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Bioinformatics
10/19/2022 - Speaker: Ron Germain, M.D., Ph.D. NIH Distinguished Investigator NIAID, NIH Dr. Germain received his Sc.B. and Sc.M. from Brown University in 1970 and his M.D. and Ph.D. from Harvard Read More...
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Bioinformatics
02/06/2025 - This lesson is part of a course, B4B: Unix and Biowulf. This course will focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading and Read More...
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Bioinformatics
What is Biowulf? Explaining compute nodes, cores, CPUs, and the idea of connecting to a remote system Why work on Biowulf? Available software, increased computation power, high memory jobs, big data Connect to Biowulf Explain Read More...
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Bioinformatics
What is Biowulf? Explaining compute nodes, cores, CPUs, and the idea of connecting to a remote system Why work on Biowulf? Available software, increased computation power, high memory jobs, big data Connect to Biowulf Explain Read More...
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Bioinformatics
Upon logging on to Biowulf, the user is taken to a log in node, which should not be used for computation intensive tasks. To perform computation intensive tasks, the user should work on a compute Read More...
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Bioinformatics
Upon logging on to Biowulf, the user is taken to a log in node, which should not be used for computation intensive tasks. To perform computation intensive tasks, the user should work on a compute Read More...
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Bioinformatics
Biowulf and other HPC systems use SLURM (Simple Linux Utility for Resource Management) to manage and allocate computation resources. Note "Slurm allocates on the basis of cores." -- Biowulf swarm tutorial
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Bioinformatics
A typical RNASEQ experiment involves several steps, only one of which falls within the realm of bioinformatics. Namely the Data Analysis step. Experimental Design What question am I asking How should I do it (does Read More...
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Bioinformatics
Functional enrichment and comparison with R . ClusterProfiler, pathview, and good introductory information Article on the impact of the evolving GO Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges, PLOS Computation Biology, 2012 Pathway enrichment Read More...
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Bioinformatics
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...
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Bioinformatics
developed as early as 1991 high-level, popular, general-purpose programming language that has a readable and easy to learn syntax Key features: easy to read easy to learn interpreted multi-platform wide community open source libraries (> 300,000) Two Read More...
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Bioinformatics
06/15/2023 - Since its release in September 2005, the Gene Set Enrichment Analysis (GSEA) software and its companion gene set collections, the Molecular Signatures Database (MSigDB), have been invaluable resources for interpreting the biological significance of expression Read More...
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Bioinformatics
05/26/2022 - The Cancer Genomics Cloud (CGC), powered by Seven Bridges and funded by the NCI, is a flexible cloud platform that enables analysis, storage, and computation of large cancer datasets. The CGC provides a user-friendly Read More...
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Bioinformatics
ClusterProfiler tutorial Functional enrichment and comparison with R . ClusterProfiler, pathview, and good introductory information Article on the impact of the evolving GO Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges, PLOS Computation Biology, 2012 Read More...
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Bioinformatics
The first example will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...
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Bioinformatics
The first example will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...
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Bioinformatics
Recall The Biowulf login node is meant for job submission to the batch system and should not be used to perform any computation intensive tasks. For testing computation intensive tasks without submitting a job, request Read More...
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Bioinformatics
This class will introduce novices to essential Unix commands for getting started in bioinformatics. Unix is an operating system like Windows and MacOS. However, in Unix, users interact with the computer by issuing commands rather Read More...
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Bioinformatics
Option 1 for obtaining the class data and example Jupyter Notebook is to download the following to personal computer. Again, installation of Jupyter Lab and other computation tools is required. Example Jupyter notebook hbr_uhr_deg_ Read More...
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Bioinformatics
Given a list of numbers, it is difficult to perform mathematical operations. For instance list_of_numbers=[1,2,3,4,5] Multiplying list_of_numbers by 2 will duplicate this list. However, multiplying a list of numbers by two should Read More...
