Breakthroughs (and Hype) in Applying Proteomics and Multi-Omics to Complex Trait Genetics

Evan Williams, PhD
Staff Scientist at Eidgenössische Technische Hochschule (ETH) Zürich

Recent advances in proteomics have been permitting the analysis of progressively larger cohort sizes at higher coverage of the proteome and with lower technical error. Genes’ mRNAs and proteins do not closely covary in response to genetic and environmental stresses, raising the possibility that proteomics studies and multi-omics studies may highlight regulatory pathways and changes that were not apparent through prior nucleotidecentric approaches. We have recently followed a diverse population of 2210 mice on low-fat and high-fat diets across their natural lifespans, including tissue collection. In the livers of these cohorts, we have generated and analyzed a detailed multi-omic dataset in order to identify diverging and converging genetic factors in the etiology of complex liver diseases and general aging processes.

DATE: Monday, January 7, 2019
TIME: 2-3pm
LOCATION: Genentech Hall N-114, UCSF Mission Bay Campus
SPONSORED BY: UCSF Bakar Institute
CONTACT: angela.rizk-jackson@ucsf.edu

The Data Age

Next-Generation Biobanking in Academia

Intro to the Unix Shell

This class will introduce the UNIX shell. You’ll learn to navigate the file system, manipulate files and directories, search for files with grep and find, write simple loops and scripts, and automate basic tasks. Bring your laptop! Computers will not be provided.

Class materials available in the CLE: Introduction to Unix

This class is part of series. You must register separately for each class.

DATES
Jan 25, 10am-1pm: Intro to Unix — REGISTER for this class
Feb 7, 10am-1pm: Intro to Python, Part 1
Feb 15, 10am-1pm: Intro to Python, Part 2

SPONSORED BY: UCSF Library

When you register, the Library reserves class space for you. Since many of our classes have a waitlist, please cancel your registration if you can no longer attend.

UCSC Genome Browser Workshop @ UCSF

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.

DATE: Monday, January 28, 2019
TIME: 9am-5pm (Main session: 9am-12pm; Hands-on training: 1:30-5pm)
LOCATION: Byers Auditorium & N-114, Genentech Hall, UCSF Mission Bay Campus
SPONSORED BY: UCSF Bakar Institute, Gladstone Institutes, UCSC Genome Browser
REGISTER: More information & Registration

“Bringing AI to the Patient Bedside”
Rachael Callcut, MD, MSPH
Associate Professor of Surgery, Division of General Surgery, Zuckerberg San Francisco General Hospital and Trauma Center; Director of Data Science, Program Director of the Smarter Health Artificial Intelligence Initiative, Center for Digital Health Innovation, UCSF

Making Invisible Visible: Patient to Population Scale

Ramesh Raskar, PhD
Associate Professor at MIT, Director, Camera Culture group, MIT Media Lab

Dr. Raskar’s focus is on building interfaces between social systems and cyber-physical systems. These interfaces span research in physical (e.g., sensors, health-tech), digital (e.g., automaFng machine learning) and global (e.g., geomaps, autonomous mobility) domains. He has worked on special research projects at Google [X] and Facebook and co-founded/advised several companies.

DATE: Monday, February 4, 2019
TIME: 12-1pm
LOCATION: Mission Hall 1406, UCSF Mission Bay Campus
SPONSORED BY: UCSF Bakar Institute
CONTACT: angela.rizk-jackson@ucsf.edu

Link to Livestream video recording here

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. Bring your laptop!

Materials and set up instructions available in the CLE: Introduction to Python, Part 1

This class is part of series. You must register separately for each class.

DATES
Jan 25, 10am-1pm: Intro to Unix
Feb 7, 10am-1pm: Intro to Python, Part 1 — REGISTER for this class
Feb 15, 10am-1pm: Intro to Python, Part 2

SPONSORED BY: UCSF Library

When you register, the Library reserves class space for you. Since many of our classes have a waitlist, please cancel your registration if you can no longer attend.

Introduction to Cytoscape (Beginner)

This workshop will provide a general introduction to network biology studies and Cytoscape concepts, including a hands-on session for universal data import and demonstration of a few of the over 300 freely available apps contributed by the Cytoscape developer community.

DATE: Thursday, February 14, 2019
TIME: 10am-5pm
LOCATION: Mission Hall 1402, UCSF Mission Bay Campus
SPONSORED BY: Cancer Cell Map Initiative, UCSF Bakar Institute, Gladstone Institutes
REGISTER: More information & Registration

Intro to Python: Part 2

This workshop is a continuation of Intro to Python (Part 1). This three hour class will cover: Pandas dataframes, plotting, looping over data sets, and importing modules. In addition to Jupyter notebook, this workshop will introduce Python at the command line and scripting and programming with Python. Bring your laptop!

Materials available in the CLE: Introduction to Python, Part 2

This class is part of series. You must register separately for each class.

DATES
Jan 25, 10am-1pm: Intro to Unix
Feb 7, 10am-1pm: Intro to Python, Part 1
Feb 15, 10am-1pm: Intro to Python, Part 2 — REGISTER for this class

SPONSORED BY: UCSF Library

When you register, the Library reserves class space for you. Since many of our classes have a waitlist, please cancel your registration if you can no longer attend.

Data Visualization with Cytoscape (Intermediate)

This course is a complement to “Introduction to Network Biology and Cytoscape”. 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

DATE: Tuesday, February 19, 2019
TIME: 12:30pm-5pm
LOCATION: Byers Hall 212, UCSF Mission Bay Campus
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More information & Registration

Cytoscape Automation in R (Advanced)

This course will demonstrate 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, we will translate these into scriptable use cases for practical applications.

DATE: Wednesday, February 20, 2019
TIME: 1:30pm-5:30pm
LOCATION: Gladstone 107C/D, UCSF Mission Bay Campus
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More information & Registration

Deep Learning in Biomedicine

Come learn how researchers in academia and industry are using Deep Learning algorithms for applications in the fields of biomedicine. You will hear how these methods are being put to use in medical imaging, physiological signal processing, molecular modeling, and more. You will also have an opportunity to attend hands-on sessions in the afternoon.

DATE: Monday, March 11, 2019
TIME: 9am-5pm
LOCATION: Genentech Hall
SPONSORED BY: UCSF Bakar Institute, NVIDIA, and Google
REGISTER: More Information and Registration

Practical, Peculiar, and (perhaps) Preposterous: A personal journey of clinical informatics from applied to research

David Hanauer, MD, MS
Clinical Associate Professor, University of Michigan

In this talk I will discuss some of my experiences with clinical informatics, ranging from applied to research. On the PRACTICAL front I will discuss a long-standing effort to develop, disseminate, and support a free text search engine (EMERSE) for clinical documents. EMERSE has been used by clinical operational groups as well as by research teams in more than 1,500 studies at the University of Michigan. EMERSE is now being deployed at multiple sites across the US. On the research front I will discuss a few studies involving data mining from the medical record, one of the PECULIAR findings that was discovered (it involved cats), and the (perhaps) PREPOSTEROUS notoriety that came about once the finding became publicized.

Tuesday, March 12
3:30 – 4:30 pm
Mission Hall 1407

Link to livestream will be available here

Clinical Informatics Workshop

In this course, you will get an introduction to the field of clinical informatics, using computational methodologies to mine and analyze Electronic Health Record Data (EHR). In this workshop, we will go over examples of studies that incorporate and feature EHR data and current state of the field, including barriers, issues, and how to overcome them working with these data. We will further focus on the utility of common data models, such as Observational Medical Outcomes Partnership (OMOP) model created by the OHDSI consortium, which is in the center of the UC-Health Data Warehouse. Lastly, we will demonstrate tools and applications developed at UCSF for interfacing with such data, including an R-package: ROMOP and a visualization tool: PatientExploreR. This demonstration includes interactive tutorials.

DATE: Wednesday, March 13, 2019
TIME: 1pm-4pm
LOCATION: Mission Hall 1407
SPONSORED BY: UCSF Library
REGISTER: More Information and Registration

R Data Analysis: Intro

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.

DATE: Tuesday, March 19, 2019
TIME: 2pm-5pm
LOCATION: Bakar Auditorium (HD-160)
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

Intro to RNAseq 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 for recovering actionable insights. Attendees will learn to explore and understand RNA-seq data using Galaxy — an easy-to-use web-based platform. No data analysis or RNA-seq experience is required. Bring your laptop!

DATE: Thursday, March 28, 2019
TIME: 2pm-5pm
LOCATION: Mission Hall 1401/1402
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

Intro to Statistics and Experimental Design

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, by Reuben Thomas of the Bioinformatics Core, is open to anyone interested in designing experiments to test hypotheses (e.g., the effect of a drug treatment, gene mutation or disease on gene expression, percent reprogrammed cells, survival time or mitochondrial velocity). No background in statistics is required.

