2020 Research Data Series: Building SMART on FHIR Apps at UCSF

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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!

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Speakers: Yulin Hswen, PhD, Department of Epidemiology & Biostatistics Talk title: TBA   Tony Capra, PhD, Department of Epidemiology & Biostatistics "Beyond single variant hypotheses: machine learning to improve interpretation of candidate rare disease variants" Link to Zoom

R Geospatial Data Part 1

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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 […]

Intermediate Cytoscape: Networks and Omics Data Visualization

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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 2

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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

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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

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Knowing how to use the command line of your computer can save you a lot of time. In this workshop, you will learn how to navigate the Unix terminal. The only thing you need is a Mac or Linux laptop (you can use Windows if you can’t access a Linux machine). Topics to be covered […]

R Census Geospatial

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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

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"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

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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

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Speakers: Abhejit Rajagopal, PhD, Postdoctoral Scholar, Peder Larson Lab, Dept of Radiology and Biomedical Imaging Talk title: TBA Wagahta Semere, MD, MHS, Assistant Professor, Department of Medicine Talk title: TBA

Python Data Wrangling and Manipulation with Pandas

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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 […]

Computational Cancer Community (C3) Meeting

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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   "Single-molecule epigenomic views of chromatin architecture" Vijay Ramani, […]

Bakar Institute-wide Lab Meeting

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Speakers: Janine Lupo, PhD, Associate Professor, Department of Radiology and Biomedical Imaging Talk title: TBA Sara Murray, MD, MAS, Associate Professor, Division of Hospital Medicine along with Hossein Soleimani, PhD, Data Scientist, UCSF Health Informatics Talk title: "Automated Measurement of Resident Work Hours" For Zoom information contact edna.rodas@ucsf.edu

Computational Cancer Community (C3) Meeting

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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   “Discovering the anticancer potential of existing drugs by systematic […]

Bakar Institute-wide Lab Meeting

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Speakers: "Bayesian Reconstruction of Brain Networks with Electromagnetic Imaging" Srikantan Nagarajan, PhD, Professor in Residence of Radiology and Biomedical Imaging   "EHR as Behavioral Microscope: Studying Physician Task Switching and Implications for Outcomes" Julia Adler-Milstein, PhD, Professor of Medicine   For Zoom information contact edna.rodas@ucsf.edu

Advanced Command Line

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Knowing how to use the command line of your computer can save you a lot of time. In this advanced workshop, you will learn how to navigate the Unix terminal, process files, set permissions, etc. The only thing you need is a Mac or Linux laptop (you can use Windows if you can’t access a Linux […]

Bakar Institute-wide Lab Meeting

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Speakers: Gabriela Fragiadakis, PhD, Assistant Professor of Medicine Title: "Profiling immune state using single-cell methods"   Henry Martell, PhD, Postdoctoral Scholar, Pediatrics; Sweet-Cordero Lab Title: “Mutational Signatures In Pediatric Cancer”   Contact edna.rodas@ucsf.edu for Zoom details.

Statistics of Enrichment Analysis

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Gene set or pathway enrichment methods allow researchers to assign functional or mechanistic significance to results from high-throughput assays like RNA-sequencing. In this workshop, you’ll learn the theory behind some of these methods, and how to interpret the associated results. REGISTER HERE

Introduction to Cytoscape and Network Biology for Biologists

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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 […]

Introduction to Pathway Analysis and Visualization

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This workshop is an introduction to functional enrichment analysis and effective visualization. You will learn about different enrichment analysis tools and methods, and how to use them. You will also learn how to visualize data on pathways and GO terms resulting from enrichment analysis. No programming experience required. Visit the workshop site for more details and materials. […]

Intermediate Cytoscape: Networks and Omics Data Visualization

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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 […]

Computational Cancer Community (C3) Meeting

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Please join us as we continue to develop a community of practice around cancer research that utilizes computational methods. This month's speaker: Geoff Lyle, representing UCSC's Treehouse Childhood Cancer Initiative Title: "Harmonizing Transcriptomic Data To Discover Clinically Relevant Overexpressed Genes In Pediatric Cancer Patients" Geoff Lyle is a Data Analyst with the Treehouse Childhood Cancer Initiative at University […]

Bakar Institute-wide Lab Meeting

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Speaker: Katie Pollard, Professor, Epidemiology & Biostatistics Title:  “Deep-learning prediction of disease variants that disrupt 3D genome folding"   Contact edna.rodas@ucsf.edu for Zoom details.

