Search Results for: Cloud

11/13/2024 - This webinar will provide an overview of the generative artificial intelligence (AI) services across three major cloud service providers (CSPs) and the steps to follow for setting up AI chatbots in cloud environments with Read More...

07/23/2024 - In this presentation, we will demonstrate how to use enterprise data science platform to configure, run, share, and scale downstream bioinformatics and image analysis pipelines using cloud and HPC resources. This session is geared Read More...

11/10/2022 - Join Google’s Marcos Novaes, Ph.D., as he presents on the design of large-scale solutions for high-performance computing, machine learning, and the internet of things using the Google Cloud Platform. Dr. Norvaes will Read More...

04/28/2022 - Register for the  April Cancer Genomics Cloud  (CGC) webinar to learn more about how NCI’s  Cancer Research Data Commons  (CRDC) and one of the Cloud Resources are helping researchers with little-to-no-programming skills conduct Read More...

12/01/2021 - Speaker: James Lacey, Ph.D., M.P.H. Dr. James Lacey is a City of Hope professor and director of the Division of Health Analytics within the Department of Computational and Quantitative Medicine. His Read More...

11/12/2021 - The Cancer Genomics Cloud (CGC) is a cloud-based bioinformatics ecosystem supported by the National Cancer Institute (NCI). The CGC allows users to run computational workflows defined in the Common Workflow Language (CWL) on a Read More...

10/28/2021 - The Cancer Genomics Cloud (CGC) (link is external) , powered by Seven Bridges, is an NCI-funded resource that provides a unified platform for cancer data analysis by co-localizing three components within the cloud: 1) large cancer Read More...

03/24/2021 - Register/Join At the next Cancer Genome Cloud’s (CGC's) monthly webinar series, NCI Research Fellow, Dr. Xavier Bofill-De Ros, will share his experiences leveraging the NCI Cancer Research Data Commons (CRDC) Cloud Read More...

03/22/2021 - Join Dear NCI Staff, The NCI Cloud Resources are chief components of the NCI Cancer Research Data Commons (CRDC), helping to bring together data and computational power to advance cancer research and discovery. These Read More...

06/12/2020 - Metabolomics as a high-throughput molecular phenotyping technique is growing across all domains in the life-sciences. The data processing and analysis is often performed with many programs using conventional computing solutions but little standardisation for Read More...

11/04/2024 - This one-hour interactive training will cover how to use the ScHARe cloud and Terra platform focusing on how to utilize over 260 social determinants of health (SDoH) data sets and analytic notebooks containing ready-to-use code. Read More...

Cancer research is a complex and data-intensive field. Cloud computing offers a powerful solution for researchers to store, analyze, and share large datasets efficiently. In this month’s topic spotlight, we will explore cloud resources Read More...

09/21/2023 - Picture this… You have large amounts of siloed medical imaging data, but you don’t have the time or budget to manually prepare the images and datasets for annotation and analysis. Don’t you Read More...

08/15/2023 - Picture this… You have large amounts of siloed medical imaging data, but you don’t have the time or budget to manually prepare the images and datasets for annotation and analysis. Don’t you Read More...

07/20/2023 - Picture this… You have large amounts of siloed medical imaging data, but you don’t have the time or budget to manually prepare the images and datasets for annotation and analysis. Don’t you Read More...

06/29/2023 - Please join us for a special presentation about the Fred Hutchinson’s data journal to the cloud, including an innovative cloud platform (Cirro:  https://cirro.bio/ ) to streamline data collection, Read More...

06/23/2023 - Please join us for the launch of the NIGMS Sandbox, a cloud-based learning platform that contains 12 modules developed by NIGMS-supported investigators and Google Cloud engineers. Each module is delivered through an interactive step-by-step tutorial, Read More...

06/21/2023 - Picture this… You have large amounts of siloed medical imaging data, but you don’t have the time or budget to manually prepare the images and datasets for annotation and analysis. Don’t you Read More...

10/03/2022 - Join Drs. Andrey Fedorov and Hugo Aerts for the upcoming October NCI Imaging and Informatics Community Webinar. Their presentation includes updates to the  Imaging Data Commons  (IDC)—a repository of the  NCI Cancer Research Read More...

