During the past year, BTEP has been making a number of on-line bioinformatics resources available to the CCR research community.  These may be of particular benefit  for “home-bound” researchers seeking to learn bioinformatics skills during their extended telework period.  

Remote Learning via on-line courses run by BTEP

  • “Bioinformatics for Beginners” with the Biostar Handbook (starting by 4/21, approximately)
  • DataQuest for learning programming skills (starting by 4/25, approximately)

Click here for more information

(Unfortunately, because these classes are commercial products, these resources are only available to CCR staff, and require registration before you can be provided access).

Training opportunities from other NIH organizations

  • FAES is currently offering several on-line courses for Bioinformatics and Data Science
  • NCI CBIIT has started a program for remote learning for Data Science

Webinars and Recorded Seminars that others may find useful

Re-assessing the Human Gene Catalog and Human Genome: How Much Are we Missing?  Steven Salzberg
Videocast link:  https://videocast.nih.gov/summary.asp?live=34578

Methods for Characterizing the Activity of Mutational Processes in Cancer.  Max Leiserson
Video link: https://btep.ccr.cancer.gov/wp-content/uploads/Max-Leiserson-BTEP.mp4?_=1

Marshaling Public Data for Lean and Powerful Splicing Studies. Ben Langmead
WebEx recording: https://cbiit.webex.com/cbiit/ldr.php?RCID=da15d3aface8f25f7f478b9a813f6499

To Function or Not to Function. Sridhar Hannenhalli
WebEx Recording: https://cbiit.webex.com/cbiit/ldr.php?RCID=ec72d1923ffe18a82b63ed348b75be0c

 

This page lists webinar recordings on NCI-licensed scientific software.

BioDiscovery Nexus Copy Number and Nexus Expression

Description: Nexus Copy Number software offers simple yet powerful tools for copy number (CNV) and sequence variation analysis and visualization from aCGH, SNP array as well as next-gen sequencing (NGS) data. Nexus Expression makes gene expression analysis easier than ever with user-friendly and platform independent software tools. Both programs include the TCGA Premier database.

Training Webinar and Tutorials: 

Nexus Copy Number Basics – Play recording (44 min)
Nexus Copy Number Advanced – Play recording (50 min)
Nexus Copy Expression – Play recording (44 min)


CLC Genomics Workbench

Description: The CLC Genomics Workbench enables comprehensive analysis of NGS data, including whole genome and transcriptome data, de novo assembly, targeted resequencing analysis, variant calling, ChIP-seq and DNA methylation (bisulfite sequencing analysis). The software also includes a streamlined workflow for taxonomic and functional microbiome analysis.

Training Webinar and Tutorials: Play recording (1 hr 4 min)


Geneious Pro

Description: Geneious Pro is a bioinformatics software platform that is both ultra-powerful and easy to use. Scientists, researchers and students are able to search, organize, and analyze genomic and protein information via a single desktop program that provides publication ready images to enhance the impact of your research.

Training Webinar and Tutorials: 

Introduction to Geneious Prime – Play recording (56 min)


Ingenuity Pathways Analysis (Qiagen)

Description: Ingenuity Pathway Analysis (IPA) is a web-based functional analysis tool for comprehensive omic data.

Training Webinar and Tutorials:

Ingenuity Pathway Analysis Basics – Play recording (1 hr 4 min)

Ingenuity Pathway Analysis Advanced – Play recording (57 min)

Qiagen Ingenuity Pathways Analysis Resources


Lasergene

Description: Lasergene Core Suite is a comprehensive DNA and protein sequence analysis software suite comprised of nine applications. Lasergene Core Suite is available in four configurations, each designed with different researchers in mind. This software includes functions for sequence assembly and SNP detection, automated virtual cloning and more

Training Webinar and Tutorials: 

Lasergene Molecular Biology – Play recording (1 hr 2 min)

Lasergene Genomics Suite – Play recording (57 min)


MetaCore

Description: High quality biological systems content in context, giving you essential data and analytical tools to accelerate your scientific research.

Training Webinar and Tutorials:

Play recording (1 hr 1 min)

Thompson Reuters MetaCore Resources


Partek Flow

Description: Partek Flow software is designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. With an easy-to-use graphical interface and the ability to build your own custom analysis pipelines or download pipelines built by Partek scientists, you can perform:

  • Alignment
  • Quantification
  • Quality control
  • Statistics
  • Visualization

SupplierPartek Incorporated

Software Access: For access to Partek Flow, NCI users must first:

  • have a Helix account — a Helix account can be obtained here https://hpc.nih.gov/docs/accounts.html
  • have a /data directory with enough disk space to hold their Partek Flow files — please fill out this online form here https://hpc.nih.gov/nih/storage_request.html if you do not already have a /data directory or if you require more disk space.
  • have a Partek Flow account created for them — please contact staff@helix.nih.gov.

Once these steps have been accomplished, Partek Flow is available at https://partekflow.cit.nih.gov/flow.

Training Webinar and Tutorials:

Play recording (57 min)

Partek Flow Resources


Partek Genomics Suite

Description: Partek Genomics Suite software offers an intuitive user interface and built-in workflows for a variety of genomic applications that guide researchers though every step of the analysis process.

Training Webinar and Tutorials:

Play recording (57 min)

Partek Genomics Suite Resources


Qlucore Omics Explorer (QOE)

Description: The QOE is an interactive data analysis and visualization software that enables biologists to find groups, structures, variable networks and discriminating variables in large Omics data sets, including public datasets.  Data types include gene expression data (NGS and arrays), DNA methylation, metabolomics, proteomics, etc.  QOE supports multiple visualization plots (e.g. 3D PCA, t-SNE, heat maps with hierarchical clustering etc.), a number of statistical methods (t-test, F-test (ANOVA), etc.) and an inbuilt Gene Set Enrichment Analysis (GSEA) workbench for pathway analysis.

Training Webinar and Tutorials: Play recording (42 min)


SnapGene

Description: SnapGene enables an easy and secure way to plan, visualize, and document everyday molecular biology procedures. With an intuitive interface, the software enables DNA sequence visualization, sequence annotation, sequence editing, cloning, protein visualization, and simulating common cloning methods. The software also enables documentation and sharing of data.

Training Webinar and Tutorials:  Play recording (55 min)

 

This list contains pointers to recorded Webinars of CBIIT sponsored Informatics Technology for Cancer Research (ITCR) tools.

 

  • UCSC Genome Browser Basics (Part One) 
  • cBioportal is hosting a webinar series to teach cBioPortal features to beginner and advanced users. Sessions will be held on five consecutive Thursdays at 11 AM EDT, starting on April 30th. Please register here: https://bit.ly/cbioportal-webinar-2020

    What is cBioPortal

    The cBioPortal for Cancer Genomics is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. The goal of cBioPortal is to significantly lower the barriers between complex genomic data and cancer researchers by providing rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects, and therefore to empower researchers to translate these rich data sets into biologic insights and clinical applications.
  • Past webinars featuring Partek Flow that Partek® has hosted. Partek Flow is a CCR licensed product