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dkNET community events and announcements in February, 2020

  • 03:48pm February 4, 2020
  • Ko-Wei Lin

Dear dkNET Community,

dkNET provides updates on activities of interest to the NIDDK-supported community. You could keep up to date on these activities through our Twitter feed @dkNET_info, through our Community Calendar, or through dkNET e-mail list. If you have an event or funding opportunities you'd like to advertise, please contact us info_at_dknet.org.


dkNET News

Funding opportunities:

  • dkNET New Investigator Pilot Program in Bioinformatics The pilot program is to provide support for Early Stage and New Investigators seeking to apply computationally-intensive methods to important questions in Diabetes, Endocrinology and Metabolic Diseases (DEMD) research. These awards will provide funding for preliminary studies that can serve as a foundation for the development of future grant applications in DEMD-focused topic areas. Application Due Date: February 14, 2020.
  • 2020 dkNET Summer of Data Student Internship To support researchers with the use of on-line resources, the 6-week dkNET Summer of Data Student Internship program provides students an opportunity to utilize the dkNET tools and resources in a research project and to provide feedback on their experience to the dkNET team. Students will learn best practices to enhance rigor and reproducibility and learn the basics of good data management by following the FAIR (Findable, Accessible, Interoperable, Reusable) data principles. dkNET will award a $1,000 scholarship to a limited number of high school, undergraduate or graduate (Masters or PhD) students who are working in a research lab during summer 2020. Awards will be determined by a competitive selection process. Application due date: April 5, 2019.

New publications

The Research Resource Initiative lead Dr. Anita Bandrowski and the dkNET PI Dr. Maryann Martone have released a new preprint "Rigor and Transparency Index, a new metric of quality for assessing biological and medical science methods". You can also check out the article published in Nature News "Software searches out reproducibility issues in scientific papers"and the article publiched in Retraction Watch "Has reproducibility improved? Introducing the Transparency and Rigor Index".


New research tools added:

  • GeneLab (RRID:SCR_017658) is an omics database for spaceflight experiments. It is an interactive and open access resource where scientists can upload, download, store, search, share, transfer, and analyze omics data from spaceflight and corresponding analogue experiments, and it enables exploration of molecular network responses of terrestrial biology to space environment. It contains curated omics data, metadata and radiation dosimetry for model organisms. It supports standard guidelines for submission of datasets, MIAME for microarray, ENCODE Consortium Guidelines for RNA-seq and MIAPE Guidelines for proteomics.

  • TCGAbiolinks (RRID:SCR_017683) is a software R Bioconductor package for integrative analysis with TCGA data. Users can access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.

  • Mousebytes (RRID:SCR_017904) is an open access database for mouse cognition, imaging and genomics data integration. It contains open-access high-throughput pipeline and database for rodent touchscreen-based cognitive assessment.

  • Primate Cell Type Database (RRID:SCR_017963) is a database of intracellular recordings of non-human primates (NHP) cells sampled from the lateral prefrontal cortex. 249 patch clamp recordings for 2 protocols: 1 second current pulse and 3 millisecond pulse. It contains morphology obtained by biocytin injections and confocal imaging at 63x magnification.

  • Cistrome (RRID:SCR_017663) is an integrative platform for transcriptional regulation studies, and it is a data analysis platform based on the Galaxy open source framework. Besides standard Galaxy functions, Cistrome has ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery. It is used to conduct data integration to mine hidden biological insights from publicly available high throughput data.

dkNET upcoming webinar:

  • Save the date! Our February's webinars will be on February 14 and 28, 2020 at 11 am pacific time. Come learn resources, services, and tools offered by Mutant Mouse Resource & Research Centers (MMRRC Repository) and AMP Type 2 Diabetes Knowledge Portal (T2D Knowledge Portal)!


Events in February, 2020

Feb. 11-12, 2020

NIH Workshop: Role of Generalist Repositories to Enhance Data Discoverability and Reuse

The Office of Data Science Strategy at the National Institutes of Health and the National Library of Medicine are hosting a workshop(link is external) on the Role of Generalist Repositories to Enhance Data Discoverability and Reuse on Feb. 11-12. The workshop will be held at the Lister Hill Auditorium on the NIH main campus in Bethesda, Md. The primary goals of the workshop are to: (1) Hear from generalist repositories about how they see themselves in the larger biomedical data repository landscape. (2) Understand from institutional data repositories how they are creating suites of solutions for their researchers and how they see generalist repositories fitting in this landscape. (3) Consider desired characteristics of data repositories and how they relate to institutional expectations of data storage/preservation solutions. (4) Explore adoption of common infrastructure, standards and federated search solutions to enable greater discoverability of NIH research data across federated data repositories. (5) Address the role of data curators in ensuring that data and metadata are sufficiently well curated to enhance discovery and enable reuse. Registration deadline: February 4, 2020.