DATE: Tuesday, April 2, 2019
TIME: 2pm-5pm
LOCATION: Bakar Auditorium (HD-160)
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

R data analysis: intermediate Data visualization with ggplot2

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 in using R and are looking to take their R skills to the next level. We shall learn how to generate high-quality and publication-ready data visualizations using ggplot2. A beginner-level knowledge of R is required. Bring your laptop with R and RStudio installed.

DATE: Thursday, April 11, 2019
TIME: 2pm-5pm
LOCATION: Mission Hall 1406
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

Intermediate R: RNAseq analysis

The learning objectives for this workshop include: 1) How to go from a matrix of raw gene expression counts to differentially expressed genes. 2) How to analyze experimental designs that go beyond 2-group comparisons using edgeR’s generalized linear modeling capabilities. 3) Ways to test specific hypotheses using a joint model fit. Prerequisites: A minimum of 4 to 6 months experience programming in R and have taken the RNAseq Analysis in R workshop or something equivalent.

DATE: Monday, April 22, 2019
TIME: 2pm-5pm
LOCATION: Genentech Hall N114
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

New approaches to generating and leveraging narrative in the medical record

Thomas Payne, MD, FACP
Professor, University of Washington School of Medicine

Tuesday, April 23
3:00 – 4:00 pm
Rock Hall Pottruck Auditorium

There has been rapid growth both in use of narrative text within the medical record and in methods to leverage it for clinical and scientific purposes.  We’ll review new approaches to creating text to mitigate current EHR weaknesses, and opportunities to use it to improve care.

LINK to livestream webcast

Predicting Inpatient Deterioration: From Quality Improvement to Research (A Story in 5 Acts)

Benjamin A. Goldstein, Ph.D.
Associate Professor, Duke University

Thursday, May 2
11:00am — 12:00pm
Mission Hall 1407

As Electronic Health Record (EHR) systems mature, the opportunity exists to implement real-time clinical decision support tools. One area of focus has been the prediction of who will deteriorate while in the hospital. In 2015, the National Early Warning Score (NEWS), with an associated best practice alert, was implemented into the Duke University Health Systems EHR system. After the score had been used for over year, we were asked to evaluate its effectiveness (Act 1). With effectiveness found lacking, we were asked to develop a better score (Act 2). After developing a better score, we implemented our model and evaluated its performance prospectively (Act 3). This raised additional questions about how much better we could do if our prediction model was not constrained by the limitations of the implementation environment of the EHR system. In response, we have developed a time-to-event deep learning recurrent neural network (RNN) model (Act 4). As we built out and tried to refine our models, new questions were raised regarding how changing clinical measurements relate to risk of deterioration (Act 5). Ultimately, what started as a question of quality improvement, turned into a research investigation. This story illustrates how partnerships with the health system can lead (hopefully) to better patient care and spur academic research. This work is joint with a variety of faculty, students and staff who are statisticians, clinicians and informaticians.

LINK to livestream webcast

Introduction to Machine Learning Workshop

The UCSF Bakar Institute is partnering with the UC Berkeley D-Lab to offer an introductory machine learning workshop for UCSF faculty, students, and staff.

In this workshop, D-Lab instructors will review the basics of supervised machine learning and take you through R coding walkthroughs of k-nearest neighbor, linear regression, decision tree, random forest, and gradient boosted machine algorithms, as well as SuperLearner ensemble methods.

Prerequisite: Basic familiarity with R programming environment

Bring your own laptop in order to participate!

Single Cell Technology and Analysis Symposium

During this one-day symposium, we will cover techniques, platforms and methods that are used in analyzing single cell data. The symposium has two sessions: a series of seminars in the morning and hands-on workshops in the afternoon. The morning session will start with the introduction of single cell platforms, followed by talks focusing on applications of various technologies to diverse research areas. In the afternoon, we will have three consecutive hands-on sessions with increasing difficulties, ranging from how to use Cell Ranger and Seurat to advanced analyses beyond these common tools.

DATE: Tuesday, May 14, 2019
TIME: 9am-6pm (Main session: 9am-12:30pm; Hands-on training: 2-6pm)
LOCATION: Mahley Auditorium, Gladstone Institutes and Genentech Hall N114
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

University of California AI in Biomedicine Conference

Please join us this summer for this first-of-its-kind meeting focused on the application of Artificial Intelligence methods to topics in biology, health, and medicine across the entire University of California system. Affiliates from ALL UC CAMPUSES are welcome.

Presentations will feature efforts taking place across the University of California, however we will be joined by a small number of external speakers.

GUEST SPEAKERS

Jeff Dean, PhD
Lead, Google AI

Wendy Nilsen, PhD
Program Director, Smart & Connected Health, CISE/IIS at National Science Foundation

DATE: June 17-18, 2019
TIME:  June 17 @ 8am-6pm; June 18 @ 8am-2pm
LOCATION: UCLA Luskin Conference Center
SPONSORED BY: UC Health
REGISTER: More Information and Registration

Introduction to Clinical Informatics

This is an introductory lecture in clinical informatics, including an overview of computational methodologies available to mine and analyze Electronic Health Record Data (EHR), and of recent studies that incorporate and feature EHR data. We will also focus on the utility of common data models, such as the Observational Medical Outcomes Partnership (OMOP) model created by the OHDSI consortium, which is in the center of the UC-Health Data Warehouse.

Prerequisites
There are no prerequisites for this course other than having an interest in clinical informatics and EHR data analysis.

Instructor
Benjamin Glicksberg, PhD is a Postdoctoral Scholar in Atul Butte’s lab in the Bakar Computational Health Sciences Institute at UCSF.

DATE: Monday, July 22, 2019
TIME: 3-5pm
LOCATION: Mission Hall 2100, UCSF Mission Bay Campus
SPONSORED BY: UCSF Bakar Institute
REGISTER: More Information and Registration

Workshop on Whole Genome and Exome Analysis

This course will be both theoretical and hands-on. We will learn the main tools used to do alignment, variant calling, annotation and visualization. We will start with raw FASTQ reads and get to annotated variants (VCF files).

DATE: Thursday, July 25, 2019
TIME: 1-5pm
LOCATION: Mission Hall 1401, UCSF Mission Bay Campus
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

Intro to Python: Part 2

This workshop is a continuation of Intro to Python (Part 1). This three hour class will cover: Pandas data frames, plotting, looping over data sets, and importing modules. In addition to Jupyter notebook, this workshop will introduce Python at the command line and scripting and programming with Python. Bring your laptop!

DATE: Thursday, July 25, 2019
TIME: 10am – 1pm
LOCATION: Mission Hall 1402, UCSF Mission Bay Campus
SPONSORED BY: UCSF Library
REGISTER: More Information and Registration

Programming Hacky Hour

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? Get away from your desk and join us for an hour of coding in a friendly environment. We provide the space and pizza. You: bring your laptop and a current project. Your programming peers may be able to answer a couple of questions. If you need 1:1 help, sign up for Office Hours.

Preparation
Bring something you want to work on, e.g. an image analysis project or a programming exercise. Find collaborators by sharing your project topic for 1-2 minutes. You’re also welcome to use the space to work on your own.

Instructor
This event is attendee-driven. No instructors.

DATE: Thursday, July 18, 2019
TIME: 12-1pm
LOCATION: Mission Hall 2100, UCSF Mission Bay Campus
SPONSORED BY: UCSF Library
REGISTER: More Information and Registration

Single Cell RNA-Seq Data Analysis Workshop

During this one-day hands-on workshop, they will cover techniques, platforms and methods that are used in analyzing single cell data. The workshop has two hands-on sessions: an introductory session in the morning and a more advanced session in the afternoon. The morning session will focus on analysis using Seurat and Monocle. In the afternoon, we will have three advanced hands-on sessions ranging from network analysis of single cell datasets in Cytoscape, normalization and differential analysis outside of Seurat and querying a Single Cell Atlas for cell types. Laptop required.

DATE: Tuesday, August 20, 2019
TIME: from 9am-5pm
LOCATION: UCSF Mission Bay Campus, Mission Hall 1401/1402
SPONSORED BY: UCSF Bakar Institute & Gladstone Institute
REGISTER: More Information and Registration

Twitter workshop for Faculty

This workshop is offered to UCSF Faculty and will feature tips and tricks from two UCSF “power tweeters” and a presentation on best practices for advanced tweeting. The workshop is primarily targeted towards faculty who have some experience with Twitter. Please plan to attend in person. There is no web conference option, but the recording will be available at a later date.