04/28/2021 - Register/Join This month’s Cancer Genomics Cloud (CGC) webinar welcomes two bioinformaticians, Dr. Vesna Pajic and Nevena Vukojicic, to show attendees how CGC features can be used to perform multi-omics analysis. Dr. Pajic Read More...

03/12/2021 - Register now at https://nih.webex.com/nih/onstage/g.php?MTID=e8b0c0c0e7a6b9c4d221051fb038e4e59 . This seminar is open to the public, so please feel Read More...

11/13/2020 - https://ncihub.org/resources/2404 Abstract: In many applications in genomics, large data sets are created and lightly used before being shared with other researchers (ideally) or simply tossed away on hard drives. The Cancer Read More...

09/30/2020 - Register Through large collaborative research projects, the field of neuroscience is gaining access to unprecedented amounts of information about the structure and function of the brain. These datasets are already having a profound impact Read More...

02/12/2020 - This two-day instructor-led course gives participants a broad study of networking options on Google Cloud Platform. Through presentations, demonstrations, and hands-on labs, learners explore and deploy GCP networking technologies, such as Google Virtual Private Read More...

04/09/2025 - Please note: Registration is required to get the Meeting Link for this event. Please pre-register. The Human Tumor Atlas Network (HTAN) is a National Cancer Institute (NCI)-funded initiative to construct 3-dimensional atlases of Read More...

09/18/2024 - Frederick National Laboratory Science and Technology Group: Work in Progress Seminar Series presents:  “Modernization of Next Generation Sequencing Big Data Analysis Pipelines Leveraging NIH’s on-prem High Performance Computing Cluster … and Cloud.” Meeting ID: 225 592 603 654  Read More...

12/14/2021 - Speaker: Alisa Goldstein, Ph.D. Senior Investigator NCI, Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch Dr. Alisa Goldstein is a Senior Investigator in NIH’s Division of Cancer Epidemiology and Genetics (DCEG), Read More...

11/04/2021 - FireCloud (Powered by Terra (link is external) ) is a data analysis platform that contains a system of workspace functionalities centered on data sharing and analysis. Researchers can use FireCloud to perform a variety of Read More...

05/03/2021 - Join via WebEx Summary: Storing and querying massive datasets can be time-consuming and expensive without the right tools. Google BigQuery is one of several enterprise data warehouse technologies that solves this problem by enabling Read More...

06/26/2018 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. A point-and-click web environment provides ready access to powerful tools for the analysis, integration Read More...

03/20/2024 - Meeting number (access code): 2303 344 1474 Meeting password: 2K9AfEmfN@2

10/13/2021 -

The above video was shared with permission from Chunhua Yan.

HALO HALO is a powerful 2D image analysis tool with AI capabilities to perform annotations and analysis on bright-field and immunofluorescent images for digital pathology and numerous other applications.  It offers a set of algorithms Read More...

10/07/2024 - This one hour training, presented by speakers from  NIH Cloud Lab , will provide an overview of the generative artificial intelligence (AI) services across three major cloud service providers (CSPs), including Amazon Web Services (AWS), Read More...

Discover expert help with analysis, processing applications, and licensed software packages.

12/11/2024 - This session of the BTEP Coding Club introduces NIH CloudLab, a free 90-day sandbox environment partnered with AWS, Google Cloud, and Azure, and demonstrates how to run Nextflow pipelines, a powerful workflow management system Read More...

The Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability (STRIDES) Initiative The STRIDES Initiative aims to help NIH and its institutes, centers, and offices (ICOs) accelerate biomedical research by reducing barriers in utilizing Read More...

Proteomic Data Common (PDC) represents the NCI’s largest public repository of proteogenomic comprehensive tumor datasets, essentially a Proteogenomic Cancer Atlas. It was developed to advance our understanding of how proteins help shape the risk, Read More...

CREx News & Updates December 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight FACILITY HIGLIGHTS Learn more about services from the STRIDES Initiative. VIEW STRIDES INITIATIVE NIH Cores Read More...

This is part II of the article highlighting nf-core pipelines and specifically addresses the use of these pipelines in the DNAnexus cloud environment. Part I of the article can be found in the October 2023 topic Read More...

nf-core is a community effort to generate a curated set of standardized, best-practice, reproducible, documented, NGS analysis pipelines. All these workflows are built using the versatile workflow manager, Nextflow , and have been released under the Read More...

