SPEAKER: Meliha Yetisgen, PhD. In this talk, I will summarize the ongoing research in my lab on building generalizable machine learning based Natural Language Processing (NLP) approaches to process clinical text for secondary use applications in the domains of cancer and substance abuse.
Programming Hacky Hour
Overview Hacky Hour is an opportunity for you to get feedback on a current programming project from your peers at UCSF or to work independently. Dedicate an hour to working on your programming project. Have you been trying to learn programming but can’t find the time? Bring your lunch, get away from your desk, and […]
Introduction to Python Part 1
This workshop will provide an introduction to programming in Python for people with little or no previous programming experience. We will cover basic variable assignment, loops, conditionals, and lists. Exercises will be hands on and use the Jupyter notebook environment. For installation instructions and course material, please see the CLE course page for Intro To Python Part […]
After the Algorithm: Making Machine Learning Work in Healthcare
Innovate For Health presents Dr. Leonard D’Avolio, Assistant Professor Brigham & Women’s Hospital & Harvard Medical School Co-founder, Cyft Abstract: In his talk, titled “After the Algorithm: Making Machine Learning Work for Healthcare,” Leonard D’Avolio, Ph.D. shares lessons learned from 15 years of experience designing, developing, and deploying machine learning-enabled systems in academic, government, philanthropic, and […]
Precision Medicine World Conference
PMWC, the “Precision Medicine World Conference” is the largest & original annual conference dedicated to precision medicine. PMWC’s mission is to bring together recognized leaders, top global researchers and medical professionals, and innovators across healthcare and biotechnology sectors to showcase practical content that helps close the knowledge gap between different sectors, thereby catalyzing cross-functional fertilization […]
Intro to Python Part 2
This workshop will provide a continuation of the topics from Intro to Python Part 1. We will cover basic additional programming constructs, including dictionaries, tuples, functions, file input/output, and tabular data with pandas. Exercises will be hands on and use the Jupyter notebook environment. For installation instructions and course material, please see the CLE course page for Intro To […]
Chalk Talk
UCSF-Stanford Joint Symposium Series on Biomedical Informatics
Presentations: 2-4 pm Reception: 4-5 pm Speakers: Ida Sim, MD, PhD – Professor of Medicine; Co-director of Informatics and Research Innovation, Clinical and Translational Sciences Institute; Director of Digital Health, Division of General Internal Medicine, UCSF Andrew Gentles, PhD – Assistant Professor of Medicine in Biomedical Informatics and Biomedical Data Science, Stanford University Courtney Lyles, […]
Advanced computational methods with UCSF clinical data on Information Commons
In this 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.
Intro to Python, Part 3
Bakar Institute-Wide Lab Meeting
Featured Labs Computational Modeling and Machine Learning of Brain Diseases Presenter: Ashish Raj, PhD Lab: Ashish Raj Mutational landscape of the non-coding regulatory regions in metastatic prostate cancer: insights from integrative modeling Presenter: Ruhollah Moussavi-Baygi, PhD Lab Hani Goodarzi and Felix Feng
NLP@UCSF Meetup
Agenda In the first NLP@UCSF meetup of 2020, we will learn about extracting structured information from clinical text with APACHE cTAKES and do a hands-on demo of the UCSF’s pre-configured cTAKES pipeline, built by Bakar’s Research Computing team and offered as a free self-service tool for UCSF community. APACHE cTAKES – In-Depth Overview. Gundolf Schenk, PhD, Principal Data Scientist, […]
Introduction to Cytoscape and Network Biology for Biologists
The course will introduce the basic concepts of biological network analysis and provide practical instruction on commonly used tools and databases with a focus on Cytoscape to analyze and visualize biological networks. The course will comprise theoretical and practical sessions where course participants will learn how to perform different biological network analyses and how to […]
Biostatistics and Bioinformatics Seminar
Title: Machine Learningbased Design of Proteins and Small Molecules Presenter: Jennifer Listgarten, PhD Professor Dept of Electrical Engineeriing and Computer Sciences, University of California, Berkeley With the advent of more and more highthroughput technologies to measure protein properties of interest such as binding, expression, fluorescence, the time for machine learning to act synergistically with protein […]