Location: Bethesda, MD, USA

More information: https://datascience.nih.gov/news/nih-to-host-workshop-on-role-of-generalist-repositories-to-enhance-data-discoverability-and-reuse

Feb. 13-15, 2020

2020 Rachmiel Levine-Arthur Riggs Diabetes Research Symposium

2020 Rachmiel Levine-Arthur Riggs Diabetes Research Symposium will be held in Universal City, CA from February 13 To 15, 2020.

More information: https://www.cityofhope.org/research/levine-symposium/levine-symposium-abstracts-and-poster-session


Feb. 14, 2020

dkNET Webinar: Mutant Mouse Resource & Research Centers (MMRRC Repository)

The Mutant Mouse Resource and Research Center (MMRRC) Program is the nation’s primary mutant mouse archive and distribution repository system. The MMRRC Program was established by the NIH 2 decades ago to ensure the preservation, dissemination, and development of valuable mutant mouse strains and data generated by research scientists. It also plays a key role in supporting rigor and reproducibility of experimental studies using mouse models. The MMRRC Program was constituted as a trans-national regionally-distributed network of four Centers each hosting an archive and distribution repository, located at the University of California Davis, University of Missouri-Columbia, The Jackson Laboratory, and the University of North Carolina-Chapel Hill, and an Informatics Coordination and Service Center (ICSC) located at UC Davis. Center members of the MMRRC Consortium serve the needs of the nation’s biomedical research community by ensuring access to and optimizing utilization of transgenic, knockout and other genetically engineered mutant mice and related biomaterials, services, and new technologies. In this webinar, Dr. Kent Lloyd will introduce the services and resources provided at MMRRC.

More information: https://dknet.org/about/blog/2016

Feb. 23-27, 2020

Keystone Symposia: Obesity and NAFLD: Mechanisms and Therapeutics (B3)

Energy metabolism underlies all facets of human health. Now, with rates of obesity and nonalcoholic fatty liver disease (NAFLD) surging, understanding how energy metabolism is governed is of the utmost interest. Halting the progression of NAFLD into nonalcoholic steatohepatitis (NASH) is considered an unmet need in human health. At this meeting, we will discuss regulatory elements underlying obesity and NAFLD, and the metabolic underpinnings of NASH. We will focus on metabolites, hormones, and cellular signaling pathways. We will also examine the leading edge of therapeutic approaches for obesity and NASH. We will bring together scientists and physicians specializing in basic, translational, and clinical research, as well as industry scientists, to create a robust exchange of ideas on how to move the field forward.

Location:  Banff, AB, Canada

More information: http://www.keystonesymposia.org/index.cfm?e=web.meeting.program&\;meetingid=1698

Feb. 28, 2020

dkNET Webinar: AMP Type 2 Diabetes Knowledge Portal (T2D Knowledge Portal)




Funding opportunities information and deadlines in February, 2020

Feb. 02, 2020

NIH Funding Opportunity Letter of Intent Due Date: Tissue Mapping Centers for the Human BioMolecular Atlas Program (U54 Clinical Trial Not Allowed)

The purpose of this Funding Opportunity Announcement (FOA) is to establish state-of-the-art Tissue Mapping Centers (TMCs) that will generate high-resolution, high-content, multiscale maps of non-diseased human organs and systems. Centers will be expected to integrate and optimize all parts of the data generation pipeline, from tissue collection and preservation through to data integration, analysis and interpretation. Centers will also be expected to work closely with the other funded projects as part of the Human BioMolecular Atlas Program to catalyze development of a framework for mapping the human body in 3D with high resolution.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-RM-20-002.html

Feb. 02, 2020

NIH Funding Opportunity Letter of Intent Due Date: Transformative Technology Development for the Human BioMolecular Atlas Program (UG3/UH3 Clinical Trial Not Allowed)

