Transforming Genomics with 5 PB Big Omics Data Engine Cray CS300-AC Supercomputer

使用 5 PB 大组学数据引擎 Cray CS300-AC 超级计算机转变基因组学

• 批准号: 8734830
• 负责人: Patricia Kovatch
• 金额: $ 194.7万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-03 至 2015-07-02
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8734830
• 关键词: Autistic Disorder; Behavior Disorders; Biology; Cardiac; Caring; Categories; Chemicals; Communities; Complex; Data; Data Storage and Retrieval; Disease; Drug Addiction; Explosion; Funding; Genomics; Institution; Insulin Resistance; Mental Depression; Productivity; Research; Research Infrastructure; Research Personnel; Resources; Runaway; Schizophrenia; Scientist; Supercomputing; Time; United States National Institutes of Health; base; cost; critical period; diabetic; instrument; success; supercomputer; tumor progression

DESCRIPTION: Our genomics-based scientists and their external collaborators are at a critical point in their research: now, and increasingly over the next years, their discoveries will be limited by the quantity and quality of computing and storage that they can access. While Mount Sinai has funded an excellent supercomputing and storage infrastructure along with professional staff to operate and maintain it, it has been a runaway success and it is now under-provisioned, negatively impacting its largest group of users the greatest: the genomics-based researchers. The scientific productivity of these researchers is greatly inhibited on this existing infrastructure due to long queue wait times especially during critical periods compounded by the extraordinary amount of time spent managing their data storage due to a substantial under-supply. With the explosion of progressively complex scientific and data queries planned by the 20 PIs, their 24 projects and their 55 external collaborating institutions comprising over $43 million in NIH funding, these limited resources are severely restricting the ability of the researchers to collaborate and to share their data with the broader scientific community. To enable these researchers instead to flourish, we propose a "Big Omics Data Engine" (BODE) instrument: a dedicated, specialized data analytic supercomputer customized for Mount Sinai's specific scientific needs. Such an instrument will increase their throughput by at least 3X and up to 10X by using 2,484 Intel Haswell enterprise cores. The available storage space will expand by over 3X to 5 petabytes, thus greatly enhancing the genomics-based research in a spectrum of disease categories including autism, insulin resistance in diabetics, schizophrenia and related behavioral disorders, cardiac care, the origins of drug addiction and depression, and cancer progression. Moving the genomics researchers to a new machine will also have the secondary effect of freeing up compute cycles and storage on our existing supercomputer for our next highest demand group of users: the structural and chemical biology researchers. In recognition of the intense scientific need for this instrument, Mount Sinai has agreed to fund up to $4 million in operating costs.

产品说明：我们的基因组科学家和他们的外部合作者正处于研究的关键时刻：现在，以及未来几年，他们的发现将受到他们可以访问的计算和存储的数量和质量的限制。虽然西奈山已经资助了一个优秀的超级计算和存储基础设施，沿着专业人员来操作和维护它，但它已经取得了巨大的成功，现在配置不足，对其最大的用户群体产生了最大的负面影响：基于基因组学的研究人员。这些研究人员的科学生产力在这种现有的 由于排队等待时间长，特别是在关键时期，加上由于供应严重不足而花费大量时间管理其数据存储，因此基础设施受到严重影响。随着20个PI计划的日益复杂的科学和数据查询的爆炸，他们的24个项目和他们的55个外部合作机构包括超过4300万美元的NIH资金，这些有限的资源严重限制了研究人员与更广泛的科学界合作和分享数据的能力。为了使这些研究人员能够蓬勃发展，我们提出了一个“大组学数据引擎”（BODE）仪器：一个专门的，专门的数据分析超级计算机定制西奈山的特定科学需求。这样的仪器将通过使用2，484个英特尔Haswell企业内核将其吞吐量提高至少3倍至10倍。可用的存储空间将扩大超过3倍至5 PB，从而大大增强了一系列疾病类别中基于基因组学的研究，包括自闭症，糖尿病患者的胰岛素抵抗，精神分裂症和相关行为障碍，心脏护理，药物成瘾和抑郁症的起源以及癌症进展。将基因组学研究人员转移到一台新机器上也会产生第二个影响，即为我们下一个需求最高的用户群体释放我们现有超级计算机上的计算周期和存储空间：结构和化学生物学研究人员。由于认识到对这一仪器的强烈科学需求，西奈山已同意资助高达400万美元。 在运营成本上。

