The ISB Cancer Gateway in the Cloud (ISB-CGC) offers multiple avenues for accessing and analyzing large-scale cancer datasets, including TCGA, TARGET, CPTAC and important references such as GENCODE and COSMIC. ISB-CGC users can process petabytes of data using complex workflows written in the language of their choice (including but not limited to CWL, WDL, Snakemake, Nextflow, etc). They can develop new analyses using SQL, Python, and R to mine data including gene expression, protein abundance, and somatic mutations in easily accessible and queryable tables. Updated interactive web tools at isb-cgc.org allow cohort creation, data discovery, and exploration. In our cloud computing session, we will demonstrate common bioinformatic workflows using both Python and R while integrating various omic data types such as gene mutations, copy number, gene expression, methylation, and proteomics. We will show how this can be interactively and iteratively performed in the cloud using the ISB-CGC platform. Attendees will receive hands-on training on optimizing analyses using “burstable” cloud tools, which enables the user to rapidly combine and interrogate their cancer datasets with those available at the Cancer Research Data Commons.
Creating a good scientific poster can be difficult. This class provides participants with tips and best practices to develop an engaging poster that conveys information clearly. This session is a short introduction for those new to creating a scientific poster and a refresher for those more experienced.Training Category: Writing and Editing Classes
In this class, you will learn tips that can help increase your chances of being published. Topics include: publishing strategies; evaluating and choosing a target journal; formatting your cover letter and manuscript; responding to peer-review comments; and how to make your research stand out. Join us as we discuss writing, editing, and publishing issues from an editor’s perspective.Training Category: Writing and Editing Classes
Publons is a profiling tool that integrates with ORCID to help you track your publications, citation metrics, peer reviews, and journal editing work in one, easy-to-maintain profile. In this session, learn how you can use Publons to: easily prepare tenure/review documentation by downloading a record summarizing your publications, editorial board memberships and verified peer review activities; train early career researchers how to conduct high-quality peer review with the Publons Academy; and take control of your Author Record & ResearcherID in the Web of Science to ensure that all of your work is correctly attributed to you.Training Category: Databases and Searching Classes
This is an introductory level class for participants to familiarize themselves with Deep Learning concepts and techniques using MATLAB. These techniques can be used to solve complex problems related to images, signals, text and controls. The training session will be held on two days.
On day one of the training, attendees will become familiar with Deep Learning concepts and techniques using MATLAB Online to train deep neural networks on GPUs in the cloud and create deep learning models from scratch for images and signal data.
On day two of the training, attendees will explore pretrained models and use transfer learning. We will touch on how MATLAB can interoperate with other deep learning frameworks as well as automatically generate optimized code for embedded targets.Training Category: Data Services Classes
Join this session to learn how Web of Science and InCites can help you understand the scientific impact of a research organization. In this session, COVID-19 will be used as an example topic, but the search, discovery and analytics workflows presented can be utilized for any research landscape analysis. This class will cover how to:
- Navigate the global research activities around COVID-19 research and find key researchers who are impacting the trajectory of this research area
- Use analytical tools to fully understand the research landscape, discover public and private sector collaborations and funding activities, and visualize your results
- Include real-world patient data in your analyses to drive more informed strategies
Bibliometric data from Web of Science and InCites can be used to analyze the impact of a research institution’s funding portfolio. Join this training session to learn how to:
- Identify the disease areas for which the NIH has provided funding and the institutions that are benefitting from this support
- Examine the key opinion leaders in your area of interest to identify funding opportunities and potential external reviewers
- Use data from publisher-neutral experts to measure NIH progress towards funding goals
Cortellis Drug Discovery Intelligence is an online tool that supports pharma and drug development by providing biological, chemical, and pharmacological data from disparate sources in a single platform. This training will cover how you can use Cortellis to benchmark, design and improve methods and models to predict a drug’s behavior in humans.
Embase is a biomedical and clinical database of bibliographic information. This seminar will explain Embase's features and how it compares to other databases like PubMed. It will include designing queries, using form-based queries, multiple search strategies, combining searches, and conference and literature coverage. This class was designed for beginners and intermediate NIH users.Training Category: Databases and Searching Classes
This class will provide valuable tips on how to use EndNote to make the systematic review process easier. Participants will learn how to download a copy of the EndNote software, add references, create and use groups for screening references, manage duplicates, and full text PDF’s, how to add reviewer comments to a record, and finally insert and format references into your systematic review manuscript. Tips will also be provided on the best way to share your EndNote library with your colleagues on the systematic review team.
Key Pathway Advisor (KPA) is a web application for biological pathway analysis of OMICs data. This session will demonstrate using KPA to: explore the biological meaning of data; predict key protein activity changes that could be the root cause of gene expression alterations; understand how biological pathways are impacted by data; create hypotheses about new targets, mechanisms of action, biomarkers and disease associations; and align results with current knowledge of biomarkers and drug targets. Bioinformatics experience is not required to use this tool.