UCSC Genome Browser Workshop
The UCSC Genome Browser is a powerful web-based tool for interacting with genome assemblies of many organisms. This workshop will introduce you to the wealth of data contained in the browser and related databases, and will allow you to integrate and compare results of your genomic and transcriptomic experiments. The main morning session, held in […]
Training procedures and regulatory policies for safe machine learning models in healthcare
Introduction to Cytoscape and Network Biology for Computer Scientists
The course will introduce the basic concepts of biological network analysis and provide practical instruction on commonly used tools and databases with a focus on Cytoscape to analyze and visualize biological networks. The course will comprise theoretical and practical sessions where course participants will learn how to perform computational analyses of biological networks and how […]
Intermediate Cytoscape: Networks and Omics Data Visualization
This course is a complement to “Introduction to Network Biology and Cytoscape” from the previous day. Following a brief review of the key concepts of network analysis, we will embark on a deep dive into data visualization and advanced Cytoscape features. We will work through three prepared use cases demonstrating various omics data types and […]
Biostatistics and Bioinformatics Seminar
Speaker: Mark Segal Professor, Department of Epidemiology and Biostatistics University of California San Francisco Abstract: It can arise that underused data analytic methodology may enjoy wide-ranging applicability. I showcase use of the Patient Rule Induction Method (PRIM) at two radically different scales: (1) identifying genomic ‘3D hotspots’ — localized regions wherein an attribute superposed on […]
Intro to R data analysis
The high-level language of R is considered one of the most powerful languages for quantitative analysis, statistics, and graphics. This workshop will help you get started with analyzing your datasets and creating graphs for visualization. No background in statistics or computing necessary. *Bring your laptop with RStudio and R installed.
Bakar Institute-Wide Lab Meeting
Featured Lab Computational discovery of therapeutic candidates for preventing preterm birth Presenter: Brian Le, PhD Marina Sirota Lab Read the UCSF story here! Please make sure to RSVP as food will be provided Zoom Join from a PC, Mac, Linux, iOS or Android device: https://ucsf.zoom.us/j/215774568 Meeting ID: 215 774 568 Telephone: US: +1 669 900 6833 […]
Postponed: Bakar Institute Seminar Series
Please note that this seminar is postponed. A new date will be determined. Speaker: Hyun Min Kang, Associate Professor of Biostatistics University of Michigan, Ann Arbor Title : Robust and scalable methods for massively sequenced genomes and single-cell transcriptomes Abstract : The rapidly accelerating pace of genome and single-cell transcriptome sequencing holds great promise for […]
Intro to RNA-seq analysis
Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. To quantify the expression levels, RNA-seq has become one of the most popular experimental methods. This workshop will provide an introduction to a typical bulk RNA-seq protocol and focus on the data analysis steps […]
Seminar Series
Robust and scalable methods for massively sequenced genomes and single-cell transcriptomes Speaker: Hyun Min Kang, Ph.D. ABSTRACT: The rapidly accelerating pace of genome and single-cell transcriptome sequencing holds great promise for precision medicine but also sets us tremendous computational and statistical challenges at an unprecedented scale. These challenges include accurately calling genetic variants from petabytes […]
Intermediate R data visualization
The high-level language of R is considered one of the most powerful languages for quantitative analysis, statistics, and graphics. This hands-on workshop will be taught as a two-part webinar. It is designed for folks who have some experience in using R and are looking to take their R skills to the next level. We shall […]
Gladstone Institute of Data Science and Biotechnology Virtual Chalk Talk
Bakar Institute Presentations – UCSF COVID-19 Response Town Hall
Watch the UCSF Health and Campus COVID-19 Response Town Hall for presentations from: Bakar Institute director Atul Butte MD, PhD on UC-wide COVID data efforts Bakar Institute affiliated faculty Vivek Rudrapatna MD, PhD, on the new COVID-19 County Tracker – a data visualization app to help all of us better understand the impact of the COVID-19 pandemic at the local level. The app features plots of […]
