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.
DNA Variant Analysis with R Bioconductor
In this 4 hour workshop over 2 days, we will use R to analyze DNA variants from Variant Call Format files to identify those likely to have a functional impact. Offered biannually.
RNA-Seq Analysis with R Bioconductor
In this 4 hour workshop over 2 days, we will use R to analyze bulk RNA-seq data to perform differential expression analysis, enrichment analysis, and visualizations. Offered biannually.
Single-cell RNA-seq Analysis with R Bioconductor
In this 4 hour workshop over 2 days, we will demonstrate how to process and analyze single cell RNA-seq data using R Bioconductor packages, focusing primarily on the Seurat package. Offered biannually.
Data Cleaning with OpenRefine
Got messy spreadsheets? Open Refine is a powerful, free, open-source software tool for cleaning and transforming data in a way that is easy to reproduce. This class is targeted at people who need to clean messy data, including spreadsheets of survey responses, patient encounters, financial records, or workshop attendance. If you want something more powerful than Excel but don’t want to spend the time to learn a programming language like R or Python, OpenRefine could be the perfect tool for you! Offered quarterly.
How to Share De-Identified 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 de-identified 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 class is to get you up to speed with these new requirements and help you work reproducible and painless data sharing into your research process. Offered biannually.
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.
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.
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.
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.
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. Offered quarterly.
Python, JSON, Web API
Read JSON data from a web based API using NLM web services. Offered quarterly.
Python and MongoDB
Index and search collections of JSON documents using MongoDB. Offered quarterly.
Python Background and Prep for Natural Language Processing
Review of python techniques to work with text data. Offered quarterly.
Document Classification and Natural Language Processing
Review of python techniques to work with text data. Offered quarterly.
Cloud Tools for Machine Leaning and NLP
Survey of Google AutoML tools for document classification, image recognition, and text extraction from images and video. Offered quarterly.
R for Everyone, Part 1 & 2
In this workshop, we’ll cover: R and Rstudio; Computer Programming; Variables, Conditions, and Loops; Functions; Vectors and Matrices; Data Frames. Offered biannually.
R for Data Manipulation, Part 1 & 2
In this workshop, we’ll cover: The Tidyverse; Subsetting with select() and filter(); Transforming Variables with mutate(); Aggregating Data with group_by() and summarise(); Relational Data; Types of joins. Offered biannually.
R for Visualization, Part 1 & 2
In this workshop, we’ll cover: Grammar of Graphics; ggplot2 library; Expressiveness vs Effectiveness; Creating Communicative Visuals. Offered biannually.
Introduction to ggplot2 with R
In this 3 hour workshop, we cover how to use ggplot2to create common statistical plots using the R programming language. Offered biannually.
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 biannually.
R for Statistics, Part 1 & 2
In this workshop, we’ll cover: Descriptive Statistics vs Inferential Statistics; Types of Statistical Variables; Describing Numerical Variables; Describing Categorical Variables; Statistical Testing Basics; Correlational Tests; Comparison of Means Tests. Offered biannually.
Univariate and Bivariate Statistics with R
In this 2 hour workshop, we will use R to describe single variables and test for relationships between two variables. Offered biannually.
Regression Modeling with R, Part 1 & 2
This 2-part hands-on workshop (each part 2 hours, offered separately) covers how to build regression models using the R programming language. Offered biannually.
Power and Sample Size Calculations with R
In this 3 hour workshop, we provide a review of the concepts underlying power and sample size analysis followed by a demonstration of how to implement calculations in R. Offered annually.
Introduction to Inclusive and Collaborative Open Science
This interactive, hands-on class will cover some of the most prevalent trends in open science including open access publishing, open research data, open protocols, and open code. We will introduce emerging biomedical funder and publisher requirements for open science, describe how you can get credit and citations for your work, and share best practices for integrating open science practices into your research workflow. Offered annually.
Reproducibility for Biomedical Researchers
Have you heard about the reproducibility crisis in the sciences? Want to know how you can make your research more transparent and rigorous? Or maybe you just want to save yourself time and effort by implementing better research workflows? Then this is the workshop series for you! Offered annually.
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.