DATE: Tuesday, September 10, 2019
TIME: 12pm to 1:30pm
LOCATION: UCSF Mission Bay, Rock Hall 102 (auditorium)
SPONSORED BY: Bakar Computational Health Sciences Institute Institute and Precision Medicine
REGISTER: More Information and Registration

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.

DATE: Monday, September 16, 2019
TIME:  1pm-5pm
LOCATION: UCSF Mission Hall 1400
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

ROCK Health Summit

Rock Health Summit is a two-day digital health conference in San Francisco that brings together 700 diverse minds from technology, medicine, policy, and beyond to tackle healthcare’s most challenging problems. Through interactive programming, the Summit showcases the expertise of thought leaders who are creating real transformation in healthcare.

With informed discussions from the most innovative minds in healthcare and technology and data-driven insights from Rock Health’s industry-leading research, attendees will walk away empowered and inspired to effect change. Attendees will also have the opportunity to forge meaningful connections with individuals and organizations committed to producing impact-driven solutions. From curated networking sessions to an event app tailored for attendee matchmaking and meeting scheduling, you’ll be a part of one of the strongest communities in digital health.

DATE: Tuesday – Wednesday, September 24-25, 2019
LOCATION: Mission Bay Conference Center
SPONSORED BY: ROCK Health
REGISTER: More Information and Registration

Intro to Basic Programming for Scientists: Python, Unix, Git (2-day workshop)

An example-driven two-day boot camp taught by volunteers who are scientists and programmers. The workshops will introduce the basics of Unix Shell and Git, along with Python. Short tutorials alternate with hands-on practical exercises, and participants are encouraged both to help one another, and to try applying what they have learned to their own research problems during and between sessions.

Participants must bring their own laptop to work on. This should be a “real” laptop – not a Chromebook, tablet, etc. You should also be sure to have admin privileges on this computer.

DATE: Friday- Saturday, September 27-28 2019
TIME:  9:30am-5pm
LOCATION: UCSF Mission Hall, 550 16th Street, Rooms 1401/1402
SPONSORED BY: Bakar and Gladstone Institute and UCSF Data Science Initiative
REGISTER: More Information and Registration

RNA — Seq Analysis with R Bioconductor

Workshop Overview

This workshop is intended for individuals who are already comfortable with R programming and who are interested in learning to use R for standard RNA-Seq analyses. We will take you through a complete RNA-Seq workflow using R Bioconductor packages.

Learning Objectives

By the end of the workshop, participants should be able to:

• Estimate gene expression levels based on raw RNA-Seq read data
• Filter and normalize gene expression data
• Perform unsupervised clustering of expression data
• Perform differential expression analysis
• Perform gene set enrichment analyses (GSEA)
• Create common visualizations of results (heatmaps, etc.)

Prerequisites

You must have some R programming experience and a basic understanding of the purpose of RNA-Seq analysis to benefit from this course. Feel free to contact the instructors (see below) if you have questions about these requirements.

Software

Please have the latest versions of R and R Bioconductor installed on your laptop prior to the workshop. RStudio (the free version) is highly recommended as well, since we will be teaching in this environment.

• Install R
• Install R Bioconductor
• Install RStudio

DATE: Thursday, October 3, 2019
TIME:  1pm-4pm
LOCATION: UCSF Mission Bay, BH 215
SPONSORED BY: Bakar and Gladstone Institute and UCSF Data Science Initiative
REGISTER: More Information and Registration

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 workshop 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 learn how to generate high-quality and publication-ready data visualizations using ggplot2. A beginner-level knowledge of R is required. *Bring your laptop with R and RStudio installed.

DATE: Thursday, October 3, 2019
TIME: 1pm-5pm
LOCATION: UCSF Mission Hall 1407
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

Intro to pathway modeling

An introduction to Pathway Modeling for Biologists. We will being with slides on “why” and “how” to use pathways in research and paper figures. Before the hands-on section, we will provide an overview of pathway drawing, covering tools and curation steps, including PathVisio, WikiPathways, Curation Guidelines and the WikiPathways Curation Process. The hands-on portion will get you familiar with pathway drawing tools. You will then build your own pathways model based on a figure. You can use your own pathway of interest in this exercise.

DATE: Monday, October 7, 2019
TIME: 1pm-5pm
LOCATION: UCSF Mission Hall 1407
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

Hypothesis Testing

As we attempt to make discoveries, we test new hypotheses using experimental data and hope that a sceptical and discerning person would start to believe the claims we make. Hypothesis testing, a branch of statistics, is a step we can rely on to bolster our claims. In this workshop, you will gain a fundamental understanding of common hypothesis-testing concepts and terms, such as null hypothesis, alternative hypothesis, type I error, type II error, p-value, and power.

DATE: Wednesday, October 9, 2019
TIME: 3pm-5pm
LOCATION: UCSF Rock Hall, Pottruck Auditorium (Room 102)
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

Introduction to Cytoscape and Network Biology

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 visualize and interpret the results of such analyses. By the end of this course you will be able to: (1) Understand the major applications of network biology, (2) Find relevant sources for networks and pathways, (3) Import your data into Cytoscape, (4) Perform network layouts and data visualization, and (5) Know where to find relevant Cytoscape apps and tutorials. Prerequisites: No prior experience required.

*Bring your own laptop. Instructions on installing Cytoscape will be provided prior to the course.

DATE: Monday, October 14, 2019
TIME: 1-5pm
LOCATION: UCSF Mission Hall 1407
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

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 strategies. You are encouraged to bring your own data as well. By the end of this course you will be able to: (1) Know when and how to use Cytoscape in your research, (2) Handle multiple data types in Cytoscape, (3) Transform and merge data with networks from multiple sources, (4) Master customized data visualization, (5) Navigate the greater Cytoscape ecosystem. Prerequisites: You should already be familiar with Cytoscape and the fundamentals of network analysis (see prior course).

*Bring a laptop with the latest version of Cytoscape installed.

DATE: Friday, October 18, 2019
TIME: 1-5pm
LOCATION: UCSF Mission Hall 1407
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

Intro to Machine Learning

The UCSF Bakar Institute is partnering with the UC Berkeley D-Lab to offer an introductory machine learning workshop for UCSF faculty, students, and staff.

In this workshop, D-Lab instructors will review the basics of supervised machine learning and take you through R coding walkthroughs of lasso, decision tree, random forest, and xgboost algorithms, as well as SuperLearner ensemble methods.

Prerequisite: Basic familiarity with R and RStudio. Bring your own laptop in order to participate!

By registering to attend, you are agreeing to provide feedback on the workshop to the organizers in follow-up communications.

DATE: Friday, October 18, 2019
TIME: 12pm-5pm
LOCATION: UCSF Mission Hall 1406
SPONSORED BY: UCSF Bakar Computational Health Sciences Institute & UC Berkeley D-Lab
REGISTER: More Information and Registration

Intermediate: Scripting Pathway Analysis

An introduction to Pathway Analysis using R. We will being with a survey of common software tools and methods for functional enrichment analysis, including WikiPathways, Cytoscape, RStudio, and the R packages: clusterProfiler, rWikiPathways and RCy3. The hands-on portion will walk through a basic enrichment analysis, including basic data visualization and exploration. We will also cover advanced topics on pathway visualization and publishing figures. We will reserve time to work with your own data and project topics.

DATE: Monday, October 21, 2019
TIME: 1-5pm
LOCATION: UCSF Mission Hall 1407
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

Intro to pathway modeling

An introduction to Pathway Modeling for Biologists. We will being with slides on “why” and “how” to use pathways in research and paper figures. Before the hands-on section, we will provide an overview of pathway drawing, covering tools and curation steps, including PathVisio, WikiPathways, Curation Guidelines and the WikiPathways Curation Process. The hands-on portion will get you familiar with pathway drawing tools. You will then build your own pathways model based on a figure. You can use your own pathway of interest in this exercise.

DATE: Friday, October 25, 2019
TIME: 1pm-5pm
LOCATION: UCSF Mission Hall 1407
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

BHCSI Annual Retreat

This event is open to BCHSI Members only.

Bakar Computational Health Sciences Institute is hosting our Annual Retreat on October 29th. There is a lot to look forward to, including a snapshot of the work taking place across BCHSI-affiliated labs and some insight into the Institute’s strategic priorities.

We have a great keynote presentation scheduled, followed by Atul Butte’s State of the Institution address then lightning talks by members of our Institute.

Lunch will take place at Spark Social. Did we mention unlimited s’mores? Join the fun, we have a great team activity planned for the afternoon session.