Batch Correction with Bulk RNA-Seq
Bulk RNA-seq has become routine for unbiased transcript/gene expression quantification in samples across multiple conditions. There is currently data for literally hundreds of thousands of samples on public databases like the Gene Expression Omnibus (GEO). We may be tempted to include data from some of these samples in our own analyses to either enrich or provide […]
Webinar: Introduction to R for Data Analysis
The scripting language of R is considered one of the most powerful languages for quantitative analysis, statistics, and graphics. This workshop will help you get started with analyzing your datasets and creating graphs for visualization. We’ll do hands-on exercises to demystify data analysis using R. From our previous experience in teaching this workshop, we know […]
Webinar: Introduction to Unix Command Line
High dimensional data integration
Biological processes like gene regulation are complex involving multiple modalities. It is becoming more common to query biological processes using multiple orthogonal and related assays to get a more complete understanding. For example, one may assay expression of genes using RNA-seq and chromatin state using Atac-seq in the samples associated with the underlying conditions of […]
Webinar: Intermediate R RNA Seq Analysis
The learning objectives for this workshop include: How to go from a matrix of raw gene expression counts to differentially expressed genes. How to analyze experimental designs that go beyond 2-group comparisons using edgeR’s generalized linear modeling capabilities. Ways to test specific hypotheses using a joint model fit. Prerequisites: A minimum of 4 to 6 […]
Intro to RNA-Seq Analysis
Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. To quantify the expression levels, RNA-seq has become one of the most popular experimental methods. This hands-on workshop will provide an introduction to a typical bulk RNA-Seq protocol and focus on the data analysis […]
Intro to Python Part 1
This workshop will provide an introduction to programming in Python for people with little or no previous programming experience. We will cover basic variable assignment, loops, conditionals, lists, and functions. Exercises will be hands on and use the Jupyter notebook environment. Note: This workshop will be offered online through UCSF Zoom. You will receive an email […]
Intro to Pathway Analysis and Visualization
This workshop introduces biologists to functional enrichment analysis (including pathways and GO) and effective visualization. You will learn about different enrichment analysis methods, and will get hands-on experience using online functional enrichment tools. You will also learn how to visualize data on pathways resulting from enrichment analysis. No programming experience required. Visit the workshop site […]
Intro to Python Part 2
This workshop is designed to be a follow up course 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, Note: This workshop will be offered online over UCSF Zoom. You […]
Intermediate R RNA-Seq Analysis
RNA-Seq is a powerful tool to interrogate cellular functions. This intermediate workshop will teach you the skills you need to get the most out of your RNA-Seq data through analysis in R. By the end of the workshop, you will know how to: Go from a matrix of raw gene expression counts to differentially expressed […]
Intro to SQL
This course will provide an introduction to SQL, the structured query language used to access relational databases. In this workshop, 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. The focus of this class is on gaining familiarity with the […]
Intro to Pathway Modeling
This workshop will teach you both why and how to use pathways in research and paper figures. First, you’ll get an overview of pathway drawing, covering tools and curation steps, including PathVisio, WikiPathways, Curation Guidelines, and the WikiPathways Curation Process. Then, you’ll have a chance to put your new knowledge to work in a hands-on […]
UCSF AI4ALL Symposium
Please join us for the AI4ALL Program Symposium! Schedule of Events 1 pm: Symposium Keynote Marylyn Ritchie, PhD “The Future is Now: How Technology and AI Have Advanced Genomics and Medicine” 2 pm: AI4ALL Project Presentations: Project 1: AI for Global Health – AI and COVID-19 Time Series Data Project 2: COVID-19 Protein-Protein Interactions (PPI) […]
Whole Genome Sequence Analysis
This course will be both theoretical and hands-on. You will learn the main tools used to do alignment, variant calling, annotation, and visualization. You will start with raw FASTQ reads and get to annotated variants (VCF files). Intermediate Level: This is an intermediate workshop in the Whole Genome and Exome Analysis series. Prior experience with […]