12/17/2024 - In this one-hour session we will describe resources available to NIH researchers for performing bioinformatics data analysis. These include trainings by specific groups or institutes (NCI, NIH Library, ODSS), licenses available for online learning ( Read More...

05/29/2024 - This talk will cover a scRNA-seq workflow available to NCI researchers on NIDAP. NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform that hosts user-friendly bioinformatics Read More...

RStudio is an integrated development environment for R, and now python. RStudio includes a console, editor, and tools for plotting, history, debugging, and work space management. It provides a graphic user interface for working with Read More...

Josh Meyer, bioinformatics analyst (CCBR), will cover a scRNA-seq workflow available to NCI researchers on NIDAP . NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform that hosts Read More...

02/22/2024 - Join us for an introduction to bioinformatics resources for NCI CCR researchers.  Featuring:  NIH Bioinformatics Calendar Programming Classes (R, Unix, Python) Class documentation Website resources working on high performance compute cluster (Biowulf/Helix) Next-Gen Read More...

RStudio is an integrated development environment for R, and now python. RStudio includes a console, editor, and tools for plotting, history, debugging, and work space management. It provides a graphic user interface for working with Read More...

DNAnexus provides a secure cloud based platform for the analysis and sharing of next generation sequencing data. This class will use a pre-built teaching environment, the GOLD platform, which includes all of the software needed Read More...

Once the job is running, wait about 4 minutes before clicking on the web address shown to the right of job status line. (It will look similar to this " https://job-GBb1xFQ0YKq8PqYJKx1bVv6 Read More...

11/21/2023 - Dear Colleagues,    This presentation will provide an overview of OpenCRAVAT.   Annotation and interpretation of cancer variants is critical to the design of personalized molecular therapies, and Read More...

11/15/2023 - This session introduces two versions of the R/ Bioconductor package OmicCircos to generate high-quality circular plots for visualizing multi-dimensional omics data: coding in the R environment for programmers; point-and-click OmicCircos R Shiny app on Read More...

10/12/2023 - In this one-hour session we will describe various resources available to NIH researchers to learn bioinformatics skills. These include trainings by specific groups or institutes (NCI, NIH Library, ODSS), licenses available for online learning, Read More...

09/14/2023 - In this 90-minute session, participants will learn to improve and optimize their MATLAB code to boost execution speed by orders of magnitude. The course covers common pitfalls in writing MATLAB code, explores the use Read More...

DNAnexus provides a secure cloud based platform for the analysis and sharing of next generation sequencing data. This class will use a pre-built teaching environment, the GOLD System, which includes all of the software needed Read More...

DNAnexus provides a secure cloud based platform for the analysis and sharing of next generation sequencing data. This class will use a pre-built teaching environment, the GOLD platform, which includes all of the software needed Read More...

CCR staff have access to a number of resources Biowulf (Helix) - CIT maintained large cluster with a huge software library (Unix command line) CCBR Pipeliner (Biowulf) Partek Flow (Local Web Service) DNAnexus (Cloud Solution) Read More...

Pathway Analysis IPA (Qiagen - CCR License) Future talk Functional Analysis Gene Set Enrichment Analysis (GSEA) https://www.gsea-msigdb.org/gsea/index.jsp DAVID https://david.ncifcrf.gov/ Enrichr https://maayanlab.cloud/Enrichr/ Other Types Read More...

Our operational objectives are to provide state-of-the-art OMICS technologies in support of the Genetics Branch (GB) investigators and collaborators. Research Services Wet Lab Single cell isolation from fresh, frozen, and FFPE tissue, DNA/RNA extractions Read More...

CREx News & Updates October 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGLIGHTS Learn more about services from the CPTR Read More...

Cores & Facilities From centralized laboratories to collaborative resources and technologies available to CCR Investigators. NCI Cores Centralized laboratories providing broad access to cutting-edge technologies and specialized expertise. Browse NCI Cores Collaborative Resources are technologies and Read More...

The research conducted within the Synthetic Biologics Core (SBC) Facility has a dual role: Generate chemical biology tools and drug candidates for molecular targets identified by NCI research groups, Develop novel effective methods and tools Read More...