Hypothesis Testing

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When you attempt to make discoveries, you test new hypotheses using experimental data and hope that a skeptical and discerning person would start to believe your claims. Hypothesis testing, a branch of statistics, is a step you can rely on to bolster your claims. In this workshop, you will gain a fundamental understanding of common […]

Bakar Institute-wide Lab Meeting

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This month's meeting will have two speakers. Please join us!   Title: "SPOKE: a biomedical knowledge graph enables precision medicine at scale" Speaker: Sergio Baranzini, PhD, Professor, UCSF Department of Neurology   Title: "Semantic interoperability for wearable data" Speaker: Simona Carini, MA, Programmer, Ida Sim Lab   Contact edna.rodas@ucsf.edu for Zoom details.

Introduction to RNA-Seq Analysis

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Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. RNA-Seq has become one of the most popular experimental methods to quantify gene expression levels. This 2-day hands-on workshop will provide an introduction to a typical bulk RNA-Seq protocol and focus on the data […]

Computational Cancer Community (C3) Meeting

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Please join us as we continue to develop a community of practice around cancer research that utilizes computational methods. This month’s speaker: Jay Shendure, Professor of Genome Sciences, University of Washington Talk title: Global views of development and cancer Speaker Bio: Jay Shendure is an Investigator of the Howard Hughes Medical Institute, Professor of Genome Sciences at […]

Working with Biomedical Graph Databases

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Scientific databases are a critical resource for modern biomedical researchers and practitioners. Graph databases are a specialized type of database that offer distinct advantages for storing and representing biomedical knowledge. Major NIH initiatives are funding the development of new biomedical graph databases to support advanced queries and reasoning not possible with traditional relational databases. Learn […]

Single Cell RNA-Seq Analysis

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This 4-session workshop will focus on the analysis of single-cell RNA-Seq data, starting from raw count matrices and progressing to network analysis of single-cell datasets. You’ll analyze data using R and Cytoscape. Attendance at all four sessions is required.  Register here! October 22, 10am–12pm: Loading data, quality control, normalization, feature selection, dimensionality reduction October 22, 2–4pm: Dimensionality […]

NLP@UCSF: Applications of NLP in Radiology

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This presentation will explore how Natural Language Processing can be used to extract information from reports in radiology, from breast density extraction in structured text to brain tumor characteristics in unstructured descriptions. The use of regex, cTAKES, and LSTM-based models will be highlighted. Here are some optional pre-reading materials to brush up on topics related […]

Computational Cancer Community (C3) Meeting

HD 160 1450 3rd Street, San Francisco

Please join us as we continue to develop a community of practice around cancer research that utilizes computational methods. This month's meeting will consist of several exciting lightning talks. Attendees may attend in person (HD-160) or virtually.  For Zoom information or to be added to the C3 calendar invite, contact edna.rodas@ucsf.edu    

Bakar Institute-wide Lab Meeting

This month’s meeting will have two speakers. Please join us! Title: "Improving Diagnostic Strategies for Injured Children: Machine Learning for Pediatric Abdominal Ultrasound" Speaker: Aaron Kornblith, Associate Professor, Departments of Emergency Medicine and Pediatrics   Title: TBA Speaker: Kate Rankin, Professor, Division of Memory and Aging, Department of Neurology   Contact edna.rodas@ucsf.edu for Zoom details.

Advanced Cytoscape Using R

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In this course, you’ll learn about the integration of Cytoscape into programmatic workflows and pipelines using R. Following a brief review of the goals and capabilities of Cytoscape in network analysis, you’ll learn how to translate these into scriptable use cases for practical applications. The bulk of the course will be a hands-on demonstration of […]

Data Science Hacky Hour (AI and Bias)

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Welcome to Data Science Hacky Hour!  We will first do a short presentation on a data science topic, and then you will have the opportunity to apply what you've learned to solve a data science challenge! We'll also leave sufficient time in the end for you to discuss your specific data science questions with us […]

Whole Genome Sequence Analysis

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When you are working with whole genome sequencing data, finding the information you need can be a daunting challenge. This course offers both theoretical and hands-on training so you can learn the main tools used to do alignment, variant calling, annotation, and visualization. You’ll learn how to go from raw FASTQ reads to annotated variants […]

Introduction to Statistics and Experimental Design

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Why do we perform experiments? What conclusions would we like to be able to draw from these experiments? Who are we trying to convince? How does the “magic” of statistics help us reach conclusions? This talk is open to anyone interested in designing experiments to test hypotheses (e.g., the effect of a drug treatment, gene […]

Intermediate R for Data Visualization

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The high-level language of R is considered one of the most powerful languages for quantitative analysis, statistics, and graphics. This workshop is designed for folks who have some experience using R and are looking to take their R skills to the next level. You’ll learn how to generate high-quality and publication-ready data visualizations using R […]

Intermediate RNA-Seq Analysis Using R

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RNA-Seq is a powerful tool to interrogate cellular functions. In this intermediate workshop you’ll learn  the skills you need to get the most out of your RNA-Seq data through analysis in R. This is a 2-day workshop, December 6th and 7th @ 2-4pm.  Attendance at both sessions is required.   By the end of the […]