2020 Research Data Series: COVID-19 Data Sources at UCSF
COVID-19 Data Sources at UCSF Presented by: Eugenia Rutenberg and Dima Lituiev Description: UCSF has several data sources available for COVID-19 research. In this session, we will review the data sources — including UCSF COVID-19 Data Mart, UC-wide CORDS data, and de-identified data for research. We will describe the sources of this data, the structures where […]
2020 Research Data Series: UCSF De-Identified Clinical Data Warehouse in Epic-based and OMOP Format
De-Identified CDW and OMOP Data Presented by: Research Data Team (IT ARS and BCHSI Information Commons): Rick Larsen, Eugenia Rutenberg, Evan Phelps, Brian Chan, Dima Lituiev, Hunter Mills, Oksana Gologorskaya, Ellen Clary Description: This session will feature an overview of the structured de-identified UCSF research data assets, De-Identified Clinical Data Warehouse, and De-Identified OMOP. We […]
2020 Research Data Series: Mapping COVID-19: UCSF Health Atlas and Citizen Science Study
Mapping COVID-19: Health Atlas and Citizen Science Study Presented by: Debby Oh and Mark Pletcher Description: In this session, learn about how mapping COVID-19 data in the context of population health factors can help elucidate the drivers of the pandemic. Important Notes This is an online event. A link to join will be sent by […]
2020 Research Data Series: UCSF Research Data Overview
Overview of Research Data and Resources Available at UCSF Presented by: Rick Larsen and Eugenia Rutenberg Description: An overview of the resources, including data, tools, compute, and support available to you at UCSF and how to get started. Important Notes A link to join online will be sent by email 1 hour prior to the event. Registrations […]
2020 Research Data Series: UCSF Compute Environments
High Performance Comuputing Environments at UCSF Presented by: Henrik Bengtsson and Sandeep Giri Description: Overview of options including Wynton, AWS and RAE (Research Analysis Environment) and upgraded MyResearch. Important Notes A link to join online will be sent by email 1 hour prior to the event. Registrations close 1 hour prior to the event. Events may […]
2020 Research Data Series: Meet RAE – The New MyResearch
Meet “RAE” – The New MyResearch Presented by: Rhett Hillary Description: The MyResearch platform you already know and love has just gotten better – meet “RAE”. Short for Research Analysis Environment, RAE offers free, premium, and new AWS cloud options to support UCSF researchers and collaborators. Join us for a demo and discussion of how RAE’s secure […]
2020 Research Data Series: Information Commons and AI Modeling
Information Commons and AI Modeling Presented by: Sharat Israni Description: Information Commons is a fast and easily searchable and accessible repository of all UCSF clinical data and models, and related basic science and population data, that enables UCSF research and discovery of new health insights underlying precision medicine, to improve patient and health care. Important […]
2020 Research Data Series: De-mystifying Data Sharing … your questions answered by UCSF experts
Join this session to learn about “data sharing,” from 1) sharing research data with external partners, 2) taking in research data from somewhere else, and 3) requirements for sharing data for reproducibility of results, as required for publication. Experts from Privacy, IRB, Academic Research Systems, Security, Contracts, & Library will answer your questions! REGISTER HERE […]
2020 Research Data Series: Medicare Data and other External Datasets
Medicare Data and other External Datasets Presented by: Joanne Spetz Description: Join us for an overview of various pathways (and their tradeoffs) to accessing CMS and MarketScan Data at UCSF. Joanne Spetz PhD will share information about the datasets and on how to access them for your own research. REGISTER HERE Important Notes A link to […]
2020 Research Data Series: Patient ExploreR- A user interface to navigate UCSF’s electronic health records
Patient ExploreR– A user interface to navigate UCSF’s electronic health records Presented by: Oksana Gologorskaya Description: Learn about Patient ExploreR, an application that produces patient-level interactive and dynamic reports and visualization of clinical data, without requiring programming skills. REGISTER HERE Important Notes A link to join online will be sent by email 1 hour prior to […]
2020 Research Data Series: Navigating Digital Innovation at UCSF: One researcher’s experience