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Bioinformatics
Given a list of numbers, it is difficult to perform mathematical operations. For instance list_of_numbers=[1,2,3,4,5] Multiplying list_of_numbers by 2 will duplicate this list. However, multiplying a list of numbers by two should Read More...
Rockville, MD
Collaborative
Repositories
The NCI Cloud Resources are components of the NCI Cancer Research Data Commons (CRDC) that bring data and computational power together to enable cancer research and discovery. These cloud-based platforms eliminate the need for researchers Read More...
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October 6, 2022 crex.nih.gov CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Science & Technology Seminars and Training Events Upcoming Seminars and Educational Opportunities The following Read More...
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Bioinformatics
While bracket notation is useful, it is not always the most readable or easy to employ, especially for beginners. This is where dplyr comes in. The dplyr package in the tidyverse world simplifies data wrangling Read More...
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Bioinformatics
We can filter features observed in only a single sample. qiime feature-table filter-features \ --i-table filtered-table-1.qza \ --p-min-samples 2 \ --o-filtered-table filtered-table-2.qza Unless we explicitly remove them, removed features will remain in our FeatureData (Representative Sequences). This Read More...
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Bioinformatics
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...
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Bioinformatics
Module 1 Week 1 Introductions and File systems L1 Why bioinformatics? L2 Intro to statistics? Lesson 1 Intro to Course, learning objectives Intro to Unix operating system What is a shell (how to proceed Windows vs Mac) What Read More...
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Bioinformatics
Module 1 Week 1 Introductions and File systems L1 Why bioinformatics? L2 Intro to statistics? Lesson 1 Intro to Course, learning objectives Intro to Unix operating system What is a shell (how to proceed Windows vs Mac) What Read More...
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Bioinformatics
Let's start our exploration of sequencing read alignment by discussing the reference genome for human chromosome 22. For this, change into our ~/biostar_class/hbr_uhr/refs folder. In Lesson 9, we discussed why we need Read More...
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Bioinformatics
Let's start our exploration of sequencing read alignment by discussing the reference genome for human chromosome 22. For this, change into our ~/biostar_class/hbr_uhr/refs folder. In Lesson 9, we discussed why we need Read More...
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Bioinformatics
Biowulf is the Unix/Linux-based high-performance computing (HPC) cluster at NIH. If you do not currently use Biowulf for your data analysis needs, consider the following advantages: Much more compute power as compared to a Read More...
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Bioinformatics
A common question posed to the Bioinformatics Training and Education Program (BTEP) is “How can I learn R and Python to analyze my data?”. First, it’s important to state that learning any programming language Read More...
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Bioinformatics
09/28/2022 - We invite you to join us for the Neuro-Oncology Visiting Scholar Lecture scheduled for next week by Eytan Ruppin, M.D. Ph.D: Next Generation Transcriptomics-based Precision Oncology Eytan Ruppin received his M.D. Read More...
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Bioinformatics
08/24/2022 - Precision oncology has made significant advances, mainly by targeting actionable mutations and fusion events involving cancer driver genes. Aiming to expand treatment opportunities, recent studies have begun to explore the utility of tumor transcriptome Read More...
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Bioinformatics
12/17/2021 - Register Now Faculty: Yi Xing, PhD – Children's Hospital of Pennsylvania/University of Pennsylvania; NCI Cancer Moonshot IOTN Moderator: Kellie N. Smith, PhD – Johns Hopkins School of Medicine Target Audience This series will serve Read More...
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Bioinformatics
11/17/2021 - Register Now Faculty: Joao Xavier, PhD – Memorial Sloan Kettering Cancer Center; NCI CSBC Moderator: Matthew J. Reilley, MD – University of Virginia Target Audience This series will serve as an excellent resource for all stakeholders Read More...
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Bioinformatics
10/20/2021 - Register Now Faculty: Joao Xavier, PhD – Memorial Sloan Kettering Cancer Center; NCI CSBC Moderator: Matthew J. Reilley, MD – University of Virginia Target Audience This series will serve as an excellent resource for all stakeholders Read More...
