GCB Academy

Computational Biology Word Art

FAll 2019 Course Offerings

GCB Academy is a series of stand-alone workshops in genome topics offered to Duke faculty, postdocs, graduate students and staff at little to no fee. Sabbatical scholars and other collaborating visitors may request registration and will be accommodated on a space-available basis. The workshops, taught by faculty and staff in GCB, range from 101-style introductions in genomic technologies, computational approaches and mass spectrometer analyses to more focused topics of molecular analysis. They are intended to introduce Duke community members to the field and build capacity in areas to further their own research.

Enrollment for each course is capped at 20 students, and registration closes 10 days before each class. You will receive an enrollment confirmation 10 days before each class. For all courses, a $100 no-show fee will be assessed if you fail to notify us 24 hours before the class begins. In the event you are unable to attend your registered course(s), please contact Alexis Kessenich. Many courses have a waitlist and we can offer your spot to another person.

Register Now

View Past Course Offerings


Introduction to DNA Sequencing Technology **Waitlist Only**

Date: Sept. 30; noon – 4 P.M.
Registration Deadline: Sept. 23
Instructor: Nicolas Devos
Location: 2240 CIEMAS
Cost: Free

During the past decade, a new generation of high-throughput DNA sequencers has transformed biomedical and biotechnology research. These new technologies have fostered the development of a wide range of applications to basic and clinical research, including SNP discovery, transcriptome profiling, genome sequencing, and epigenetics. The goal of this introductory course is to teach the basic principles of next generation sequencing technology (NGS) and to present an overview of various library preparations and their applications. Advantages and limitations of various methods will be discussed and compared across technologies/platforms (Illumina, PacBio, Oxford Nanopore, Ion Torrent). This course will also provide an introduction to primary data analysis and data quality assessment steps. Attendees will become familiar with NGS technology terms and fundamentals, NGS data format and quality, and will acquire a better understanding of how to choose a suitable NGS sequencing method or instrument for their study.

Top of page


Introduction to Scientific Computing for Genomics

Dates: Nov. 4 – 5; 8:30 A.M. - 4:30 P.M.
Registration Deadline: Oct 28
Instructor: Hilmar Lapp
Location: 127 Bostock
Cost: $200 for faculty, postdocs and staff; Free for grad students

Computing has become an integral and indispensable part of genomic biology. This course teaches basic skills in scientific computing, with a focus on applications for genomic science, aimed at making you more productive, your computational work more reliable, and your research easier to reproduce and extend, including by your future self. The course includes introductions to (1) using Unix shell commands to efficiently find, organize, and stage data for analysis; (2) basic data types, control flows, functions, and 3rd party packages for the Python programming language commonly encountered in scientific computing; (3) using version control to manage with confidence the numerous directions research code takes from inception to publication; and (4) effectively using a high-performance computing cluster to run computational analyses. The format of the course is inspired by the acclaimed Software Carpentry-style bootcamps. Hence, this is a fully hands-on workshop, and students are expected to bring a laptop.

*Prerequisites: “Introduction to Unix” (or equivalent experience)

Top of page


Fundamentals of Mass Spectrometry for Proteomics and Metabolomics

Date: Nov. 8; 1 – 5 P.M.
Registration Deadline: Nov. 1
Instructor: Arthur Moseley
Location: 2240 CIEMAS
Cost: Free

Liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) continues to be the key technology for the qualitative and quantitative analysis of peptides, proteins and metabolites for both basic and clinical research projects. This GCB Academy session is designed as an introduction for researchers needing to expand their knowledge of the use of LC/MS/MS-based methods for proteomics and metabolomics, and thus help researchers better understand how these technologies can help inform their research goals. Background material in basic protein/metabolite chemistries will be provided, with an emphasis on how to use the physicochemical characteristics of these biomolecules for sample preparation specifically for LC/MS/MS analyses. In addition, the fundamentals of liquid chromatography and mass spectrometry will be discussed to enable students to understand the nuances of the experimental designs required to address their specific project. Real-world examples will be used to illustrate sample preparation and analysis strategies, including basic identification projects, characterization of Post-Translational Modifications and differential expression analyses (including 'omic biomarker discovery and targeted biomarker verification).

Top of page


RNA-Seq Analysis (Limited to 12 participants) **Waitlist Only**

Date: Nov. 11; 9 A.M. - 1 P.M.
Registration Deadline: Nov. 4
Instructor: David Corcoran
Location: Old Chem 003
Cost: $50 for faculty, postdocs and staff; free for grad students

This 4-hour tutorial will provide you with a better understanding of the data processing and analysis methods that are used in RNA-seq analysis. We will cover topics such as data quality control, normalization, and calling differentially expressed genes. We will provide hands-on experience that will allow you to go back to your lab and work with your own data.

*Pre-requisites: "Introduction to Unix" and "Introduction to Scientific Computing for Genomics" (or equivalent experience).