California Academy of Bioengineering – Distinguished Lecture Series

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Engineering Medicine for a Global Society by Roderick Pettigrew, MD, PhD ABOUT Roderick I. Pettigrew, M.D., Ph.D. CEO EnHealth, Robert A Welch Professor and Executive Dean EnMed Intercollegiate School of Engineering Medicine, Texas A&M University and Houston Methodist Hospital Biography Pettigrew is a graduate of Morehouse College as a Merrill Scholar (BS in physics), Massachusetts […]

Computational Cancer Community (C3) Meeting

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Please join us as we continue to develop a community of practice around cancer research that utilizes computational methods. Speaker: Dan Landau, MD, PhD, New York Genome Center Title: Charting differentiation topologies in somatic evolution via single-cell multi-omics   C3 Faculty Leadership: Joe Costello, Hani Goodarzi, Franklin Huang, Marina Sirota, Alejandro Sweet-Cordero For Zoom information or to […]

Intermediate Cytoscape: Networks and Omics Data Visualization

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This course is a complement to “Introduction to Network Biology and Cytoscape.” Following a brief review of the key concepts of network analysis, you’ll embark on a deep dive into data visualization and advanced Cytoscape features. Work through three prepared use cases demonstrating various omics data types and strategies. You’re also encouraged to bring your […]

Unix Command Line

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Knowing how to use the command line of your computer can save you a lot of time. In this workshop, you’ll learn how to navigate the Unix terminal. For this workshop, you’ll need a Mac or Linux laptop (you can use Windows if you can’t access a Linux machine). Topics to be covered include: File […]

Introduction to Statistics and Experimental Design

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Why do we perform experiments? What conclusions would we like to be able to draw from these experiments? Who are we trying to convince? How does the “magic” of statistics help us reach conclusions? This workshop is open to anyone interested in learning more about experimental design, biological and technical aspects to consider, confounding factors, […]

Recurring

Python Intro to Machine Learning: Parts 1-2

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Python Intro to Machine Learning is a 2-part series running from 10am-1pm each day: Part 1: Wednesday, February 23 Part 2: Monday, February 28 This workshop introduces students to scikit-learn, the popular machine learning library in Python, as well as the auto-ML library built on top of scikit-learn, TPOT. The focus will be on scikit-learn syntax […]

Recurring

Python Intro to Machine Learning: Parts 1-2

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Python Intro to Machine Learning is a 2-part series running from 10am-1pm each day: Part 1: Wednesday, February 23 Part 2: Monday, February 28 This workshop introduces students to scikit-learn, the popular machine learning library in Python, as well as the auto-ML library built on top of scikit-learn, TPOT. The focus will be on scikit-learn syntax […]

Recurring

R Introduction to Machine Learning with tidymodels: Parts 1-2

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This workshop is a 2-part series that runs from 9am-12pm each day: Tuesday, March 1 Thursday, March 3 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. During this two […]

Recurring

R Introduction to Machine Learning with tidymodels: Parts 1-2

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This workshop is a 2-part series that runs from 9am-12pm each day: Tuesday, March 1 Thursday, March 3 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. During this two […]

Recurring

Introduction to RNA-Seq Analysis

Zoom Only

Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. RNA-seq has become one of the most popular experimental methods to quantify gene expression levels. This 2-day hands-on workshop will provide an introduction to a typical bulk RNA-seq protocol and focus on the data […]

Recurring

Introduction to RNA-Seq Analysis

Zoom Only

Gene expression is central to cell biology. Disease pathways often involve changes in the expression levels of at least some genes. RNA-seq has become one of the most popular experimental methods to quantify gene expression levels. This 2-day hands-on workshop will provide an introduction to a typical bulk RNA-seq protocol and focus on the data […]

Computational Cancer Community (C3) Meeting

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Please join us as we continue to develop a community of practice around cancer research that utilizes computational methods. Speaker:  Francisca (Paquita) Vazquez, PhD, Broad Institute Title: TBA   C3 Faculty Leadership: Joe Costello, Hani Goodarzi, Franklin Huang, Marina Sirota, Alejandro Sweet-Cordero For Zoom information or to be added to the C3 calendar invite, contact edna.rodas@ucsf.edu

Intermediate RNA-Seq Analysis Using R

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RNA-Seq is a powerful tool to interrogate cellular functions. In this intermediate workshop you’ll learn  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'll know how to: Go from a matrix of raw gene expression counts to differentially expressed genes […]

Recurring

R Introduction to Deep Learning: Parts 1-2

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R Introduction to Deep Learning is a 2-part series that runs from 10am-1pm each day: Tuesday, March 29 Thursday, March 31 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 […]