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Bioinformatics
09/08/2021 - Register Now Faculty: Bing Zhang, PhD – BCM, NCI CPTAC Moderator: Carsten Krieg, PhD – Medical University of South Carolina Target Audience This series will serve as an excellent resource for all stakeholders interested in expanding Read More...
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Bioinformatics
08/10/2021 - Register Now Faculty: Evan Newell, PhD – Fred Hutchinson Cancer Institute Moderator: Carsten Krieg, PhD – Medical University of South Carolina Target Audience This series will serve as an excellent resource for all stakeholders interested in Read More...
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Bioinformatics
07/15/2021 - Register Now Faculty: Michael Angelo, MD, PhD – Stanford University, Moonshot Cancer Atlas Moderator: Carsten Krieg, PhD – Medical University of South Carolina Target Audience This series will serve as an excellent resource for all stakeholders Read More...
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Bioinformatics
06/17/2021 - Register Now Faculty: Dana Pe’er, PhD – Memorial Sloan Kettering Cancer Center; NCI Cancer Moonshot HTAN Moderator: Daniel Wells, PhD – Immunai Target Audience This series will serve as an excellent resource for all stakeholders Read More...
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Bioinformatics
06/08/2021 - Do you want to know how to use Machine Learning (ML) for accelerating drug discovery? Join us on June 8, 1:00 pm – 2:00 pm ET, for the first in a series of workshops on how to use Read More...
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Bioinformatics
05/27/2021 - Register Now Faculty: Shannon McWeeney, PhD – Oregon Health & Science University; NCI Cancer Moonshot DRSN Moderator: Santosh Putta, PhD Target Audience This series will serve as an excellent resource for all stakeholders interested Read More...
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Bioinformatics
05/11/2021 - Register Now Faculty: Eliezer M. Van Allen, MD – Harvard University/Dana-Farber Cancer Institute/BROAD; NCI Cancer Moonshot IOTN Moderator: Kellie N. Smith, PhD – Johns Hopkins School of Medicine Target Audience This series will serve Read More...
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Bioinformatics
04/21/2021 - Register Here Inherited and environmental influences can put people at greater risk of cancer and impact their response/resistance to treatment. In this presentation, Dr. Eliezer Van Allen will describe how a patient’s Read More...
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Bioinformatics
11/17/2020 - Please join us for a brief overview of NCI’s HALO cloud deployment and the first in a series of talks describing HALO-enabled research. Dr. Noemi Kedei, MD, CCR, will cover examples of using Read More...
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Bioinformatics
11/13/2020 - New computational opportunities and challenges have emerged within the cancer research and clinical application fields, as the size, source and complexity of cancer datasets have grown. Simultaneously, advances in computational capabilities, with exceptional growth Read More...
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Bioinformatics
06/24/2020 - Traditional methods of epidemic modeling continue to be used fruitfully for characterizing outbreaks and predicting the spread of disease in populations. However, these methods, typically rely on what are known as “compartment models”, requiring Read More...
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Bioinformatics
The example below will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...
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Bioinformatics
The example below will use Python code to demonstrate the utility of Jupyter Notebook for keeping code, output, and analysis steps all in one place. First, the import command of Python will be used to Read More...
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Bioinformatics
Here, we will download some high throughput genomic sequences from NCBI SRA. The data that we will download were derived from sequencing of the Zaire Ebola virus. See the NCBI SRA page for this study Read More...
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Bioinformatics
Recall that we are not supposed to use the login nodes to perform any computation intensive tasks on Biowulf. Instead, we should either submit a job (if staying in the log in node) with sufficient Read More...
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Bioinformatics
Here, we will download some high throughput genomic sequences from NCBI SRA. The data that we will download were derived from sequencing of the Zaire Ebola virus. See the NCBI SRA page for this study Read More...
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Confocal
Wide-field microscopy This is the technical term for a conventional fluorescence microscope. Typically the entire field of view of the specimen is illuminated with excitation light and then all of the emitted fluorescence is collected Read More...