DATE: Friday, October 29, 2019
TIME: 8am-4pm
LOCATION: UCSF Byers Auditorium + Spark Social
SPONSORED BY: UCSF Bakar Computational Health Sciences Institute
REGISTER: More Information and Registration

BHCSI Presents Seminar Series

Genomics for the world: a comprehensive framework for genetic studies in diverse populations

Alicia Martin, PhD
DATE: October 31, 2019
TIME: 10-11 am
Location: UCSF Mission Hall 1407
SPONSORED BY: UCSF Bakar Computational Health Sciences Institute
PRESENTATON LINK

Interpreting genetic variation using massive genomic datasets

Konrad Karczewski, PhD
DATE: October 31, 2019
TIME: 11:05am-12pm
Location: UCSF Mission Hall 1407
SPONSORED BY: UCSF Bakar Computational Health Sciences InstituteThis will be recorded.
PRESENTATION LINK

Intro to Deep Learning

The UCSF Bakar Institute is partnering with the UC Berkeley D-Lab to offer an introductory deep learning workshop for UCSF faculty, students, and staff.

This workshop introduces the basic concepts of Deep Learning – the training and performance evaluation of large neural networks. 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 R interface to Keras to become familiar with basic concepts like input and output layers, batch sizes and output dimensions, dropout rates, weight parametrization and bias, backpropagation, and loss, activation, and optimization functions for image classification applications in biomedicine. You will also gain confidence exploring more complex approaches that utilize pretrained and fine-tuned models.

By registering to attend, you are agreeing to provide feedback on the workshop to the organizers in follow-up communications.

DATE: Friday, November 1, 2019
TIME: 12pm-5pm
LOCATION: UCSF Mission Hall 1407
SPONSORED BY: UCSF Bakar Computational Health Sciences Institute & UC Berkeley D-Lab
REGISTER: More Information and Registration

Want to hear from one of the newest elected members of the National Academy of Medicine?

Turning Digital Fumes into a Breath of Fresh Air
Julia Adler-Milstein, PhD
Director of Center for Clinical Informatics and Improvement Research
Associate Professor, Department of Medicine

While EHR Data is heavily used for clinical research there is also significant potential for behavioral and social science research. In her talk, she will describe EHR access log data that captures individual and team behaviors in APeX (the UCSF EHR) and give examples of how such data can be applied to address questions related to user interface design, clinician burnout and clinical workflow.

DATE: Friday, November 1, 2019
TIME: 12:30-1:30pm
Location: UCSF Mission Hall 1400
SPONSORED BY: Department of Epidimiology and Biostatistics

UCSF Clinical Data Colloquium 2019

In addition to pragmatic information on how to use and access clinical data for research, we will introduce new data assets and tools and we’ll cover topics including population health, endeavors in the digital health space, and more. Plan for a plenary session in the morning and break-out sessions on specific topics in the afternoon.

DATE: Tuesday, November 6, 2019
LOCATION: UCSF  Mission Bay Campus
SPONSORED BY: Clinical Data Colloquium
REGISTER:  More Information 

AMIA 2019 Annual Symposium

by the The American Medical Informatics Association

The AMIA 2019 Annual Symposium, to be held at the Washington Hilton in Washington, D.C., November 16-20, 2019, will build on more than 40 years of sharing pioneering research and insights for leveraging information to improve human health.

Under the overall theme of “Informatics: From Data to Knowledge to Action” the Annual Symposium will have topics across the spectrum from deciphering the underpinning phenomena of disease, to managing information and communications for improving patient care, to tracking the health of populations.

The AMIA 2019 Annual Symposium brings together informatics professionals from diverse backgrounds committed to transforming health through informatics. From the leading experts in the field, to the students eager to get started, the AMIA 2019 Annual Symposium provides an opportunity to learn and to grow professionally, to network, and to flesh out ideas with colleagues and start new collaborations.

DATE: Saturday- Wednesday, November 16-20, 2019
LOCATION: Washington Hilton in Washington, D.C.
SPONSORED BY: The American Medical Informatics Association
REGISTER: More Information and Registration

Intermediate R: RNAseq analysis

The learning objectives for this workshop include: 1) How to go from a matrix of raw gene expression counts to differentially expressed genes. 2) How to analyze experimental designs that go beyond 2-group comparisons using edgeR’s generalized linear modeling capabilities. 3) Ways to test specific hypotheses using a joint model fit.

Prerequisites: A minimum of 4 to 6 months experience programming in R and have taken the RNAseq Analysis in R workshop or something equivalent.

DATE: Monday, November 18, 2019
TIME: 2pm-5pm
LOCATION: UCSF Mission Hall 1400
SPONSORED BY: UCSF Bakar Institute & Gladstone Institutes
REGISTER: More Information and Registration

How to Share Research Data to Meet Requirements and Promote Open Knowledge

If you are funded by the NIH, HHMI, or Gates Foundation, or plan to publish in PLOS, PNAS, Science or Nature it is very likely that you will be asked to make your research data publicly available. This is part of a global effort to make research results more transparent, reproducible, and equitable. But what data do you share and how exactly should you share it? The goal of this mini workshop is to get you up to speed with these new requirements and help you work reproducible and painless data sharing into your research process.

Learning Objectives

By the end of this workshop learners will be able to:

• Describe data sharing policies and motivations
• Identify relevant data and documentation for sharing
• Select an appropriate place to share their data
• Prepare data for sharing
• Plan for ethical and reproducible data sharing

DATE: Friday, November 22, 2019
TIME: 11am-12pm
LOCATION : ZSFG Library – Bldg. 30 – 1st Floor – Computer Lab
SPONSORED BY: UCSF Data Science Initiative
REGISTRATION: More Information and Registration

Python and SQL

Data obtained from the web or other outside sources is often messy and difficult to manage.  Pandas, a popular tabular data frame library in Python, and SQL, a structured query language for databases, provide two different but effective tools for getting a better handle on your data.  This workshop is designed to introduce you to both tools in the context of managing research data, demonstrate the strengths of each approach, and review how the two approaches can be particularly effective when used in combination.

Through a series of in class exercises, participants will review how to sort, filter, and aggregate data in Pandas and SQL, and review the benefits and drawbacks of each approach.  We will also review how Pandas and SQL can be used in combination to handle more difficult data analysis problems.

This workshop has recommended prerequisites. For more information please see the CLE page for Data Analysis with SQL and Python.

DATE: Friday, November 22, 2019
TIME: 9am-11am
LOCATION : Mission Bay, CC151
SPONSORED BY: UCSF Data Science Initiative
REGISTRATION: More Information and Registration

Python and JSON

Finding, reading, and parsing data is often the most challenging and important part of a data science project. JSON is a common standard used by web APIs to provide machine readable access to data over the web. This workshop will introduce basic JSON parsing through Python using a web based API.

Prerequisites: Unix Shell and Python

Materials and set up instructions are available in the CLE: Reading Data from an API with Python and JSON

DATE: Friday, December 6, 2019
TIME: 9am-11:30pm
LOCATION : Mission Bay, CC151
SPONSORED BY: UCSF Data Science Initiative
REGISTRATION: More Information and Registration

PRISM Health Symposium

Promoting Research in Social Media and HealthThe Promoting Research in Social Media and Health Symposium (PRISM Health Symposium) is a one-day research symposium that fosters a collaborative learning community for researchers in social media and health. The burgeoning field of social media and health research is broad, but distinct from health information technology and mobile health. The PRISM Health Symposium planning committee does far-ranging research on health and social media. Prior work presented at PRISM include vaccination attitudes, infectious disease outbreaks, tobacco cessation, and tanning bed use, all using online communication.PRISM provides a one-of-a-kind opportunity for participants to meet, collaborate, and advance their work. Now in its fourth year, PRISM has hosted researchers, industry partners, and patients from over 40 unique institutions. PRISM is one of the few symposiums dedicated to social media and health research.Featuring Susannah Fox, former Chief Technology Officer at HHS

DATE: Friday, December 6, 2019
TIME: 8:30am-6pm
LOCATION: Presidio Officers’ Club – Ortega Ballroom
SPONSORED BY: CTSI, UCSF Cancer Center, Center for Vulnerable Populations, Dept of Epi and Biostats
REGISTRATION: More Information and Registration

Intro to Basic Programming for Scientists: Python, Unix, Git (2-day workshop)

An example-driven two-day boot camp taught by volunteers who are scientists and programmers. The workshops will introduce the basics of Unix Shell and Git, along with Python. Short tutorials alternate with hands-on practical exercises, and participants are encouraged both to help one another, and to try applying what they have learned to their own research problems during and between sessions.

Participants must bring their own laptop to work on. This should be a “real” laptop – not a Chromebook, tablet, etc. You should also be sure to have admin privileges on this computer.