Biowulf is a Linux cluster designed for large numbers of simultaneous jobs common in the biosciences. It is a powerful tool; one node in Biowulf has more memory than a typical desktop computer. NIH CIT now has a MATLAB site license on Biowulf, so any investigator at the NIH can use MATLAB. In conjunction with the High Performing Computation team, this beginner/intermediate two-hour course covers setting up an account and accessing Biowulf, as well as running MATLAB on Biowulf, from routine beginner MATLAB applications to operating MATLAB on thousands of cores.Training Category: Data Services Classes
OFF-X is a translational safety intelligence portal built to help organizations identify toxicology and safety signals, mitigate safety liabilities, and de-risk early-stage assets. In this session, participants will learn how to use OFF-X API calls to integrate OFF-X translational safety data with in-house information sources. Attendees will then learn how to: build artificial intelligence models with high-quality curated data; assess potential safety liabilities to evaluate risk-benefit profiles; determine optimal secondary pharmacology drug screens to anticipate potential off-target toxicities; use reverse-pharmacology to identify the cause and mechanisms behind unexpected adverse events; and analyze biomedical literature to assess the potential safety signals identified in real-world evidence databases, such as FAERS (FDA Adverse Event Reporting System Electronic Submissions) or JADER (Japanese Adverse Drug Event Report). Please note: OFF-X is not licensed by the NIH Library,
This introductory training will cover how to develop hypotheses for off-target interactions and guide experimental assay planning using OFF-X. OFF-X is a safety and toxicity intelligence portal for drugs and targets of pharmacological interest. Early identification of off-target interactions is essential to help reduce patient burden and attrition rates related to toxicology and safety issues. Note: the NIH Library is currently reviewing this product but does not have a subscription to it at this time. For more information, contact the NIH Library Bioinformatics Support Team.
This course will demonstrate how an Author Profile can be used to showcase and track an author research impact, h-index, citations, and references. The session will also show you how to validate and correct your author profile on Scopus.
This session will demonstrate how you can track the research progress and impact of an institution. It will also demonstrate how to compare institution performance using sophisticated analytical tools built into Scopus.
Cortellis Drug Discovery Intelligence supports pharma and drug development by providing biological, chemical, and pharmacological data from disparate sources in a single platform. The Biomarkers Module of Cortellis Drug Discovery Intelligence provides continually updated information that supports biomarker research at every stage of drug research and development. This introductory training will cover two main features of the Cortellis Drug Discovery Intelligence Biomarkers Module: how to assess the biomarker landscape around research areas of interest and how to find efficacy biomarkers for clinical studies. Note: the NIH Library is currently reviewing this product but does not have a subscription to it at this time. For more information, contact the NIH Library Bioinformatics Support Team.
Evaluating variants according to the American College of Medical Genetics and Genomics (ACMG) guidelines can be an extensive process that requires an in-depth understanding of all available criteria for any cell variant. VSClinical is software that uses a single testing paradigm to automate the complex ACMG guidelines process. Copy Number Variation (CNV) is a type of structural variation in which sections of the genome are duplicated or deleted. This class will show examples of the new CNV analysis guidelines, assess the impact of CNV on Gene and Gene Dosage, and demonstrate how the Golden Helix CNV caller can streamline the analysis process. Golden Helix’s VarSeq-CNV (VS-CNV) is a calling algorithm that uses one testing paradigm to provide a true simplification of a clinical workflow. Attendees will learn how to simplify and streamline this process without losing user-control of final results or overlooking any crucial criteria components necessary for final classification.
VSClinical is designed for researchers to efficiently process the clinical interpretation of variants based on Association for Molecular Pathology (AMP) and American College of Medical Genetics and Genomics (ACMG) guidelines. This class will review the importance and value of automating the search for available clinical trials for the improvement of cancer treatment and prevention. Attendees will explore content and examples leveraged by VSClinical for site, inclusion criteria, relevant drugs, and matching biomarkers. The following topics will be covered: somatic guidelines inclusion of reporting on clinical trials, NCI source database clinical trial content, automated integration of accessing clinical trial content from VSClinical, and example biomarkers to demonstrate the process to report.
Clinical variant analysis is a three-stage process that entails quality control and processing of data, creating a draft report for cell variant evaluations using different genomic databases and annotation sources, assessing the draft report, and signing-off on the final report. VSClinical is software that uses a single testing paradigm to consolidate and automate the workflow of this three-part analysis. Participants will learn how to use VSClinical to transfer data between different users, evaluate germline and somatic cell variants according to the American College of Medical Genetics (ACMG) and Association for Molecular Pathology (AMP) guidelines, and create clinical reports with the new Word-based templates.