Search Results for: Cloud Storage

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...

10/11/2021 - This course uses lectures, demos, and hands-on labs to give you an overview of Google Cloud products and services so that you can learn the value of Google Cloud and how to incorporate cloud-based 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...

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...

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...

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.

06/10/2022 - Join the upcoming NCI Containers and Workflows Interest Group (CWIG) webinar to learn about the research and functionality available through the University of California, San Francisco’s (UCSF) Information Commons. As an open-source platform, Read More...

02/11/2022 - Dr. Jeremy Goecks will share how cancer researchers are using the machine learning capabilities of the Galaxy project, one of the largest and most widely used open-source platforms for biomedical  data science , to predict Read More...

10/08/2021 - Dr. Pjotr Prins and Arun Isaac will present their Concise Common Workflow Language (CCWL). CCWL makes code reusable and adaptable across a variety of software and hardware environment while following FAIR+ (Findable, Accessible, Interoperable, Read More...

01/10/2020 - In this introductory course, you will learn about AWS products, services, and common solutions. You will learn the fundamentals of identifying AWS services so that you can make informed decisions about IT solutions based Read More...

As the NCI Center for Biomedical Informatics and Information Technology, CBIIT provides training classes, data sharing and storage solutions, seminars and blogs on data science and bioinformatics. Upcoming data science and informatics presentations, conferences, workshops, Read More...

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...

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

03/10/2021 - Register now to watch the presentation The term “data commons” is used across NIH to describe data-hosting repositories. But data commons can differ widely in what they offer, from simple storage and infrastructure to Read More...

04/12/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...

04/11/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...

04/09/2019 - DNAnexus provides a secure cloud based platform for the analysis, storage and sharing of many different types of genomic data. CCR has recently established a Pilot program to enable CCR researchers to use this Read More...

Note This is not an exhaustive list. cBioPortal cBioPortal is a platform for exploratory and interactive visualization, analysis, and download of cancer genomics data. With cBioPortal You can quickly view genomic alterations across a set 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...

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...

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...

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

The Central Repository provides the research community at the NCI with various cryogenic services, including low-temperature storage from +4° C to -196° C, controlled-rate freezing, computerized inventory and distribution of samples. The Central Repository is operated 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...

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...

10/29/2024 - In this presentation, you will get an overview of the Cancer Digital Slide Archive (CDSA) platform. CDSA is an open source, web-based platform for storage, visualization, and management of digitized whole slide images.& 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...

Due to limits on computational resources, you may be interested in running your analysis on an HPC. Biowulf is the NIH high performance compute cluster. It has greater than 90k processors, and can easily perform 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...

Factors are an important data structure in statistical computing. They are specialized vectors (ordered or unordered) for the storage of categorical data. While they appear to be character vectors, data in factors are stored as 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...

Globus (https://hpc.nih.gov/storage/globus.html) HPCDME BOX OneDrive (s)FTP Network Drives Flash Drives

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...

These are considered appropriate if you are planning on doing all the data analysis yourself. High performance Linux computer (multi core, high memory, and plenty of storage) Familiarity with the “command line” and at least Read More...

Two introductory lessons on Biowulf were presented in this course series. You can access those here and here . The first contains an introduction to Biowulf including information regarding storage space and the module system. The Read More...

Biowulf is the high performance computing cluster at NIH. When you apply for a Biowulf account you will be issued two primary storage spaces: 1) /home/$User and 2) /data/$USER , with 16 GB and 100 GB of default 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...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Spotlight The NIH Lab Managers Working Group have developed a new NIH-wide database of cold Read More...

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

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...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Derive Greater Insights and Accelerate your Research Using Bioinformatic Tools! CREx is an NIH 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...

Back Services: Biophysics Facility offers Tycho as an open-access instrument.  This instrument is very easy to use, and no formal training is required.  Core staff will help with their first experiment of new 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...

Learning Objectives Understand the components of an HPC system. How does this compare to your local desktop? Learn about Biowulf, the NIH HPC cluster. Learn about the command line interface and resources for learning. What 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...

03/19/2024 - Vinton “Vint” Cerf, Ph.D., is the special guest for the 2024 J. Edward Rall Cultural Lecture, The Promises and Perils of AI in Biomedical Research and Health Care Delivery. Dr. Read More...

03/06/2024 - The NCI Cancer Diagnosis Program in the Division of Cancer Treatment and Diagnosis is hosting a workshop, “Digital Pathology Imaging (DPI) in Cancer Clinical Trials and Research.” This workshop will 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...

The data type of an R object affects how that object can be used or will behave. Examples of base R data types include numeric, integer, complex, character, and logical. R objects can also have 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...

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...

Data Analysis Overview RNASEQ - Data Analysis WorkFlow Mostly Computational intensive task requiring signigicant computer hardware. Quality Control Sample quality and consistency Is Trimming appropriate - quality/adaptors Alignment/Mapping Reference Target (Sequence and annotation) 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...

Electron Microscopy Laboratory (EML) The EML offers investigators access to unique expertise and EM technologies that allow our partners to explore new avenues of research to enhance the knowledge of biological systems. To assist our Read More...

The EML offers investigators access to unique expertise and EM technologies that allow CCR Investigators to explore new avenues of research in order to enhance the knowledge of biological systems. To assist our customers, we Read More...

Total end-to-end system for single-cell research [embed]https://youtu.be/vMzhSzg1rUw[/embed] The BD Rhapsody Single-Cell Analysis system empowers and streamlines your research with a complete system of tools, including reagents and analysis software, Read More...

The Blood Processing Core monitors viral load in patients with HIV and performs sequential studies using samples obtained from patients with cancer, AIDS, chronic granulomatous disease, or other diseases associated with immunologic dysfunction. The core Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. If you haven’t Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Research Festival The NIH Research Festival highlights the groundbreaking science and the vibrant NIH community driving our Read More...

The NIH Biowulf Cluster provides researchers with a world-class system to assist in solving complex biomedical problems as diverse as gene variation in worldwide human populations, deep learning to model protein structures, and PET brain Read More...

The AgingResearchBiobank was officially launched in January 2019 with a mission to provide a state-of-the-art inventory system for the storage, maintenance, and distribution of de-identified biospecimens and associated phenotypic, clinical, and imaging data from numerous NIA-funded Read More...

Home About the Biophysics Core Biophysics Core Services [tabby title="Instrumentation"] NHLBI Biophysics Core The Biophysics Core Facility: Overview Core Facilities provide scientific resources, cutting-edge technologies and novel approaches to support DIR scientists. Availability of 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...

Most BTEP courses include detailed course materials including lesson content, additional resources, and lesson associated data. These course materials are listed here so that learners can easily return to and review concepts taught in class 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...

What is bioinformatics? Bioinformatics integrates biology, statistics, and computer science to develop and apply theory, methods, and tools for the collection, storage, and analysis of biological and related data. Bioinformatics plays a critical role in 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...

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...

Objectives To understand some of the most basic features of the R language including: Creating R objects and understanding object types Using mathematical operations Using comparison operators Creating, subsetting, and modifying vectors By the end 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...

Learning Objectives Learn about data structures including factors, lists, data frames, and matrices. Load, explore, and access data in a tabular format (data frames) Learn to write out (export) data from the R environment 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...