DATE: Wednesday – Saturday, December 9-12, 2019
TIME:  1pm-5pm
LOCATION: UCSF Mission Hall, 550 16th Street, Rooms 1407
SPONSORED BY: Bakar Computational Health Sciences Institute and UCSF Data Science Initiative
REGISTER: More Information and Registration

BHCSI Presents Seminar Series

Technology and Team Science for Person-centered Care:  A Health Informatics Research Agenda from Data to Wisdom

Katherine Kim, PhD, MPH, MBA

Abstract: Mobile and interactive technologies that enable collaboration can be applied to improve social health processes that are highly individualized such as care coordination and shared decision making.  Technologies such sensors, mobile applications, and decision aids support not only data collection but also analytics that turn those data into information.  However, information alone may not lead to outcomes.  Engagement with users—patients, families, clinicians—turns information into knowledge that can be applied to the health/healthcare challenge at hand and generalized to benefit populations.  In this talk, I will share my research program in which I apply an ensemble of methods to innovate research ideas, develop applications, create and evaluate interventions for care coordination and shared decision making, and incorporate predictive analytics into decision support.  I will illustrate with examples from my research in Oncology, Cardiology, and chronic conditions.

DATE: Tuesday, December 10, 2019
TIME: 4-5pm
Location: UCSF Mission Hall 1401
SPONSORED BY: UCSF Bakar Computational Health Sciences Institute
PRESENTATON LINK: View Here

Python and Natural Language Processing

This workshop will provide a hands-on introduction to natural language processing and text classification using Python. This workshop will focus on the programming skills necessary to prepare and format data, build and run a model, and read and interpret results.

We want to emphasize that while this is an intro to NLP class, it’s not an intro to Python class! Prerequisites: Familiarity with python programming, including lists, dictionaries, loops, pandas data frames, and functions.

Bring your laptop. Computers will not be provided.

DATE: Friday, December 13, 2019
TIME:  9am-11am
LOCATION: Mission Bay, CC151
SPONSORED BY: UCSF Data Science Initiative
REGISTER: More Information and Registration

Programming Hacky Hour

Hacky Hour is an opportunity for you to get feedback on a current programming project from your peers at UCSF or to work independently. This event is a brown bag lunch.

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 join us for an hour of coding in a friendly environment. You: bring your laptop and a current project. Your programming peers may be able to answer a couple of questions. If you need 1:1 help, sign up for Office Hours.

Preparation: Bring something you want to work on, e.g. an image analysis project or a programming exercise. Find collaborators by sharing your project topic for 1-2 minutes. You’re also welcome to use the space to work on your own.

Software: No requirements. Optional – if you want to install software, here are instructions:

• Unix, Bash, and Python Installation
• Install R
• Install RStudio

Materials: This is not a class and there are no materials. If you’re new to programming, we can point you to a few tutorials like Intro to R, Intro to Python, or Data Cleaning with OpenRefine. Find more class materials in the Data Science Initiative CLE and take a look at our recommended reading list.

Instructor: This event is attendee-driven. No instructors.

DATE: Thursday, December 19, 2019
TIME:  12pm-1pm
LOCATION: Mission Bay, CC151
SPONSORED BY: UCSF Data Science Initiative
REGISTER: More Information and Registration

SQL for Beginners

Register here

TIME: 1:00pm – 3:00pm
LOCATION: Mission Bay, Mission Hall 1406
SPONSORED BY: UCSF Library

Programming and Pizza

TIME: 4:00pm – 6:00pm
LOCATION: Mission Bay FAMRI Library: Room CC150 (main reading room)
SPONSORED BY: UCSF Library / ICHS

Register here

Deep Learning in Biomedicine

TIME: 9:30am – 6:00pm
LOCATION: Genentech Hall
SPONSORED BY: ICHS & NVIDIA

Precision Medicine World Conference (PMWC) 2018, Silicon Valley

The Precision Medicine World Conference (PMWC), formerly known as the Personalized Medicine World Conference, is an independent and established conference that attracts recognized authorities and experts across healthcare and biotechnology sectors. The Conference – an outstanding forum to touch upon the different directions and aspects of precision medicine and attended by all the multi-disciplinary stakeholders – showcases practical content that helps close the knowledge gap by different sectors, thereby catalyzing cross-functional collaboration to further adoption of personalized medicine in the clinic.

Topics Include:

AI & Machine Learning, All of Us Research Program, Big data, Biomarker and companion diagnostics, Cancer and rare disease diagnostics, Clinical NGS, Clinical trial developments, Clinical-decision support, CRISPR, Data and regulatory policies, Digital, mHealth, and Telehealth, Drug discovery, PM Economics and socio-political aspects, Immunotherapy, Infectious disease ID and monitoring, Large scale human genetics, Liquid biopsy, Metabolomics, Overcoming data sharing, PM initiatives, Microbiome, Patient engagement, Valued-based healthcare, Wellness & Aging

For more information & to register, visit: https://www.pmwcintl.com/2018sv/

Machine Learning in the Genome and Phenome
to Understand Complex Traits:

Discovery Science for Precision Medicine

TIME: 3:00pm – 5:00pm (followed by reception)
LOCATION: Parnassus Campus, Nursing Building, N225
SPONSORED BY: PREMIER

Introduction to the Unix Shell

TIME: 10:00am – 12:00pm
LOCATION: UCSF Mission Bay, Mission Hall, MH 1406
SPONSORED BY: UCSF Library

Programming and Pizza

Data Analysis with SQL and Python

Data Cleaning with Open Refine

Related LibGuide: Data Sharing & Data Management by Ariel Deardorff

Register Here 

DATE: Thursday, February 15, 2018

TIME: 1:00pm – 2:30pm

LOCATION: UCSF Parnassus Library, CL214

Winter Genetics Day

Building on the momentum of a highly successful Genetics Day in the Fall, the Institute for Human Genetics will host Winter Genetics Day on Thursday, February 15, 2018, beginning at 1:00pm at Parnassus in HSW-301.

Special guest and keynote speaker Dr. Michael F. Hammer will present “Genomic approaches to identifying genes associated with epilepsy severity in two patient populations.” Dr. Hammer is Research Scientist in the Division of Biotechnology at the University of Arizona, with appointments in the Department of Neurology, Ecology and Evolutionary Biology, School of Anthropology and University of Arizona Cancer Center.

Also speaking: Deepak Srivastava, President of the Gladstone Institutes and Professor of Pediatrics and Biochemistry & Biophysics, will begin the program with a talk on “Complex genetic inheritance of congenital defects.” Helen Kim, Assoc. Professor of Anesthesia and Investigator at the Center for Cerebrovascular Research will present “Familial cerebral cavernous malformations: Modifiers of disease severity and progression.” Yin Shen, Asst. Professor of Neurology, will speak on “Regulation of gene expression in the 3D genome.”

A special new component of Winter Genetics Day will be 5-minute “flash talks” by genetic trainees, scheduled between faculty presentations. Please join us for an afternoon of exciting scientific discourse and community.

More info available at the IHG event page

TIME: 1:00pm – 5:00pm
LOCATION: UCSF Parnassus, Health Sciences West Bldg., HSW301
SPONSORED BY: Institute for Human Genetics

Intro to Github

DATE: Tuesday, February 20, 2018

TIME: 11:00am – 1:00pm

LOCATION: UCSF Parnassus Library, CL214

Introduction to R with Basic Statistics

Related LibGuide: Bioinformatics and Statistics Resources by Karla Lindquist

DATE: Thursday, February 22, 2018

TIME: 9:00am – 1:00pm

LOCATION: UCSF Mission Bay, Mission Hall 1402

Introduction to Python

DATE: Friday, February 23, 2018

TIME: 10:00am – 1:00pm

LOCATION: UCSF Mission Bay, Mission Hall 1406

Translating Big Data to Practice:
Navigating Politics, Policy and Coverage

Christoph Lee, MD, MS  is Associate Professor of Radiology at the University of Washington (UW) School of Medicine. He earned his BA cum laude from Princeton and MD cum laude from Yale. He completed his radiology residency at Stanford and a health policy fellowship as a Robert Wood Johnson Foundation Clinical Scholar. He holds additional faculty appointments at the UW School of Public Health, Fred Hutchinson Cancer Research Center, the Pacific Northwest Evidence-Based Practice Center, and the Kaiser Permanente Washington Health Research Institute.