The CCR Collaborative Bioinformatics Resource (CCBR) is a centrally funded resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals. The group has Read More...

This archive contains past and present issues of the  BTEP BioInformatics Bulletin. The BTEP Bioinformatics Bulletin features select upcoming bioinformatics events offered across NIH and is distributed monthly via email to the Center Read More...

04/17/2025 - Cardinal Bernardin Cancer Center Virtual Grand Rounds Interested in learning about various cancer indicators, approaches for data integration , and how to leverage data to drive scientific discovery? Then join NCI CBIIT’s Read More...

Register now for an upcoming seminar on January 22, 2025 , “Revealing Tumor-Promoting Signals in Breast Cancer Subtypes: A NIDAP Analysis of Single-Cell Data” . This one-hour talk will feature guest speaker and NIDAP developer, Josh Meyer, who will Read More...

12/04/2024 - Galaxy is a web-based computational workbench for analyzing and visualizing biomedical datasets that is used by thousands of scientists daily.   Galaxy enables accessible, reproducible, and scalable biomedical data science by any scientist Read More...

11/12/2024 - In this hour and half online training, attendees will learn how to improve and optimize their MATLAB code to boost execution speed by orders of magnitude. The training covers common pitfalls in writing MATLAB Read More...

10/16/2024 - The CRDC will celebrate its 10th anniversary with this one-and-a-half-day event highlighting its accomplishments and looking ahead to exciting initiatives. We are planning many informative sessions and report-outs on new work, including our AI Read More...

10/09/2024 - This session will give an overview of the NCI Cancer Research Data Commons and the variety of available cancer data such as RNA expression and protein abundance. These data are hosted in openly accessible Read More...

08/09/2024 - We cordially invite you to attend the upcoming Data Sharing and Reuse Seminar featuring Dr. Robert Schuler and Dr. Jifan Feng. Dr. Schuler, a Senior Computer Scientist and Lead Scientist at the University of Read More...

07/24/2024 - As a cancer researcher, did you know that  data sharing  is now required by many funding agencies and journals? Join NCI CBIIT’s  Dr. Jill Barnholtz-Sloan & Read More...

The CCBR Single-cell RNA-seq Workflow on NIDAP Josh Meyer, bioinformatics analyst (CCBR), will cover a scRNA-seq workflow available to NCI researchers on NIDAP . NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative Read More...

04/12/2024 - This session will outline the All of Us Researcher Workbench registration process for NIH researchers. Access to the Researcher Workbench is free, and all registered researchers are provided $300 initial computational credits. Some analyses in Read More...

::: columns ::: {.column width="75%"} - No install of R or RStudio required. We will access RStudio server through the DNAnexus platform. Course documentation available at https://bioinformatics.ccr.cancer.gov/docs/rintro/index.html . ::: ::: {. Read More...

01/23/2024 - Looking for  data sharing  platforms to enhance your research and advance communal knowledge of childhood cancers? Join the first NCI Childhood Cancer Data Initiative (CCDI) webinar of the new year! Read More...

DNAnexus Basics Setting up the R-Studio environment outside of Class hours These instructions should be followed if you are setting up the R-Studio Web environment outside the normal class hours. Log into DNAnexus Each student Read More...

12/14/2023 - NIDAP , the NIH Integrated Data Analysis Platform, is a cloud-based, collaborative data aggregation and analysis platform that hosts user-friendly bioinformatics workflows and other component analysis and visualization tools. The NCI CCR Collaborative Bioinformatics Resource ( Read More...

12/06/2023 - NIDAP, the NIH Integrated Data Analysis Platform, is a cloud-based and collaborative data aggregation and analysis platform. The NIDAP platform hosts user-friendly bioinformatics workflows (Bulk RNA-Seq, scRNA-Seq, Digital Spatial Profiling) and other component analysis Read More...

09/19/2023 - The NIH is home to a number of groups aimed at supporting bioinformatics, genomics, computational biology and various related topics. Many of these groups meet regularly to host talks or provide training opportunities, while Read More...

09/18/2023 - The NIH is home to a number of groups aimed at supporting bioinformatics, genomics, computational biology and various related topics. Many of these groups meet regularly to host talks or provide training opportunities, while Read More...