The purpose of this Funding Opportunity Announcement (FOA) is to solicit transformative technologies that will significantly expand throughput, multiplexing and discrimination of biomolecules in human tissues for comprehensive mapping of individual cells and their context in human tissues. This FOA supports the accelerated proof-of-principle demonstration and validation of promising tools, techniques and systems that can be integrated, scaled and applied to multiple human tissues, particularly for characterizing functional modifications, lipids and the extracellular environment. The initial two-year UG3 phase will support accelerated development and demonstration of feasibility of these emerging, high impact technologies. The subsequent two-year UH3 phase will support validation in human tissues, optimization, scale-up, and generation of data. Funded projects will be expected to work closely as part of the Human BioMolecular Atlas Program to catalyze development of a framework for 3D mapping the human body with high resolution.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-RM-20-001.html

Feb. 02, 2020

NIH Funding Opportunity Letter of Intent Due Date: 4DN Organization and Function in Human Health and Disease (U01 Clinical Trial Not Allowed)

To support projects that apply new or existing tools to monitor and/or manipulate the 4D nucleome in the context of human health and disease. Any human disease or biological process relevant to NIH’s mission may be proposed including environmental exposures (e.g. addictive substances, toxins, psychosocial stress), or studies across development or lifespan. Other relevant timeframes may include but are not limited to: circadian rhythms, fasting and feeding cycles, reproductive cycles, and sleep/wake cycles.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-RM-20-005.html

Feb. 02, 2020

NIH Funding Opportunity Letter of Intent Due Date: New Investigator Projects on 4DN Organization and Function in Human Health and Disease (U01 Clinical Trial Not Allowed)

To support projects from scientists who are in the early stages of establishing an independent research career that apply new or existing tools to monitor and/or manipulate the 4D nucleome (4DN) in the context of human health and disease. Any human disease or biological process relevant to NIH’s mission may be proposed including environmental exposures (e.g. addictive substances, toxins, psychosocial stress), or studies across development or lifespan. Other relevant time frames may include but are not limited to: circadian rhythms, fasting and feeding cycles, reproductive cycles, and sleep/wake cycles.

Feb. 10, 2020

National Kidney Foundation Funding Opportunity Application Deadline: 2020 Young Investigator Research Grant Program

The National Kidney Foundation recognizes the importance of the accomplishments of individuals who are early in their investigative careers in the advancement of our knowledge about the treatment and prevention of kidney disease. To raise awareness and create interest in the challenge of developing better treatments for kidney disease and its complications, the NKF has established a Young Investigator grant program to support clinical research studies addressing important issues for patients with kidney disease. Promising young scientists are encouraged to submit proposals for investigating clinical research questions in nephrology, or closely related fields. Projects must be patient-oriented. Elements of patient- oriented research activities may include but are not limited to development of new technologies, mechanisms of human disease, educational or therapeutic interventions, epidemiological studies, health policy studies, and clinical trials. Individuals who have completed fellowship training in an ACGME- accredited training program and who hold junior faculty positions (Instructor or Assistant Professor) at university-affiliated medical centers in the United States are eligible to apply.

More information: https://www.kidney.org/sites/default/files/2020%20YI%20Grant%20Eligibility%20%26%20Instructions.pdf


Feb. 13, 2020

NIDDK Funding Opportunity Letter of Intent Due Date: Type 1 Diabetes in Acute Pancreatitis Consortium - Clinical Centers (T1DAPC-CCs) (U01 Clinical Trial Optional)

This Funding Opportunity Announcement (FOA) invites U01 applications for the establishment of a clinical consortium, composed of one Data Coordinating Center (DCC) and up to 10 Clinical Centers (CC), to conduct studies on diabetes mellitus, with an emphasis on Type 1 diabetes (T1D), that occurs after or as a consequence of one or more episodes of acute pancreatitis. The Consortium will form multi-disciplinary teams composed of members from the CCs and DCC to undertake a prospective longitudinal observational study of the occurrence of diabetes that occurs during an acute pancreatitis episode or subsequently, with an emphasis on type 1 diabetes (T1D). The study will be designed to gain insight into the incidence, clinical evolution, etiology, type and pathophysiology of the T1D and other forms of diabetes that occurs during or after one or more episodes of acute pancreatitis. The teams will also undertake studies on the identification of immune and genetic risk factors and biomarkers which predict the development of T1D in a racially, ethnically, and geographically diverse population of subjects who have impaired glucose tolerance or diabetes mellitus after one or more episodes of acute pancreatitis due to various identifiable etiologies. Applications for the Data Coordinating Center (DCC) will be submitted in response to a separate FOA: RFA-DK-19-023: Type 1 Diabetes in Acute Pancreatitis Consortium Data Coordinating Center (T1DAPC-DCC) (U01 Clinical Trial Optional). To achieve the goal of a comprehensive characterization of diabetes with an emphasis on T1D that results or occurs after acute pancreatitis, each CC should include researchers and clinicians with multi-disciplinary expertise. CCs will be expected to share results freely within Consortium and to develop trans-consortium collaborative projects that make use of the combined expertise and technological capabilities present in all of the CCs. In addition, a major collaborative effort within the Consortium will be the establishment of an annotated repository of bio-specimens (e.g., blood, saliva, urine, pancreatic and duodenal juice, stools and when feasible pancreatic tissue) to allow for the identification and validation of biomarkers for risk stratification, early detection, and to inform the development of future treatment strategies to prevent or reverse T1D after acute pancreatitis.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-DK-19-022.html