Dr. Lee is the lead author and editor of five books spanning the basic sciences, evidence-based medicine, and medical imaging, distributed internationally by McGraw-Hill and Oxford University Press. He has obtained research funding from the National Institutes of Health, American Cancer Society, and Agency for Healthcare Research and Quality. Dr. Lee is the author of more than 150 peer-reviewed journal articles and book chapters, and serves on the editorial boards of three leading journals: Radiology, the American Journal of Roentgenology (AJR), and the Journal of the American College of Radiology (JACR). He is a national thought leader in imaging-related health services and policy research, with a focus on improving the value of breast cancer care.

RSVP

TIME: 8:00-9:00am
LOCATION: Parnassus, HSW 301
SPONSORED BY:Radiology and Biomedical Imaging

Crowdsourcing & Interactive Digital Media for Research

Come and interact with a Consortium of NIH BD2K Investigators implementing exciting projects involving crowdsourced data and gamification methodology in their research. The following software will be showcased, and the Investigators will be on-hand, along with Program representatives from NIH, to share their insights. This showcase coincides with GDC (Game Developers Conference) taking place in San Francisco that same week, and GDC attendees are encouraged to join!

Eterna                 Rhiju Das, Stanford University

Solve puzzles to design molecular medicines. (Web)

Fold It                 Seth Cooper, Northeastern University

Solve puzzles to help researchers find out if humans’ pattern-recognition and puzzle-solving abilities make them more efficient than existing computer programs at pattern-folding tasks, informing models of protein structure prediction. (Web)

EyeWire II           Amy Sterling, Princeton University

EyeWire is a 3D puzzle game that allows players to solve puzzles of neuron configurations to help researchers map the brain. (Web)

Quorum              Jimmy Lin, Rare Genomics Institute

Project Quorum is a flexible gaming platform that will crowdsource the analysis of visual data — such as microscopic images or graphical charts — that are provided directly by research scientists.

MDCAS               Stephen Intille, Northeastern University

Mobile Data Crowdsourced Annotation System (MDCAS) is a crowd game for annotating and integrating the vast amount of motion data from mobile phones, wearables, and other everyday sensors.

Cancer Crusade Sandy Anderson, Moffitt Cancer Center

This project represents a collaboration between cancer biologists at Moffitt Cancer Center and the game development team at Spry Fox to prototype a game in which players can help improve our scientific understanding of combination therapies that fight cancer.

GraphSpace       T.M. Murali, Virginia Tech

GraphSpace is an easy-to-use web-based platform that collaborating research groups can use for storing, interacting with, and sharing networks. (Web)

EMR Labeling     Daniel Fabbri, Vanderbilt University

This project is developing a crowdsourcing solution for generating a wide range of labeled data sets from electronic health records.

StarGEO              Dexter Hadley
University of California, San Francisco

The Search Tag Analyze Resource for the Gene Expression Omnibus (STARGEO) project aims to crowdsource annotations of open genomics big data that allows users to discover the functional genes and biological pathways that are defective in disease. (Web)

TIME: 1:00pm – 4:00pm
LOCATION: Mission Bay, Mission Hall 1400
SPONSORED BY: ICHS

Intro to Geographic Information System (GIS)

This 2-hour workshop is designed for those with little or no GIS (Geographic Information System) experience. GIS software is widely used to manage, display, and analyze/model spatial information as well as to publish maps.

Class Agenda:

• Explore common file types
• Explore the user interface
• Perform basic analysis
• Publish a map

Instructor: Mono Simeone, Mono.Simeone@ucsf.edu

Mono is the UCSF GIS Manager, his primary work is to support the university in utilizing spatial information and mapping to support operations and communications. He is also the UCSF Esri Site License Administrator. Before joining UCSF, Mono taught intro and intermediate GIS for 10 years at the GIS Education Center at CCSF before directing the program for the past 3 years. Other projects include: SF Department of Elections, SFPD, and Point Reyes National Seashore. Mono is now past-President of BayGeo, the Bay Area’s professional association for users of GIS and mapping technology. Mono loves maps and is passionate about sharing the benefits of maps and spatial analysis to empower communities.

When you register, the Library reserves class space for you. Since many of our classes have a waitlist, please cancel your registration if you can no longer attend.

Register here

TIME: 10:00am – 12:00pm
LOCATION: Mission Bay, Mission Hall 1407
SPONSORED BY: UCSF Library

Introduction to Machine Learning

This 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 to create a “bag of words”, train an algorithm to recognize patterns in text, and apply the algorithm to classify new documents.

We want to emphasize that while this is an intro to machine learning class, it’s not an intro to Python class! Prerequisites: Familiarity with python programming, including lists, dictionaries, loops, pandas data frames, and functions.

Bring your laptop! Computers will not be provided.

Register here

TIME: 1:00pm – 5:00pm
LOCATION: Mission Bay, Mission Hall 1406
SPONSORED BY: UCSF Library

Programming and Pizza

Learning Python or R? Need dedicated practice time where you can ask questions? Like pizza? This 2-hour work session is designed to give people a chance to work on their Python/R projects alongside other beginners, and receive support from other users and our in-house experts. Bring your laptop, questions, and anything you are working on.

April 5 & 19: Introducing data science book clubs! Want to learn a new programming language with a group? Love pizza? Join us twice a month from 4-5pm in the Mission Bay FAMRI Library as we work through the following books:

simpleR – Using R for Introductory Statistics
https://cran.r-project.org/doc/contrib/Verzani-SimpleR.pdf

Python For Data Analysis (UCSF WPA users have a free subscription to the online version)
https://proquest.safaribooksonline.com/book/programming/python/9781491957653
For the reading schedule and more information, see the Data Science Initiative CLE

Have a general programming question? Drop-in programming help will run from 5-6pm.

Brought to you by the UCSF Library Data Science Initiative and the Institute for Computational Health Sciences.

Bring your laptop! Computers will not be provided.

TIME: 4:00pm – 6:00pm
4/5 & 4/19 LOCATION: Mission Bay FAMRI Library: Room CC150 (main reading room)
4/12 LOCATION: Parnassus, CL221-222
SPONSORED BY: UCSF Library / ICHS

Statistical Methods and Software for the Study of Stem Cell Differentiation Using Single-Cell Transcriptome Sequencing

TIME: 3:00pm – 4:00pm (reception 4-5pm)
LOCATION: Mission Bay, Mission Hall 2103
SPONSORED BY: UCSF Biostatistics and Bioinformatics & ICHS

Identifying the location and functional impact of transcription factor binding sites using neural networks

Martin Hemberg, Ph.D.

Cellular Genetics, Wellcome Sanger Institute

Intro to SQL

LOCATION: Parnassus, CL221-222
SPONSORED BY: UCSF Library

Intro to Python

Programming and Pizza

TIME: 4:00pm – 6:00pm
LOCATION: Mission Bay FAMRI Library: Room CC150 (main reading room)
SPONSORED BY: UCSF Library / ICHS

ImageXD 2018: Image processing across domains

NLP @ UCSF

Have you ever wanted to extract medical information from clinical notes, biomedical textbooks, tweets or other unstructured text data? Have you tried to extract it yourself and hit roadblocks? Or, perhaps you were successful and but want to raise the bar and meet people doing similar work at UCSF.

Join us on May 18, for a morning dedicated to using natural language processing (NLP) techniques to process medical text, specifically focused on research applications.

This will be a two-part event:

The first part of the morning will highlight current work by researchers on campus who have successfully used NLP to enable their research. Expect to learn what’s possible with text analysis and information retrieval, and the support available to conduct medical research using NLP at UCSF.
The second part of the morning is a deep dive into the code and techniques used by analysts and programmers, with the goal of enabling participants to get started with NLP. It will feature tools, examples, challenges and technical particulars in the use of NLP.
We hope you can attend and encourage others to attend either or both parts of this event!

Agenda & additional info can be found on the event website

Videocapture of the event can be viewed here

TIME: 9:00am – 12:30pm
LOCATION: Mission Bay, Byers Auditorium, Genentech Hall
SPONSORED BY: UCSF Research Data Guild

TIME: 4:00pm – 5:00pm
LOCATION: Mission Bay, BYERS HALL 215
SPONSORED BY: UCSF Bioengineering and Therapeutic Sciences

Data Acquisition with JSON and Python

TIME: 10:00am – 12:00pm
LOCATION: Parnassus, Main Library CL220-223
SPONSORED BY: UCSF Library

Programming and Pizza

TIME: 4:00pm – 6:00pm
LOCATION: Mission Bay FAMRI Library: Room CC150 (main reading room)
SPONSORED BY: UCSF Library / ICHS

June 14

Learning Python or R? Need dedicated practice time where you can ask questions? Like pizza? This 2-hour work session is designed to give people a chance to work on their Python/R projects alongside other beginners, and receive support from other users and our in-house experts. Bring your laptop, questions, and anything you are working on. Brought to you by the UCSF Library Data Science Initiative and the Institute for Computational Health Sciences.

