genes as drivers of endocrine resistance in breast cancer
-
批准号:10605355
-
项目类别:
-
资助金额:$56.76万
-
财政年份:2021
-
负责人:Adrian V Lee
-
依托单位:
Estrogen receptor fusions genes as drivers of endocrine resistance in breast cancer
-
批准号:10373094
-
项目类别:
-
资助金额:$56.59万
-
财政年份:2021
-
负责人:Adrian V Lee
-
依托单位:
Developing and credentialing murine models of ILC
-
批准号:10830524
-
项目类别:
-
资助金额:$14.84万
-
财政年份:2021
-
负责人:Adrian V Lee
-
依托单位:
Credentialing Models of Invasive Lobular Breast Cancer for Translational Research
-
批准号:10378642
-
项目类别:
-
资助金额:$56.81万
-
财政年份:2021
-
负责人:Adrian V Lee
-
依托单位:
Targeting the IGF Pathway for Treatment of Breast Cancer
-
批准号:7385535
-
项目类别:
-
资助金额:$15.94万
-
财政年份:2007
-
负责人:Adrian V Lee
-
依托单位:
IGF-1& its Cross-Talk with Estrogen in Breast Tumor Grow
-
批准号:6989330
-
项目类别:
-
资助金额:$17.46万
-
财政年份:2004
-
负责人:Adrian V Lee
-
依托单位:
IRS1 and 2 Signaling in Mammary Development and Cancer
-
批准号:6620551
-
项目类别:
-
资助金额:$26.62万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
IRS-1 and -2 signaling in mammary development and cancer
-
批准号:8237036
-
项目类别:
-
资助金额:$28.84万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
IRS1 and 2 Signaling in Mammary Development and Cancer
-
批准号:6887645
-
项目类别:
-
资助金额:$12.02万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
IRS-1 and -2 signaling in mammary development and cancer
-
批准号:8433433
-
项目类别:
-
资助金额:$0.0万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
IRS-1 and -2 signaling in mammary development and cancer
-
批准号:8624531
-
项目类别:
-
资助金额:$26.01万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
IRS-1 and -2 signaling in mammary development and cancer
-
批准号:8840542
-
项目类别:
-
资助金额:$29.14万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
IRS1 and 2 Signaling in Mammary Development and Cancer
-
批准号:6418735
-
项目类别:
-
资助金额:$26.62万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
IRS1 and 2 Signaling in Mammary Development and Cancer
-
批准号:6693817
-
项目类别:
-
资助金额:$26.62万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
IRS-1 and -2 signaling in mammary development and cancer
-
批准号:7904710
-
项目类别:
-
资助金额:$30.13万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
ER Co-Repressor Function of SAFB in Breast Cancer
-
批准号:7087942
-
项目类别:
-
资助金额:$26.16万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
IRS-1 and -2 signaling in mammary development and cancer
-
批准号:8049580
-
项目类别:
-
资助金额:$28.84万
-
财政年份:2002
-
负责人:Adrian V Lee
-
依托单位:
海外基金