Feb. 13, 2020

NIDDK Funding Opportunity Letter of Intent Due Date: Type 1 Diabetes in Acute Pancreatitis Consortium - Data Coordinating Center (T1DAPC-DCC) (U01 Clinical Trial Optional)

This Funding Opportunity Announcement (FOA) invites U01 applications for the establishment of a clinical consortium, the Type 1 Diabetes in Acute Pancreatitis Consortium (T1DAPC), composed of one Data Coordinating Center (DCC) and up to 10 Clinical Centers (CC), to conduct studies on Type 1 diabetes mellitus (T1D) that occurs after or as a consequence of one or more episodes of acute pancreatitis. Applications for the Clinical Centers (CC) are submitted in response to a separate FOA: RFA-DK-19-022  : Type 1 Diabetes in Acute Pancreatitis Consortium Clinical Centers (T1DAPC-CC) (U01 Clinical Trial Optional). The applicant for the Data Coordinating Center (DCC) must have experience serving as the DCC for studies on complex, clinical conditions, like the occurrence of diabetes mellitus (DM) after or as a consequence of one or more episodes of acute pancreatitis. The Consortium will form multi-disciplinary teams composed of members from the CCs and the DCC to undertake a prospective longitudinal observational study of the occurrence of diabetes that occurs during an acute pancreatitis episode or subsequently, with an emphasis on type 1 diabetes (T1D). The study will be designed to gain insight into the incidence, clinical evolution, etiology, type and pathophysiology of the T1D and other forms of diabetes after acute pancreatitis. The Consortia will also undertake studies on the identification of immune and genetic risk factors and biomarkers which predict the development of T1D in a racially, ethnically, and geographically diverse population of subjects who have recovered from one or more episodes of acute pancreatitis due to various identifiable etiologies. The DCC will provide overall project coordination, administration, quality control, data management and biostatistical support.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-DK-19-023.html

Feb. 14, 2020

dkNET Funding Opportunity Application Due Date: New Investigator Pilot Program in Bioinformatics

The goal of the dkNET Pilot Award program is to provide support for Early Stage and New Investigators seeking to apply computationally-intensive methods to important questions in diabetes, endocrinology and metabolic diseases research. These awards will provide funding for preliminary studies that can serve as a foundation for the development of future grant applications in DEMD-focused topic areas. dkNET Pilot Award applications should focus on applying computational and/or modeling approaches to compelling research problems in diabetes, endocrinology and related metabolic disorders. Consistent with these goals, this program will support projects focused on a wide array of topics including, but not limited to: Metabolic modeling of known and unknown pathway kinetics and compartmentalization in diabetes and/or endocrine or metabolic disorders;Network and systems biology of intra and intercellular regulation and inter-tissue and organ homeostasis focused on etiology, diagnosis, prognosis or responses to treatment, including computational approaches to identify biomarkers capable of tracking disease process or progress;Structural biology/informatics and chemical informatics of endocrine and metabolic pathways in diabetes, endocrinology and related metabolic diseases;High-throughput and/or high information content image analysis of organs or tissues of relevance to diabetes or metabolic disease;Computational characterization of the normal or abnormal development of involved organs such as the formation of pancreatic islets.Of particular interest are projects that can leverage and expand the utility of existing large datasets developed in NIDDK projects and programs. For examples, see the dkNET webpage at NIDDK-specific-repositories. Research designed to address important research questions through the development of new analytical tools, or through novel secondary analyses of existing datasets are encouraged.