Register for June 14

TIME: 4:00pm – 6:00pm
LOCATION: Parnassus, Main Library, CL 221-222
SPONSORED BY: UCSF Library / ICHS

Intro to Python: Part 1

Register here

TIME: 9:00am – 12:00pm
LOCATION: Mission Bay, Mission Hall 1407
SPONSORED BY: UCSF Library

TIME: 2:00 – 5:00pm
LOCATION: Mission Bay, Mission Hall 1407
SPONSORED BY: UCSF Library

Intro to Python: Part 2

Register here

TIME: 9:00am – 12:00pm
LOCATION: Mission Bay, Mission Hall 1407
SPONSORED BY: UCSF Library

Programming and Pizza: Python/R

DATE: Thursday, July 12, 2018 Show more dates
TIME: 4-6pm
LOCATIONS: Mission Bay — Mission Hall 1108 for R; Mission Hall 1109 for Python
SPONSORED BY: UCSF Library

Basic Statistics with R

TIME: 2-5pm
LOCATION: Mission Bay, Mission Hall 1407
SPONSORED BY: UCSF Library

Invited NLP Seminar: Rui Zhang

TIME: 11am-12pm
LOCATION: Mission Bay, Mission Hall 1406
SPONSORED BY: UCSF Bakar Institute

Bakar Institute Seminar Series: Ed Boyden

Intro to SQL

Introduction to Bioconductor

Intro to Github

Greater Bay Area Cancer Registry Symposium

Introduction to Machine Learning Workshop

UCSF Clinical Data Colloquium 2.0

Intro to Basic Programming for Scientists (2-day workshop)

WikiPathways Summit 2018

Intro to the Unix Shell

Programming and Pizza: Python/R         

Join us for an R or Python discussion from 4-5pm followed by general programming help from 5-6pm. Pizza provided while supply lasts.

Want to learn more about R or Python, but don’t know where to start? Do you have a specific programming problem and need advice? Join us to talk about tools, resources, and other programming topics. Beginners welcome!

Locations: Meet in Mission Hall 1105 for R and Mission Hall 1107 for Python.

4 – 5pm: Discuss an R or Python programming question as a group

5 – 6pm: Drop in programming help

Bring your laptop! Computers will not be provided.

TIME: 4pm-6pm
LOCATION: Mission Bay, 1105/1107 Mission Hall
SPONSORED BY: UCSF Library & Bakar Institute

Intro to Python: Part 1 (Oct 18) & Part 2 (Oct 26)

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. Bring your laptop!

Materials and set up instructions available in the CLE: 

• Introduction to Python, Part 1
•  Introduction to Python, Part 2

Register Here for Part 1

Register Here for Part 2

Inaugural Artificial Intelligence & Machine Learning Symposium

Hosted by UC Davis Health, Office of Entrepreneurship and Industry Alliances in partnership with UC Davis Machine Learning Working Group

Free Breakfast + Watch Party: Building Community as Infrastructure

Related LibGuide: Data Sharing & Data Management by Ariel Deardorff

Date:

Friday, November 2, 2018

Time:

9:00am – 11:30am

Location:

Mission Hall 2110

Campus:

Mission Bay

Intro to Python: Part 2

Date:

Friday, November 2, 2018

Time:

10:00am – 1:00pm

Location:

Mission Hall 1407

Campus:

Mission Bay

Big Data in Biology:
The good, the bad, the ugly

Ewan Birney, PhD, FRS
Director of the European Molecular Biology Lab – European Bioinformatics Institute (EMBL-EBI)

Molecular biology is now a leading example of a data intensive science, with both pragmatic and theoretical challenges being raised by data volumes and dimensionality of the data. These changes are present in both “large scale” consortia science and small scale science, and across now a broad range of applications – from human health, through to agriculture and ecosystems. All of molecular life science is feeling this effect.

As molecular techniques – from genomics through transcriptomics and metabolomics – drop in price and turn around time there is a wealth of opportunity for clinical research and in some cases, active changes clinical practice even at this early stage. The development of this work requires inter-disciplinary teams spanning basic research, bioinformatics and clinical expertise.

This shift in modality is creating a wealth of new opportunities and has some accompanying challenges. In particular there is a continued need for a robust information infrastructure for molecular biology and clinical research. This ranges from the physical aspects of dealing with data volume through to the more statistically challenging aspects of interpreting it.

A particular opportunity is the switch from research commissioning genomic measurement to healthcare centric genomic measurement. This is occurring in a number of countries worldwide, including Australia, Denmark, Finland, France, United Kingdom and United States.

Coupled with this though are important aspects of communication of the results of this information, in particular in areas closer to policy and politics, for example, the concepts of “ethnicity and race” with respect to genetics. Here the scientific area of endeavour interacts with many active societal discussions.

Dr. Birney will provide an overview of this area, highlighting the role of EMBL’s European Bioinformatics Institute and the Global Alliance for Genomics and Health, and then using an exemplar from my own research group on imaging genetics. Finally he will discuss his view on how to present the intersection of this field with broad societal concepts such as ethnicity or race, and the potential pitfalls in these discussions, and welcome feedback and discussion in particular on this latter topic.

Link to livestream

Questions can be submitted remotely via slido.com/birney

DATE: November 2
TIME: 4-5pm (lecture), 5-6pm (reception)
LOCATION: Mission Bay Campus, Mission Hall 1401/1402

Intro to SQL

Date:

Thursday, November 8, 2018

Time:

1:00pm – 4:00pm

Location:

Mission Hall 1407

Campus:

Mission Bay

Programming and Pizza: Python/R          

Related LibGuide: Data Sharing & Data Management by Ariel Deardorff

Date:

Thursday, November 15, 2018

Time:

4:00pm – 6:00pm

Location:

Mission Hall 1105

Campus:

Mission Bay

Insights into genetic mechanisms of complex traits: An introduction to polygenic scores and conditional false discovery rate

DATE: November 16
TIME: 2-3 pm
LOCATION: Mission Bay Campus, Mission Hall 1407

Data Visualization 101

Related LibGuide: Data Sharing & Data Management by Ariel Deardorff

Date:

Thursday, November 29, 2018

Time:

10:30am – 12:00pm

Location:

CL221-222

Campus:

Parnassus

DATE: Friday,December 7, 2018
TIME: 9:00 am – 2:30 pm
LOCATION: UCSF Mission Bay, Genentech Hall, Byers Auditorium and Atrium 600 16th St., San Francisco CA

Precision Medicine World Conference 2017

Overview
The Precision Medicine World Conference (PMWC), formerly known as the Personalized Medicine World Conference, is an independent and established conference series considered to be the preeminent precision medicine conference that attracts 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 and collaboration. Recognized as a vital cornerstone for all constituents of the health care and biotechnology community, PMWC provides an exceptional forum for the exchange of information about the latest advances in technology (e.g. DNA sequencing technology), in clinical implementation (e.g. cancer and beyond), research, and in all aspects related to the regulatory and reimbursement sectors.
Format
The conference format consists of two main tracks (1 and 2) and two parallel tracks (3 and 4). Tracks 1 and 2 include sessions by leaders in the commercial, pharmaceutical, academic, government, regulatory, venture capital, and non-profit arenas that deliver a broad and up-to-date array of content across the various facets of precision medicine. Session discussions focus on time-relevant aspects with a selected set of key stakeholders, while commercial sessions cover the latest developments in technologies that are instrumental for the success of further adoption of precision medicine.

More info here

DATES: January 23-25
LOCATION: Computer History Museum, Mountain View CA

Rare Variants and Asthma in Multi-Ethnic Populations

Dara Torgerson, PhD

Assistant Professor, UCSF Department of Medicine

Thursday, January 26, 2017 @ 12pm – 1pm

Abstract: The prevalence and morbidity of asthma varies among racial/ethnic groups, suggesting that the genetic variation that contributes to asthma may also vary in frequency between populations. Whole genome sequencing of 2500 individuals has shown us the majority of variants in humans are rare and population specific, with 94% of nonsynonymous variants in the Thousand Genomes Project at a frequency < 1%. Thus, for complex diseases governed by multiple genes, we should expect rare variants to play an important role, and to be predominantly population-specific in their effect. In this talk, I will present the results of multiple targeted sequencing efforts of candidate genes and genetic loci that support a role of rare, and in many cases population-specific variation in asthma and asthma-related traits. Further, I will present the case for returning to hypothesis-driven science in the era of whole genome sequencing to identify rare variation that contributes to complex disease. Specifically, through the integration of population genetics, clinical sub-phenotyping, and ancestry deconvolution to empower genetic association studies in diverse populations.   