Navigating Digital Innovation at UCSF: One researcher’s experience Presented by: Ida Sim Description: Hear one frontline innovator describe her efforts to develop, deploy and study digital innovations in the clinical environment here at UCSF. Learn more about the budgeting, timelines, buy-in and approvals necessary. REGISTER HERE Important Notes A link to join online will be sent by […]
2020 Research Data Series: Images and Tools in the Imaging Commons
Images and Tools in the Imaging Commons Presented by: Jason Crane and Pablo Damasceno Description: Learn about current processes for accessing UCSF’s radiological images, and the tools and systems available for deep image analysis, along with the related clinical records. REGISTER HERE Important Notes A link to join online will be sent by email 1 hour prior […]
2020 Research Data Series: Building SMART on FHIR Apps at UCSF
Building SMART on FHIR Apps at UCSF Presented by: Eric Meeks and Andrew Robinson Description: Interested in leveraging FHIR to build and integrate digital health apps at UCSF? Come hear two developers walk through their process in creating a new SMART on FHIR app. REGISTER HERE Important Notes A link to join online will be sent by […]
2020 Research Data Series: UCSF GitHub available now!
UCSF GitHub available now! Presented by: Alina Goncharova Description: Learn about UCSF on-premise GitHub, which is safe for patient data and proprietary code. REGISTER HERE Important Notes A link to join online will be sent by email 1 hour prior to the event. Registrations close 1 hour prior to the event. Events may be recorded. Slides […]
R Fundamentals Part 1: Introduction
Students will learn how to navigate the R Studio environment. You will also learn how to store data, characteristics of basic data types and data structures, the importance of data frames (think Excel spreadsheets), and how to save your work. Overview of Workshop Series Data are the foundations of the social and biological sciences. Familiarizing […]
Python Fundamentals Part 1
This four-part, interactive workshop series is your complete introduction to programming Python for people with little or no previous programming experience. By the end of the series, you will be able to apply your knowledge of basic principles of programming and data manipulation to a real-world social science application. Part 1 Topics: Running Python Jupyter […]
R Fundamentals Part 2: Subsetting and Reshaping
Students will be introduced to loading data from files and various ways to subset it with an emphasis on bracket notation. You will also learn how to use logical vectors, search for and subset missing data, and merge data frames. Terms like subset, bracket notation, and logical vectors will be defined and reintroduced in Part […]
Python Fundamentals Part 2
This four-part, interactive workshop series is your complete introduction to programming Python for people with little or no previous programming experience. By the end of the series, you will be able to apply your knowledge of basic principles of programming and data manipulation to a real-world social science application. Part 2 Topics: Lists Loops Conditionals […]
R Fundamentals Part 3: Data exploration
Students will be introduced to data exploration and analysis in R. You will learn how to summarize data and explore it with histograms, scatterplots, and boxplots. You will also be introduced to coding statistical data analysis via t-tests, analyses of variance, correlation, and linear regression. Overview of Workshop Series Data are the foundations of the […]
Python Fundamentals Part 3
This four-part, interactive workshop series is your complete introduction to programming Python for people with little or no previous programming experience. By the end of the series, you will be able to apply your knowledge of basic principles of programming and data manipulation to a real-world social science application. Part 3 Topics: Dictionaries Files Libraries […]
R Fundamentals Part 4: For loops and functions
In the final part, you will learn the basics of automation through for loops and functions. We will also walk through a Monte Carlo simulation from scratch and examine the probabilistic “birthday problem”. Overview of Workshop Series Data are the foundations of the social and biological sciences. Familiarizing yourself with a programming language can help […]
Python Fundamentals Part 4
This four-part, interactive workshop series is your complete introduction to programming Python for people with little or no previous programming experience. By the end of the series, you will be able to apply your knowledge of basic principles of programming and data manipulation to a real-world social science application. Part 4 Topics: We will apply […]
