Experts at the library can help with a wide range of topics from literature searching to programming to 3D printing. Descriptions for our most frequently offered classes and workshops are below. To register, view upcoming Library Events and Classes
and filter by category. Have a question about a class? Ask us.
Basic Statistics With R
In this 4 hour workshop, we will use R to perform some common statistical analyses such as regression modeling with continuous, binary and survival outcomes. Although this is not an introduction to R programming or statistics, this workshop is ideal for those who are just starting to use R for data analysis. Offered biannually. Related: class materials
Computation with UCSF clinical data on Information Commons
In this 3 hour hands-on workshop, we will go through a real case study to explore de-identified UCSF Electronic Health Records using UCSF Information Commons. You will learn how to query UCSF clinical data and gain some of the skills necessary for building your own computational models in this environment. Related: class materials
Data Cleaning with OpenRefine
Got messy data? Open Refine is a powerful, free open-source software tool for cleaning and transforming spreadsheet data in a way that is easy to reproduce. This 1.5 hour workshop will cover basic data cleaning in Open Refine, including faceting, clustering, and sorting. Offered biannually. Related: class materials
DNA Variant Analysis with R Bioconductor
In this 3 hour workshop, we will use R to analyze DNA variants from Variant Call Format files to identify those likely to have a functional impact. It is intended for those with intermediate R programming skills. Offered biannually. Related: class materials
Getting Started with Information Commons
This 3 hour workshop is intended for Information Commons account holders who want guided tutorials on how to use the cluster to access and query the data. Many of the topics on the Information Commons Wiki will be covered, and we will walk you through examples. You will also have time to work on your own queries with help from the instructors. Related: class materials
How to Share Research Data
If you are funded by the NIH, HHMI, or Gates Foundation, or plan to publish in PLOS, PNAS, Science or Nature it is very likely that you will be asked to make your research data publicly available. This is part of a global effort to make research results more transparent, reproducible, and equitable. But what data do you share and how exactly should you share it? The goal of this 1 hour workshop is to get you up to speed with these new requirements and help you work reproducible and painless data sharing into your research process. Related: class materials
Intro to SQL
This 3 hour workshop will provide an introduction to SQL, the structured query language used to access relational databases. You’ll learn how to import data into a database, run queries, filter results, aggregate data, and join multiple tables based on a common element. Offered quarterly. Related: class materials
Introduction to Machine Learning
This 3 hour workshop will begin with an introduction to machine learning lecture to review overall concepts, common algorithms and applications. This will be followed by a programming workshop using Python’s scikit-learn library. Offered annually. Offered annually. Related: class materials
Introduction to Python, Part 1
This 3 hour workshop “Reading Data from an API with Python and JSON”, uses the National Library of Medicine’s Drug Interaction web services to demonstrate how to gain access to data available through a RESTful API through Python. Offered quarterly. Related: class materials
Introduction to Python, Part 2
This 3 hour workshop is designed to be a follow up workshop to Introduction to Python, Part 1. Participants will build on core programming skills and learn to use common Python libraries for data analysis including Pandas for tabular data analysis and matplotlib for graphing and plotting. Offered quarterly. Related: class materials
Introduction to R Programming
This 4 hour workshop covers the basic syntax of the R statistical programming language, best practices, how to read and write data, how to write loops and functions, and other tasks that will help you get started in performing analyses. This is intended for those with no previous R programming experience. Offered biannually. Related: class materials
Introduction to Unix
This 3 hour workshop will introduce the UNIX shell using Bash. You’ll learn to navigate the file system, manipulate files and directories, search the filesystem with grep and find, write simple loops and scripts, and automate basic tasks. Offered quarterly. Related: class materials
Reproducibility for Biomedical Researchers
In this 8-part workshop series, we will learn how to design a rigorous experiment free of bias, make our work more transparent by sharing our protocols, publications, code, and data, and build a culture of reproducibility in our labs. Related: class materials
RNA-Seq Analysis with R Bioconductor