Top of page


Experimental Design: Get the Most Out of Your Proteome

Date: Nov. 15; 1 – 5 P.M
Registration Deadline: Nov. 8
Instructor: Matt Foster
Location: 2240 CIEMAS
Cost: Free

This course will provide an in-depth overview of experimental design, focusing on proteomic analysis of protein post-translational modifications (PTMs) and protein expression in (but not limited to) mammalian cells, tissues and biofluids. Topics will be aimed at getting maximum biological information from your samples. We will discuss methods for enriching subproteomes and PTMs; best practices for insuring sample integrity and avoiding common contaminants that will be carried downstream; and how to be aware of additional factors that might influence reproducibility across biological replicates. In addition, we will discuss where discovery-based or targeted proteomic analyses may be most appropriate. Feel free to bring specific questions about your favorite proteins, model systems, or biological matrices. Prerequisite: Fundamentals of Mass Spectrometry for Proteomic and Metabolomic Analyses, encouraged, but not required.

Top of page


Single-Cell RNA-Seq (limited to 12 participants) **Waitlist Only**

Date: Nov. 18; 9 a.m. - 1 p.m.
Registration Deadline: Nov. 11
Instructor: David Corcoran
Location: 133 Soc-Psych
Cost: $50 for faculty, postdocs and staff; free for grad students

This 4-hour hands-on tutorial will provide you with experience working with data from a single-cell RNA-Seq experiment. We will cover quality control, filtering, normalization, clustering, differential expression and mark identification analysis.

*Pre-requisites: Must have previously taken the GCB Academy “RNA-Seq Analysis” course.

Top of page


Proteomic Data Analysis: Strategies and Software Solutions

Date: Nov. 22; 1 – 5 P.M.
Registration Deadline: Nov. 15
Instructor: Erik Soderblom
Location: 2240 CIEMAS
Cost: Free

Liquid chromatography coupled with mass spectrometry (LC/MS) is a versatile tool for the qualitative and quantitative characterization of peptides, proteins and metabolites for both basic and clinical research projects. One of the most important considerations in being able to translate LC-MS datasets into meaningful biological observations is to effectively use open source software packages and/or online resources geared toward LC-MS based datasets.  This GCB Academy session is designed as a complement to GCB Academy course “Fundamentals of Mass Spectrometry for Proteomic and Metabolomic Analyses” (Nov. 7) and GCB Academy course “Experimental Design: Get the most your of your proteome” (Nov. 8) and is intended for users of the Proteomics and Metabolomics Shared Resource who have or plan on generating LC/MS based Proteomic Datasets with the Shared Resource. This first portion of the course will focus on the effective use of Scaffold to characterize qualitative proteomic datasets. This will include an overview of Scaffold and features such as interpretation of spectral matches at a protein or peptide level, gene ontology classification, homology matching, spectral count data, and data export. The second portion of the course will cover common proteomic data analysis strategies from supplemental data (typically .xlsx file formats from Rosetta Elucidator) provided as part of the Shared Resource’s quantitative proteomic workflows. This will include an overview of the typical features of a quantitative data return document, various data summarization levels, calculating peptide/protein relative fold-changes and p-values, exporting data for motif analysis (PTM specific datasets), and performing Principle Component Analysis (PCA) and 2D Clustering within JMP Pro.

 Top of page


Metabolomics for Clinical and Basic Research

Date: Nov. 25; 1 – 5 p.m.
Registration Deadline: Nov. 18
Instructor: Will Thompson
Location: 2240 CIEMAS
Cost: Free

Metabolomics has emerged as a powerful approach for characterization of molecular systems and also development of biomarkers for disease progression or diagnosis. Broadly, metabolomics is the characterization of small molecules by mass spectrometry and can include both "unbiased" or non-targeted techniques, as well as "targeted" methods.   The measurement of metabolites by mass spectrometry is also directly translatable to the clinic; many common assays such as amino acids, acylcarnitines, vitamin D epimers, steroid hormones, and drugs of abuse are all clinical mass spec assays.  Whether developing a novel assay or using a validated metabolite assay, the most important aspect for a successful metabolomics study is deciding which technique to use and understanding the data each approach will likely be able to provide. In this course, we will discuss sample types which are amenable to metabolomics, and utilize case studies to discuss the critical differences in targeted and non-targeted metabolomics and an investigator might choose one over another.  We will use example datasets to demonstrate techniques for analysis of high dimensional metabolomic data.  We will also cover the methods needed for accurate quantification, how to enable longitudinal translation of metabolomics assays, and how a targeted mass spec assay may differ in utilization from a clinical ELISA.

Top of page


Introduction to Biobanking

Date: Dec. 6; 9 – 10:30 A.M.
Registration Deadline: Dec. 2
Instructor: Tom Burke
Location: 2240 CIEMAS
Cost: Free

This seminar will offer an introductory overview of key considerations and best practices in establishing and maintaining clinical biospecimen collections for genomic and precision medicine research. Topics covered will include:  basic concepts in biobank and cohort research; role of standardization, harmonization, and quality control; maintaining unique sample identification and robust chain-of-custody tracking; need for secure information and inventory management systems for samples and data; important considerations in repository design; and an overview of biobanking resources at Duke and beyond.

Top of page