For this class, we are going to work with data from and associated with two commercially available sets of RNA samples, Universal Human Reference (UHR) and Human Brain Reference (HBR). UHR - bulk RNA from 10 Read More...

Notes: PANTHER DAVID Qiagen IPA - more detailed R Bioconductor clusterProfiler GSVA goseq GOexpress (for GO annotation) pathview EGSEA seqGSEA CRAN GANPA GOxploreR geneset GSEA, GSVA, ORA https://www.rna-seqblog.com/blitzgsea-efficient-computation-of-gene-set-enrichment-analysis-in-python/ https://github.com/ Read More...

Content for this course series was adapted / inspired by the following sources: The Biostar Handbook , 2nd Edition, Istvan Albert. Malachi Griffith, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith. 2015. Informatics for Read More...

Resources Tertiary Analysis - Biological Meaning Pathway Analysis IPA (Qiagen - CCR License) Future talk Functional Analysis Gene Set Enrichment Analysis (GSEA) https://www.gsea-msigdb.org/gsea/index.jsp DAVID https://david.ncifcrf.gov/ Enrichr Read More...

References Content for this course series was adapted / inspired by the following sources: The Biostar Handbook , 2nd Edition, Istvan Albert. Malachi Griffith, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith. 2015. Informatics Read More...

mkdir rnaseq cd rnaseq curl -s http://data.biostarhandbook.com/rnaseq/projects/griffith/griffith-data.tar.gz | tar zxv Directories: * "reads" contains the sequencing reads * "refs" contains genome and annotation information using Read More...

mkdir rnaseq cd rnaseq curl -s http://data.biostarhandbook.com/rnaseq/projects/griffith/griffith-data.tar.gz | tar zxv Directories: * "reads" contains the sequencing reads * "refs" contains genome and annotation information using Read More...

mkdir rnaseq cd rnaseq curl -s http://data.biostarhandbook.com/rnaseq/projects/griffith/griffith-data.tar.gz | tar zxv Directories: * "reads" contains the sequencing reads * "refs" contains genome and annotation information using Read More...

Module 3: Pathway Analysis Lesson #: Intro to Gene ontology and pathway analysis Discuss what this is Where can we find descriptors geneontology.org organism specific databases What is KEGG? Lesson #: More on ORA, GSEA, GSVA pros Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: using trimmomatic to remove low-quality bases from a sequence Always remember to activate the bioinformatics environment. conda activate bioinfo We will be Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: using trimmomatic to remove low-quality bases from a sequence Always remember to activate the bioinformatics environment. conda activate bioinfo We will be Read More...

Listed below are the video recordings of past BTEP events (classes, seminars, workshops). Videos are hosted on various servers and may play slightly differently. Some videos may be downloaded for local viewing. Recorded Videos of Read More...

Congratulations, your experiments have been completed and you have a large amount of data. Now, it’s time to analyze these data. But where do you begin? How can you gain the most meaning from Read More...

This lesson provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat. Learning Objectives Learn about options for analyzing your scRNA-Seq data. Learn about resources for learning R programming. Learn Read More...

Welcome! Welcome to the R Introductory Series! Who: Novices and beginners\ What: A course series introducing R and RStudio. This course will introduce the foundational skills necessary to begin to analyze and visualize data in Read More...

Learning Objectives To understand: 1. the difference between R and RStudioIDE. 2. how to work within the RStudio environment including: creating an Rproject and Rscript navigating between directories using functions obtaining help how R can enhance data Read More...

Lesson 2: Getting Started with QIIME2 Lesson Objectives Obtain sequence data and sample metadata Import data and metadata Discuss other useful QIIME2 features including view QIIME2, provenance tracking, and the QIIME2 forum. DNAnexus DNAnexus provides a Read More...

NIDAP , the  N IH  I ntegrated  D ata  A nalysis  P latform, is an innovative, cloud-based, and collaborative data aggregation and analysis platform. The platform Read More...

Lesson 1: Introduction to Unix and the Shell Lesson Objectives Review the course syllabus and general structure of lessons to come. Introduce Unix and describe how it differs from other operating systems. Introduce and get set Read More...