BIDS-BCHSI Research Xchange Forum
Research Talk — Lowry Kirkby, 2019-2021 I4H Fellow. TITLE: Using a Biomedical Knowledge Graph for Medical Diagnosis Prediction ABSTRACT: Neurodegenerative diseases and dementias are heterogeneous in their underlying brain dysfunction and symptomatic experience, however, objective methods for subtyping these complex disorders are lacking. As such, patients often receive a catch-all diagnosis and undergo a trial-and-error approach to […]
UC Love Data Week – Day 1
UC Love Data Week is a week-long offering of presentations and workshops focused on data access, management, security, sharing, and preservation. All members of the University of California community are welcome to attend. Make sure to register with your UC-campus email. Register Here PUBLISHING DATA AT DRYAD @ 9:00 – 10:00 am Speakers: Wasila Dahdul […]
UC Love Data Week – Day 2
UC Love Data Week is a week-long offering of presentations and workshops focused on data access, management, security, sharing, and preservation. All members of the University of California community are welcome to attend. Make sure to register with your UC-campus email. Register Here INTRODUCTION TO LOCATING SECONDARY DATA & SEARCHING DATA REPOSITORIES: SOCIAL SCIENCES EDITION […]
UC Love Data Week – Day 3
UC Love Data Week is a week-long offering of presentations and workshops focused on data access, management, security, sharing, and preservation. All members of the University of California community are welcome to attend. Make sure to register with your UC-campus email. Register Here DATA “OWNERSHIP”: RIGHTS AND RESPONSIBILITIES @ 9:00 – 10:00 am Speaker: Michael Ladisch […]
UC Love Data Week – Day 4
UC Love Data Week is a week-long offering of presentations and workshops focused on data access, management, security, sharing, and preservation. All members of the University of California community are welcome to attend. Make sure to register with your UC-campus email. Register Here BASIC STATISTICS IN R (PART 1) @ 10:00 am – 12:00 pm Speakers: […]
UC Love Data Week – Day 5
UC Love Data Week is a week-long offering of presentations and workshops focused on data access, management, security, sharing, and preservation. All members of the University of California community are welcome to attend. Make sure to register with your UC-campus email. Register Here INTRO TO TEXT MINING AND NLP FOR HEALTH DATA @ 10:00 am – […]
Text Analysis Fundamentals in Python, Part 1
This hands on workshop goes through the common “preprocessing recipe” that is used as the foundation for a variety of other applications as well as some basic natural language processing techniques. These include: a) removal of stopwords, numbers, punctuation, b) tokenization, c) calculation of word frequencies / proportions, and d) part of speech tagging. Prior […]
Text Analysis Fundamentals in Python, Part 2
This hands on workshop builds on part 1 by introducing the basics of Python’s scikit-learn package to implement unsupervised text analysis methods. This workshop will cover a) vectorization and Document Term Matrices, b) weighting (tf-idf), and c) uncovering patterns using topic modeling. Prior knowledge: We will be using the NLTK Python package, so basic familiarity with […]
Text Analysis Fundamentals in Python, Part 3
In this workshop we will cover the most common CTA task: supervised classification. Using the Python library scikit-learn, we will implement Logistic Regression and Random Forest methods to perform sentiment analysis. Optional: introduction to word vector representations with Word2Vec. Prior knowledge: We will be using the NLTK Python package, so basic familiarity with Python is required […]
2021 Research Data Series: EMERSE and Exploring UCSF Clinical Notes
EMERSE and Exploring UCSF Clinical Notes Presented by: Alina Goncharova and Brian Turner Description: We now have a large set of 100+ million clinical notes from the UCSF Electronic Health Record available for research. While the ultimate goal is to certify these notes as fully de-identified, we are still in the midst of the certification process. So in the […]
Introduction to Cytoscape and Network Biology for Biologists
Join this course for an introduction to the basic concepts of biological network analysis and practical instruction on commonly used tools and databases, with a focus on Cytoscape to analyze and visualize biological networks. The course will comprise theoretical and practical sessions in which you will learn how to perform different biological network analyses and […]
BIDS-BCHSI Research Xchange Forum