Recurring

R Introduction to Deep Learning: Parts 1-2

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R Introduction to Deep Learning is a 2-part series that runs from 10am-1pm each day: Tuesday, March 29 Thursday, March 31 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 […]

Computational Cancer Community (C3) Meeting

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Please join us as we continue to develop a community of practice around cancer research that utilizes computational methods.   Algorithms for single-cell tumor phylogeny inference and deep learning imaging models for tumor purity estimation Iman Hajirasouliha, Ph.D, Assistant Professor of Computational Genomics, Weill Cornell Medicine   C3 Faculty Leadership: Joe Costello, Hani Goodarzi, Franklin Huang, […]

Recurring

Single Cell RNA-Seq Analysis

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This three-session workshop will focus on the analysis of single-cell RNA-Seq data, starting from raw count matrices and progressing to network analysis of single-cell datasets. You’ll analyze data using R. Attendance at all three sessions is required. April 15, 2022 • 10am–12pm: Loading data, quality control, normalization, feature selection, dimensionality reduction April 15, 2022 • 1–3pm: Dimensionality […]

Recurring

Single Cell RNA-Seq Analysis

Zoom Only

This three-session workshop will focus on the analysis of single-cell RNA-Seq data, starting from raw count matrices and progressing to network analysis of single-cell datasets. You’ll analyze data using R. Attendance at all three sessions is required. April 15, 2022 • 10am–12pm: Loading data, quality control, normalization, feature selection, dimensionality reduction April 15, 2022 • 1–3pm: Dimensionality […]

Recurring

Single Cell RNA-Seq Analysis

Zoom Only

This three-session workshop will focus on the analysis of single-cell RNA-Seq data, starting from raw count matrices and progressing to network analysis of single-cell datasets. You’ll analyze data using R. Attendance at all three sessions is required. April 15, 2022 • 10am–12pm: Loading data, quality control, normalization, feature selection, dimensionality reduction April 15, 2022 • 1–3pm: Dimensionality […]

Statistics of Enrichment Analyses Methods

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Gene set or pathway enrichment methods allow researchers to assign functional or mechanistic significance to results from high-throughput assays like RNA-sequencing. In this workshop, you’ll learn the theory behind some of these methods, and how to interpret the associated results. Intermediate: This is an intermediate workshop in both the Biostats series and the Pathway Analysis series. The demos session will […]

Recurring

Python Introduction to Machine Learning: Parts 1-2

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This workshop is a 2-part series running from 2 pm - 5 pm on April 25th and April 27th.  D-Lab workshops start 10 minutes after the scheduled start time. The Python Introduction to Machine Learning workshop introduces students to scikit-learn, the popular machine learning library in Python, as well as the auto-ML library built on […]

Recurring

Python Introduction to Machine Learning: Parts 1-2

Zoom Only

This workshop is a 2-part series running from 2 pm - 5 pm on April 25th and April 27th.  D-Lab workshops start 10 minutes after the scheduled start time. The Python Introduction to Machine Learning workshop introduces students to scikit-learn, the popular machine learning library in Python, as well as the auto-ML library built on […]

Introductory Machine Learning for Biologists

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Machine learning is becoming increasingly important not only in data science, but also in bioinformatics. Machine learning gives you the opportunity to find hidden patterns in your data and draw predictive conclusions. In this workshop, you’ll learn key machine learning concepts and categories, and get hands-on practice with simple examples. See how machine learning can […]

Computational Cancer Community (C3) Meeting

Zoom Only

Please join us as we continue to develop a community of practice around cancer research that utilizes computational methods. Computational approaches for interpreting somatic mutation events in the noncoding cancer genome. Felix Dietlein, MD, PhD Assistant Professor, Harvard Medical School PI, Computational Health Informatics Program, Boston Children’s Hospital   C3 Faculty Leadership: Joe Costello, Hani Goodarzi, […]

Information Commons Day at UCSF

Byers Auditorium, Genentech Hall 600 16th St, CA

MAY 9, 2022 @ 9am — 4pm GENENTECH HALL,  Byers Auditorium 600 16th Street, San Francisco, CA or ZOOM REGISTER HERE Today, data is everywhere, and underlies research in all medical disciplines. Information Commons is a field-leading computational research platform, designed for the multimodal, integrative research and precision medicine, combining clinical data, medical notes, radiology […]

Advanced Cytoscape Automation

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In this course, you’ll learn how to integrate  Cytoscape into programmatic workflows and pipelines using R or Python. Following a brief review of the goals and capabilities of Cytoscape in network analysis, you’ll learn how to translate these capabilities into scriptable use cases for practical applications. Gain hands-on experience accessing and controlling Cytoscape from R/Python […]