In this 3 hour workshop, we will use R to analyze bulk RNA-seq data to perform differential expression analysis, enrichment analysis, and visualizations. It is intended for those with intermediate R programming skills. Offered biannually. Related: class materials
Single-cell RNA-seq Analysis with Bioconductor
In this 3 hour workshop, we will demonstrate how to process and analyze single cell RNA-seq data using R Bioconductor packages, focusing primarily on seurat. It is intended for those with intermediate R programming skills who are familiar with the biological concepts of single cell RNA-seq. Offered biannually. Related: class materials
Version Control with Git
Git and github are widely used tools for sharing, versioning, and collaborating on code, data, and other documents. In this 2 hour workshop, you’ll learn to access code from a github repository and create and share code on your own github repository. You’ll also learn to use git to create and manage different versions of a document, save work in progress, and collaborate on a shared code base with other researchers and programmers. Related: class materials
Writing R Packages
This 3 hour workshop will cover all the steps required for writing your own R package for submission to GitHub or CRAN. This is ideal for advanced R programmers. Offered biannually. Related: class materials
Foundations in the CLE
Foundations in the CLE covers the foundation skills needed to manage a course within the CLE. Online course. Related: class materials
Advanced Techniques in the CLE
Advanced Techniques in the CLE is an online course for users with prior CLE experience to explore more advanced topics. Online course. Related: class materials
Makers Lab 101
Never been to a makerspace or used any of the equipment before? The Makers Lab 101 pop-up is designed to provide an introduction to the Makers Lab and an understanding of what is possible to create using the technology and supplies available.
3D Printing at UCSF Part I, II, and III
Did you know anyone from the UCSF community can 3D print right inside of the Parnassus Library? Are you curious about the applications for 3D printing at UCSF? We offer a series of courses that cover topics such as 3D design & modeling using the web-based application, Tinkercad, and 3D printable models from CT scans.
Virtual Reality Demo
Join us as we discover applications for virtual reality (VR) technology at UCSF. In this demo, we will review the basics for using VR in the Makers Lab and attendees will explore a number of the VR experiences currently available.
3D Carving Demo
Are you interested in subtractive processes working with a variety of materials i.e., wood, acrylic, metal? Sign up for a 3D carving demo and learn the basics of 3D carving so you can reserve the Carvey and further explore CNC routing.
Sewing Machine Demo
Whether you are a beginner with no experience or needing a refresher on the sewing machine, the sewing machine demo will cover the basics to get you up and sewing.
Die Cutting Demo
Do you want to learn how to make precision cuts on various materials like vinyl, paper, leather, or fabric? The die cutting demo will show you the basics of the Cricut software and the Cricut die cutter machine.
3D Printing Meet-up
Come together for the 3D Printing Meet-Up to discuss all things related to 3D printing. This meet-up is open to anyone interested in the topic, so bring your questions, ideas, thoughts, and perspectives. Offered quarterly.
Systematic Review Series
Provides an overview to Systematic Reviews and the various resources they use such as PubMed, Embase, and Web of Science. Related: Systematic Review guide
PubMed for Clinicians
We all use PubMed for research, but did you know that the database has features to help you quickly find evidence for clinical questions? This class will go over keyword searching vs. MeSH, filters, Clinical Queries, and some features in UptoDate. Related: class materials
Super Searching: PubMed, Embase, and Beyond
Let us show you how to get the best results from your search. Go beyond the Google searching methods to get a handle on database logic and complex search strategies.
Finding Funding Through Pivot
Are you looking for funding to support your research, training, fellowship, postdoc or program/curriculum development? This class will show you how to navigate Pivot, a comprehensive database of funding opportunities. Related: class materials and Grants guide
Manage Your Citations with Endnote
EndNote is a powerful research tool that helps you gather, organize, analyze, and share your sources. This class will show you how to set up, import, organize, and add citations to a paper you are writing.
Using Zotero for Research
Like EndNote, Zotero is a powerful research tool that helps you gather, organize, analyze, and share your sources. Unlike EndNote, Zotero is free, open source, and easy to use.
Copyright: Images, Open Content, and Fair use
Covers finding and using images in education, using open access publications and other open content, and how to apply fair use if using copyright protected materials in your lectures.