Research Talk — Haley Hunter-Zinck, 2019-2021 I4H Fellow. TITLE: Comparison of synthetic electronic health record data generation techniques for training predictive clinical models ABSTRACT: Synthetic data is gaining attention for facilitating electronic health records (EHR) data access for building predictive clinical models. Currently, there are several methodologies for generating synthetic data. Some rely on access to real and patient-level EHR […]
Introduction to R Data Analysis
The scripting language R is considered one of the most powerful languages for quantitative analysis, statistics, and graphics. This workshop will help you get started using R to analyze your datasets and create graphs for visualization. You’ll do hands-on exercises to demystify data analysis using R. This workshop is designed for those who have no […]
Bakar Institute-wide Lab Meeting
Intermediate Cytoscape: Networks and Omics Data Visualization
This course is a complement to “Introduction to Network Biology and Cytoscape.” Following a brief review of the key concepts of network analysis, you will embark on a deep dive into data visualization and advanced Cytoscape features. You will work through three prepared use cases demonstrating various omics data types and strategies. You are encouraged […]
R Geospatial Data Part 1
Geospatial data are an important component of data visualization and analysis in the social sciences, humanities, and elsewhere. The R programming language is a great platform for exploring these data and integrating them into your research. Part 1: Getting started with spatial data objects Part one of this workshop series will introduce basic methods and […]
R Geospatial Data Part 2
Geospatial data are an important component of data visualization and analysis in the social sciences, humanities, and elsewhere. The R programming language is a great platform for exploring these data and integrating them into your research. Part 2: Geoprocessing and analysis Part two of this workshop series will dive deeper into data driven mapping in […]
R Visualization
This workshop will provide an introduction to graphics in R with ggplot2. Participants will learn how to construct, customize, and export a variety of plot types in order to visualize relationships in data. We will also explore the basic grammar of graphics, including the aesthetics and geometry layers, adding statistics, transforming scales, and coloring or […]
Introduction to Unix Command Line
R Census Geospatial
Since 1790, the US Census has been THE source of data about American people, providing valuable insights to social scientists and humanists. Mapping these data by census geographies adds more value by allowing researchers to explore spatial trends and outliers. This workshop will introduce three key packages for streamlining census data workflows in R: tigris, […]
BIDS-BCHSI Research Xchange Forum
“Socioeconomic Risk Screening, Documentation, and Interventions” Speaker: Ben Lacar, PhD, Innovate for Health Fellow Abstract: Social determinants of health (SDOH) are conditions of the environments of people that affect a wide range of health, functioning, and quality-of-life outcomes. Despite the recent recognition that social adversity can negatively affect health, patient-level screening for socioeconomic adversity or […]
R Functional Programming
This workshop helps you to step up your R skills with functional programming. The purrr package provides easy-to-use tools to automate repeated things in your entire R workflow (e.g., wrangling, modeling, and visualization). The end result is cleaner, faster, more readable and extendable code. I highly recommend you to take this workshop (1) if you […]
Bakar Institute-wide Lab Meeting
Python Data Wrangling and Manipulation with Pandas
Pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with ‘relational’ or ‘labeled’ data both easy and intuitive. It enables doing practical, real world data analysis in Python. In this workshop, we’ll work with example data and go through the various steps you might need to prepare data […]
Python Visualization
For this workshop, we’ll provide an introduction to visualization with Python. We’ll cover visualization theory and plotting with Matplotlib and Seaborn, working through examples in a Jupyter (formerly IPython) notebook. The following plot types will be covered: line, bar, scatter, and boxplot. We’ll also learn about styles and customizing plots. Throughout the workshop, we’ll discuss […]
R Introduction to Machine Learning tidymodels