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Confocal
Our Team Tatiana S. Karpova Ph.D.Core Headkarpovat@nih.govBuilding 41, Room C615240-760-6637 David A. Ball Ph.D.Core Biologistballa@nih.govBuilding 41, Room B114D240-760-6577 Mohamadreza Fazel, Ph.D.Core Biologistmohamadreza. Read More...
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Confocal
Software Image Acquisition Commercial imaging systems of LRBGE Optical Microscopy Core are controlled by acquisition software specifically designed for the appropriate microscope, such as ZEN (Zeiss confocal microscopes), Nikon Elements (Nikon), Imspector (Abberior). Custom-built HILO Read More...
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Confocal
Gianluca Pegoraro, PhD gianluca.pegoraro@nih.gov Facility Head 240-760-6696 Bldg. 41, Room B909 Dr. Pegoraro received his Ph.D. in Molecular Genetics from the International School of Superior Studies in Trieste, Italy in 2004. After Read More...
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Confocal
2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...
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Confocal
2024 Date: Tuesday, October 15, 2024 Time and Location: 11 am EST, ZOOM (INVITATION BY LMIG LIST SERVER) Speaker: Dr. Diego Presman (U Buenos Aires) Title: “Insights on Glucocorticoid Receptor Activity Through Live Cell Imaging” Summary: Eucaryotic transcription factors ( Read More...
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Bioinformatics
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...
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Bioinformatics
The computational chemistry and protein modeling team in the Advanced Biomedical Computational Science (ABCS) group provides novel solutions in structural modeling and computational chemistry. Computational scientists in the group collaborate with NCI researchers by using Read More...
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Bioinformatics
This lesson will introduce data wrangling with R. Attendees will learn to filter data using base R and tidyverse (dplyr) functionality. Learning Objectives Understand the concept of tidy data. Become familiar with the tidyverse packages. Read More...
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Bioinformatics
Lesson 4: Feature table filtering, taxonomic classification, and phylogeny Learning objectives learn how to apply different types of filtering to your ASV table and representative sequence data. classify your ASVs. Generate a phylogenetic tree. Now that Read More...
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Bioinformatics
RNA-SEQ Overview What is RNASEQ ? RNA-Seq (RNA sequencing), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment. (Wikipedia) Strictly speaking this could be any Read More...
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Bioinformatics
Gene ontology and pathway analysis Objectives Determine potential next steps following differential expression analysis. Tour geneontology.org and understand the three main ontologies. Learn about different methods and tools related to functional enrichment and pathway Read More...
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Bioinformatics
Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, Read More...
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Bioinformatics
Lesson 13: Aligning raw sequences to reference genome Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 11 Review In Lesson 11 we learned to aggregate multiple FASTQC reports into one using MultiQC, Read More...
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Bioinformatics
Learning Objectives Learn about popular programming languagues in bioinformatics Compare advantages and disadvantages of Python and R Discuss what you will need to learn to use these languages Discuss learning resources Choosing a programming language Read More...
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Bioinformatics
While bracket notation is useful, it is not always the most readable or easy to employ, especially for beginners. This is where dplyr comes in. The dplyr package in the tidyverse world simplifies data wrangling Read More...
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Bioinformatics
Introduction to Data Wrangling with the Tidyverse Objectives Wrangle data using tidyverse functionality (i.e., dplyr ). To this end, you should understand: 1. how to use common dplyr functions (e.g., select() , group_by() , arrange() , mutate() , Read More...
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Bioinformatics
ggpubr allows us to easily incorporate additional information into our plots (e.g., mean, individual case information, etc.). Where this package really shines is its ability to easily include the results of common statistical tests. Read More...
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Bioinformatics
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...
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Bioinformatics
Upon connecting to Biowulf, the user lands in the login node. Warning Do not use the login node to perform any computation intensive tasks on Biowulf. Instead, we should either submit a job (if staying Read More...