More information: https://dknet.org/about/new-investigator-pilot


Feb. 17, 2020

NIH Funding Opportunity Letter of Intent Due Date: 4DN Centers for Data Integration\, Modeling and Visualization (UM1 Clinical Trial Not Allowed)

The purpose of this FOA is to solicit applications for research projects to generate reference datasets and to create navigable maps for the study of the spatial and temporal organization of the nucleus, using genomic and imaging data as well as newly developed visualization and integrative analysis tools.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-RM-20-004.html

Feb. 17, 2020

NIH Funding Opportunity Letter of Intent Due Date: Real Time Chromatin Dynamics and Function (U01 Clinical Trial Not Allowed)

To support the development and application of tools that would enable the monitoring in real-time of the dynamic three-dimensional structure of mammalian genomes and provide insight into how organizing components of 4D genome architecture affect biological processes in live cells.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-RM-20-003.html

Feb. 19, 2020

NIDDK Funding Opportunity Application Due Date: Limited Competition for the Closeout of the SEARCH for Diabetes in Youth Cohort Study (R01 Clinical Trial Not Allowed)

The purpose of this Funding Opportunity Announcement (FOA) is to complete the SEARCH for Diabetes in Youth Cohort Study. SEARCH has recruited a cohort of youth with diabetes who have been followed longitudinally. The purpose of this FOA is to complete data analyses and disseminate scientific findings regarding the evolution of diabetes-related complications, including mortality, and processes of care and quality of life.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-DK-19-507.html

Feb. 25, 2020

NIDDK Funding Opportunity Letter of Intent Due Date: New Investigator Gateway Awards for Collaborative T1D Research (R03 Clinical Trial Not Allowed)

The New Investigator Gateway Award in T1D Research is designed to ensure that a robust pipeline of talented new investigators will continue to embark on successful careers in T1D research. In addition to providing support for preliminary research, the Gateway program provides an opportunity for new Program Directors/Principal Investigators (PD/PIs) to pursue their studies within the intellectual environment of a select number of large, ongoing collaborative research programs. Embedding awardees within an established scientific framework in each of these consortia will provide unique opportunities for New and Early Stage Investigators to increase their understanding of key questions in the field, to network, and to establish unique and potentially long-lasting collaborations that will propel their careers forward. It is anticipated that the Gateway award will providethe support needed to enhance the success of future R01 submissions from New Investigators interested in pursuing careers in T1D research.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-DK-19-026.html

Feb. 26, 2020

NIDDK Funding Opportunity Letter of Intent Due Date: Mechanisms Underlying the Contribution of Type 1 Diabetes Disease-associated Variants (R01 Clinical Trial Not Allowed)

This Funding Opportunity Announcement (FOA) encourages applications from integrative teams and individual investigators for large-scale complex multi-disciplinary Functional Genomics Projects (FGPs) to determine the contributions and mechanisms underlying the contribution of associated variants for type 1 diabetes (T1D). Genome-wide association studies (GWAS) and other genomic studies of T1D have found many variants that are statistically associated with disease risk or disease protection, but they have not clearly shown which variants in genomic elements cause these effects or how they result in differences in function. Applications submitted to this RFA will systematically identify causal variants and effector transcripts associated with all known T1D risk variants, verify the role of downstream effector transcripts, build network models that explain their role(s) in T1D. These biological insights could lead to the development of reliable biomarkers and effective strategies for screening and disease prevention, rational drug design, and better-tailored therapies.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-DK-19-020.html

Feb. 26, 2020

NIDDK Funding Opportunity Letter of Intent Due Date: Treating Diabetes Distress to Improve Glycemic Outcomes in Type 1 Diabetes (R01 Clinical Trial Required)

This FOA seeks applications for clinical trials testing interventions targeting diabetes distress in individuals with type 1 diabetes and/or their caregivers, with the goal of understanding whether lowering diabetes distress will improve glycemic control and quality of life. Given the clinical care recommendation that screening for diabetes distress take place in the context of medical care, applications should reflect a practical team approach to screening and treatment that could realistically occur in a clinical setting.

More information: https://grants.nih.gov/grants/guide/rfa-files/RFA-DK-19-021.html

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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.

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dkNET Webinar: Single Cell Multi-Omics Analysis of Beta Cell Heterogeneity and Differentiation

Funding Opportunity: HTORR Pilot Award Program

dkNET community events and announcements in May, 2024

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