Getting Started with Python and Cloud Computing — NCBI North Texas Workshops and Codeathon 2021

Getting Started with Python and Cloud Computing — NCBI North Texas Workshops and Codeathon 2021

Learning to use computational tools and techniques is increasingly important for life scientists. But knowing where to start when learning relevant data-centric skills such as coding and cloud computing can be a big challenge. The NCBI education team is here to help!  As a part of the NCBI North Texas Workshops and Codeathon, we presented workshops that helped novice users learn about coding in Python, Jupyter Notebooks, and cloud computing.

Attendees from the greater Dallas area logged on to webinars and NCBI-provided cloud accounts to learn about programming in Python, Jupyter Notebooks, cloud computing services, and to perform relevant research tasks.

In the workshop, Getting Started with NCBI Data in Python, participants used Python to download, explore, and analyze biologically relevant NCBI data in a Jupyter Notebook.  Participants were able start programming immediately because their computing environment was managed by a running JupyterHub. Instead of struggling to setup computing environments, attendees focused on learning the fundamentals of coding in Python, best practices in computation, and worked with the NCBI Datasets resource. After completing this workshop, one participant stated that it was most useful to learn, “how different Python packages can help extract useful information from NCBI”.  Another said, “Now I am more confident using Python for NCBI data”. By tailoring this learning experience to the needs and interests of life scientists, we hope that all attendees new to coding or computational notebooks understand the power of both tools in reproducible research and feel comfortable continuing learning on their own.

While Getting Started with NCBI Data in Python utilized cloud computing services, workshop participants dove deeper into learning about the cloud in the next workshop, An Introduction to NCBI Cloud Computing for Biologists. Here, attendees learned why cloud computing is so valuable to life scientists, how to navigate cloud services, and which NCBI resources can be readily used inside the cloud. Participants completed biological examples with the NCBI Sequence Read Archive (SRA) and MagicBLAST in the cloud and uploaded results to the Genome Data Viewer . Many attendees were excited to learn how cloud computing can enhance their research and one remarked, “I will definitely use (Cloud Services) for our RNA-Seq research. It looks like you are able to do this effortlessly”. After this workshop, we hope that all participants feel familiar enough with cloud computing services to incorporate it into their work.

These workshops introduced a new group of life scientists to coding, computational notebooks, and cloud computing and, together, laid the foundation for attendees to build important computational skills. They can put these new skills to use in educational, research, or clinical settings. A number of the workshop participants put their new skills to use immediately, in the NCBI North Texas Codeathon, which we will discuss in our next post.

You can download materials from these two workshops and all the Texas events from the FTP site.  See our previous post for details on the two more traditional workshops we presented as part of these events.

If you have questions about these workshops or interest in participating in future NCBI workshops, please contact workshops@ncbi.nlm.nih.gov.

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