GCB Academy

Computational Biology Word Art


On Demand Courses

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.

There is no enrollment cap for online courses. Enrollment for in-person courses is capped at 20 students, and registration closes 7 days before each class. You will receive an enrollment confirmation 3 days before each class. For all in-person 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 Julia Walker. Many in-person courses have a waitlist and we can offer your spot to another person.

Additional fall courses may be added at a later date. Please check back for updates.

View Past Course Offerings

Fundamentals of Mass Spectrometry for Proteomics and Metabolomics - VIRTUAL
Date: Part I: Sept. 15, 1-2 PM; Part II: Sept. 22, 1-2 PM; Part III: Sept. 29, 1-2 PM
Registration Deadline: Sept. 10
Instructor: Arthur Moseley
Location: Zoom -- link will be emailed to participants
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).

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Introduction to DNA Sequencing Technology -- IN PERSON ** WAITLIST ONLY
Date: Part I: Oct. 7, 1 - 2:25 PM; Part II: Oct. 14, 1-2:25 PM
Registration Deadline: Sept. 30
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. 

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A high-performance computing cluster empowers users to harness computational power far beyond that of a single machine. This online course module teaches users how to run and manage computational analyses on the HARDAC cluster, Duke's high-performance computing resource tailor-designed for computational genomics. The course module consists of a set of interactive activities that take users from connecting to HARDAC all the way to running powerful array jobs. To follow the activities included in this course, users must be granted access to HARDAC, which is available to everyone on Duke's campus through the Computational Solutions service center. To inquire about access, please contact the Computational Solutions team.
View/Download Course Slides

Custom software is a common component of almost any computational workflow. Using and installing these on a shared high-performance computing environment such as HARDAC presents challenges due to frequently conflicting recursive dependency chains and versions. A number of mechanisms have been developed to isolate software environments, their versions, and their dependencies from each other, and understanding these is key in recruiting already installed software packages, and installing one's own. This course teaches the use of Environment Modules as provided on HARDAC in part 1, and Conda Environments in part 2. A third installment is planned for teaching the use of Singularity containers. To follow the material in this class effectively, you should have access to HARDAC, and you should have taken (or have full command over the material presented in) the "High Performance Computing (HPC) / SLURM Best Practices for HARDAC" online course.
View/Download Course Slides Part 1: Environmental Modules          View/Download Course Slides Part 2: Conda Environments

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