Machine learning often evokes images of Skynet, self-driving cars, and computerized homes. However, these ideas are less science fiction as they are tangible phenomena that are predicated on description, classification, prediction, and pattern recognition in data. To social scientists, such methods might be critical for investigating evolutionary relationships, global health patterns, voter turnout in local […]
R Introduction to Deep Learning
This workshop introduces the basic concepts of Deep Learning – the training and performance evaluation of large neural networks, especially for image classification, natural language processing, and time-series data. Like many other machine learning algorithms, we will use deep learning algorithms to map input data to their appropriately classified outcome labels. You will use the […]
Python Fundamentals Part 1
This four-part, interactive workshop series is your complete introduction to programming Python for people with little or no previous programming experience. By the end of the series, you will be able to apply your knowledge of basic principles of programming and data manipulation to a real-world social science application. Part 1 Topics: Running Python […]
UCSC Genome Browser Workshop
The UCSC Genome Browser is a powerful web-based tool for interacting with genome assemblies of many organisms. This workshop will introduce you to the wealth of data contained in the browser and related databases, and will allow you to integrate and compare results of your genomic and transcriptomic experiments. Prior experience with the Browser is not […]
BIDS-BCHSI Research Xchange Forum
Title: “Digital Health Platform for Corneal Opacities and Cataracts Management” Speaker: Saeed Seyyedi, PhD, Innovate for Health Fellow Abstract: Cataracts and corneal opacities are eye disorders that affect the vision and are two of the most common causes of blindness world-wide, ranking as first and fourth, respectively. Early detection of these disorders can facilitate the […]
Python Fundamentals Part 2
This four-part, interactive workshop series is your complete introduction to programming Python for people with little or no previous programming experience. By the end of the series, you will be able to apply your knowledge of basic principles of programming and data manipulation to a real-world social science application. Part 2 Topics: Lists Loops Conditionals […]
Python Fundamentals Part 3
This four-part, interactive workshop series is your complete introduction to programming Python for people with little or no previous programming experience. By the end of the series, you will be able to apply your knowledge of basic principles of programming and data manipulation to a real-world social science application. Part 3 Topics: Dictionaries Files Libraries […]
Python Fundamentals Part 4
This four-part, interactive workshop series is your complete introduction to programming Python for people with little or no previous programming experience. By the end of the series, you will be able to apply your knowledge of basic principles of programming and data manipulation to a real-world social science application. Part 4 Topics: We will apply […]
Computational Cancer Community (C3) Meeting
This recurring monthly meeting focuses on cancer genomics and computational cancer biology and oncology. It provides a forum for UCSF labs to share largely unpublished data work to get feedback and input. For Zoom information or to be added to the C3 calendar invite, contact edna.rodas@ucsf.edu Speakers: Eric Chow, PhD, Assistant Professor, Biochemistry and Biophysics […]
Bakar Institute-wide Lab Meeting
Speakers: Jean Feng, PhD, Assistant Professor, UCSF Department of Epidemiology & Biostatistics Talk title: “Bayesian Logistic Regression for Online Recalibration and Revision of Risk Prediction Models with Safety Guarantees” Ryan Hernandez, PhD, Associate Professor, UCSF Department of Bioengineering and Therapeutic Sciences Talk title: “Evolutionary Forces Shape the Genetic Architecture of Complex Traits”
2021 Research Data Series: New COVID-19 Data for Research
From UCSF data to city-wide data, UC-wide data, state-wide data, national data and more — tune in to hear about the variety of data sources available and also from investigators who are using the data for their research projects. The session will also cover how to get started with each of the datasets. REGISTER HERE […]
BIDS-BCHSI Research Xchange Forum
Join us for feature presentations by Elizabeth Smith on “Scaling the Impact of PSMA-PET in Clinical Decision Making” and Reza Eghbali on “A Treatment Recommendation System for CNS Lymphoma.” Elizabeth Smith’s Title: Scaling the Impact of PSMA-PET in Clinical Decision Making ABSTRACT: Prostate cancer is the most common cancer and third-leading cause of cancer […]