项目成果

miR-135a-5p-mediated downregulation of protein tyrosine phosphatase receptor delta is a candidate driver of HCV-associated hepatocarcinogenesis.

• DOI: 10.1136/gutjnl-2016-312270
• 发表时间: 2018-05
• 期刊: Gut
• 影响因子: 24.5
• 作者: Van Renne N;Roca Suarez AA;Duong FHT;Gondeau C;Calabrese D;Fontaine N;Ababsa A;Bandiera S;Croonenborghs T;Pochet N;De Blasi V;Pessaux P;Piardi T;Sommacale D;Ono A;Chayama K;Fujita M;Nakagawa H;Hoshida Y;Zeisel MB;Heim MH;Baumert TF;Lupberger J
• 通讯作者: Lupberger J

Molecular evidence of SARS-CoV-2 in New York before the first pandemic wave.

• DOI: 10.1038/s41467-021-23688-7
• 发表时间: 2021-06-08
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Hernandez MM;Gonzalez-Reiche AS;Alshammary H;Fabre S;Khan Z;van De Guchte A;Obla A;Ellis E;Sullivan MJ;Tan J;Alburquerque B;Soto J;Wang CY;Sridhar SH;Wang YC;Smith M;Sebra R;Paniz-Mondolfi AE;Gitman MR;Nowak MD;Cordon-Cardo C;Luksza M;Krammer F;van Bakel H;Simon V;Sordillo EM
• 通讯作者: Sordillo EM

RT-PCR/MALDI-TOF Diagnostic Target Performance Reflects Circulating SARS-CoV-2 Variant Diversity in New York City.

• DOI: 10.1016/j.jmoldx.2022.04.003
• 发表时间: 2022-07
• 期刊: JOURNAL OF MOLECULAR DIAGNOSTICS
• 影响因子: 4.1
• 作者: Hernandez, Matthew M.;Banu, Radhika;Gonzalez-Reiche, Ana S.;Gray, Brandon;Shrestha, Paras;Cao, Liyong;Chen, Feng;Shi, Huanzhi;Hanna, Ayman;Ramirez, Juan David;van de Guchte, Adriana;Sebra, Robert;Gitman, Melissa R.;Nowak, Michael D.;Cordon-Cardo, Carlos;Schutzbank, Ted E.;Simon, Viviana;van Bakel, Harm;Sordillo, Emilia Mia;Paniz-Mondol, Alberto E.;Mt Sinai PSP Study Grp
• 通讯作者: Mt Sinai PSP Study Grp

Novel substituted aminothiazoles as potent and selective anti-hepatocellular carcinoma agents.

• DOI: 10.1016/j.bmcl.2016.10.015
• 发表时间: 2016-12-01
• 期刊: Bioorganic & medicinal chemistry letters
• 影响因子: 2.7
• 作者: Lu H;Rogowskyj J;Yu W;Venkatesh A;Khan N;Nakagawa S;Goossens N;Koh AP;Higashi T;Gunasekaran G;Schwarz ME;Hiotis SP;Xu X;Kinney W;Hoshida Y;Block T;Cuconati A;Du Y
• 通讯作者: Du Y

A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci.

• DOI: 10.1101/gr.242594.118
• 发表时间: 2019-01
• 期刊: Genome research
• 影响因子: 7
• 作者: Laverty KU;Stout JM;Sullivan MJ;Shah H;Gill N;Holbrook L;Deikus G;Sebra R;Hughes TR;Page JE;van Bakel H
• 通讯作者: van Bakel H