DATE: January 26
LOCATION: Mission Bay Campus, Rock Hall Auditorium

Special Presentation by Dr. Rich Caruana

In 1997, even before Google was founded, a group of computer scientists and physicians from Carnegie Mellon and the University of Pittsburgh were asked to apply Machine Learning to predict mortality of patients hospitalized with pneumonia. The goal was to identify high risk patients for additional treatment and low risk patients for discharge. Their results were both technically and ethically profound, and paved the way for the use of machine learning in medicine. We are fortunate to have one of the original authors, Dr. Rich Caruana, give a talk in our department. Rich is a pioneer in medicine learning and artificial intelligence. Currently a Senior Researcher at Microsoft Research, Rich was previously on the faculty of Cornell University, UCLA School of Medicine, and the Carnegie Mellon Center for Learning and Discovery. Rich received an NSF CAREER Award in 2004 (for Meta Clustering), and best paper awards in 2005, 2007, and 2014. His current research focus is on learning for medical decision making, deep learning, and computational ecology.

Presentation Abstract:

In machine learning often a tradeoff must be made between accuracy and intelligibility: the most accurate models usually are not very intelligible (e.g., neural nets, boosted trees, and random forests), and the most intelligible models usually are less accurate (e.g., linear or logistic regression).  This tradeoff often limits the accuracy of models that can be applied in mission-critical applications such as healthcare where being able to understand, validate, edit, and ultimately trust a learned model is important. We have developed a learning method based on generalized additive models (GAMs) that is often as accurate as full complexity models, but remains as intelligible as linear/logistic regression models.  In the talk I’ll present two case studies where these high-performance generalized additive models (GA2Ms) are applied to healthcare problems yielding intelligible models with state-of-the-art accuracy.  In the pneumonia risk prediction case study, the intelligible model uncovers surprising patterns in the data that previously prevented complex learned models from being deployed, but because it is intelligible and modular allows these patterns to easily be recognized and removed. In the 30-day hospital readmission case study, we show that the same methods scale to large datasets containing hundreds of thousands of patients and thousands of attributes while remaining intelligible and providing accuracy comparable to the best (unintelligible) machine learning methods.

DATE: February 8
TIME: 5-6pm
LOCATION: Radiation Oncology conference rooms in Ron Conway Family Gateway Medical Building 1825 Fourth St., Second Floor

Data-Mining Health Records for Clinical Decision Support

Jonathan H. Chen MD, PhD

Instructor, Stanford Department of Medicine

Dr. Chen is a practicing physician with research interests focused on data-mining electronic medical records for insights to inform medical decision making. He co-founded a company to translate his Computer Science graduate work into an expert system to solve organic chemistry problems, with applications from drug discovery to a practical education tool distributed to students across the world. To gain first-hand perspective in tackling the greater societal problems in health care, he completed medical training in Internal Medicine and a VA Research Fellowship in Medical Informatics.

A current focus is automated generation of personalized decision support content. With the support of an NIH Big Data 2 Knowledge K01 Career Development Award, he is developing this approach to systematically extract and disseminate the undocumented collective wisdom of practicing clinicians. This will translate endpoint clinical data into a reproducible and executable form of expertise and, deploying this right at the point-of-care, will close the loop of a continuously learning health system.

ABSTRACT:

Medical decision making is fraught with both uncertainty and undesirable variability. The vast majority of our clinical decisions lack adequate evidence to determine their efficacy and inconsistent implementation compromises quality and efficiency.

The current standards in clinical decision support reinforce best-practices but are limited in scalability by manual production. “Grand challenges” thus include mining clinical data sources to automatically generate decision support content.

Statistical approaches allow us to learn patterns that reflect real-world standards of care vs. outliers. This can range from my evaluation of the national distribution of opioid prescriptions to my current NIH Big Data 2 Knowledge K01 Career Development Award directed to empower individual clinicians with the collective experience of the many.

I will review my efforts developing a collaborative filtering machine-learning approach to clinical order entry, analogous to Netflix or Amazon.com’s “Customer’s who bought A also bought B” algorithm. This automatically generated decision support content can reproduce, and even optimize, manual constructs like order sets while remaining largely concordant with guidelines and avoiding inappropriate recommendations. This has even more important implications for prevalent cases where well-defined guidelines do not exist. The same methodology is predictive of clinical outcomes comparable to state-of-the-art risk prediction models. Embedded randomization of such decision support interventions could then allow us to explicitly build knowledge for the future, even as we enhance care today, in a closed-loop learning health system.

TIME: 10-12 pm
LOCATION: Parnassus, M1296

DahShu 2017: Data Science and Computational Precision Health

Dahshu, a nonprofit organization with the mission of promoting research and education in data science, is hosting its inaugural scientific symposium in the beautiful San Francisco Bay Area February 20-22nd, 2017.

The theme for this coming year’s conference is “Data Science and Computational Precision Health.” It will be an international forum that includes keynote speeches, invited talks, demonstrations, as well as oral and poster presentations of refereed papers. The goal is to explore research, development and novel applications in the field of medical research and data science that actively promotes precision health. In this era of information explosion, great advancement to understand disease and help patients could only be achieved by successful collaborations. We aim to bring together academia, industry and policy makers into the same room to share knowledge and experiences, and to showcase innovations and achievements.

The conference venue South San Francisco Conference Center is conveniently located in the heart of the biotech region, minutes from San Francisco Airport and 15 minutes from downtown San Francisco. San Francisco Bay Area is in the Pacific Time Zone.

For more info or to register visit the conference website here

DATES: February 20-22
LOCATION: South San Francisco Conference Center

Healthcare as an Information Business

Healthcare is in great part a pure information business, but its use of technology for information is closer to a library card catalog than to a modern information business. Udi will discuss what’s missing and how to get it.

Udi Manber

Professor and Director of Digital Transformation, Department of Medicine, UCSF
Technical Advisor, Institute for Computational Health Sciences, UCSF
Former head of Google Search (2009-2014)

RSVP here 

A link to the talk can be found here

TIME: 4:00-5:00pm Lecture, 5:00-6:00pm Reception (refreshments served)
LOCATION: UCSF Mission Bay campus, Byers Auditorium & Genentech Hall Atrium
SPONSORED BY: ICHS
HOSTED BY: Robert Wachter, MD; Chair, UCSF Dept of Medicine

UCSF / UC Berkeley Computational Health Science Symposium

Come and join us for an afternoon of stimulating discussion about what’s possible when we bring together experts in biomedicine, computation, and statistics

See here for more information

A link to the talks can be found here 

TIME: 2:00 – 4:00 pm event, 4:30 – 6:00 pm reception
LOCATION: UCSF Mission Bay campus, Mission Hall rooms 1401/1402
SPONSORED BY: ICHS, Berkeley Institute for Data Science, Koret Foundation

BioData World Congress, West 2017

The worlds of science and technology have never been so closely intertwined. The potential and applications of bio data are limitless. From patients tracking their own symptoms to doctors virtually assessing patient needs; from personalized sequencing of cancer genomes to defeating aging through AI, it is safe to say the pharma industry will never be the same again.

BioData World West 2017 is bringing scientific innovation to the forefront with tracks on:

1. Genomics
2. Precision Medicine
3. NEW AI track put together in partnership with Merck

In San Francisco, over 200 participants will gather in the beating heart of innovative tech to discuss disruptive approaches
being used to drive drug development, personalized medicine, and inevitably, the clinic. This unique conference gathers
clinicians, bioinformaticians, pharmaceutical companies, start-ups and government policy advisors under one roof!

Confirmed speakers include: Merck, UCSF, Google, US Department of Veteran Affairs, University of Melbourne Centre for Cancer Research, InSilico Medicine, NIH, BERG Health, RARE, FDA, State of California, and the National Cancer Institute .

Healthcare is joining the big data club. With the advent of high-throughput genomics, the debut of artificial intelligence, and more, the industry is starting to tackle the futuristic era it finds itself in.

See more at: https://www.terrapinn.com/conference/biodata-west/

Empowering Healthcare with Advanced Data Science

The healthcare domain is now being transformed by data-driven discovery and prediction. Professionals working in healthcare are now required to have skills necessary to perform data analytics at large-scale and know the complex ecosystem of tools and platforms in healthcare BigData analytics. This five-week class will cover the foundational topics in data science useful for healthcare professionals and give them skills to sample and apply the basic data analytics techniques.

For more info, or to register, see here

TIME: 3:30 pm – 5:30 pm
LOCATION: UCSF Mission Bay campus, Mission Hall 1407
SPONSORED BY: ICHS & UCSF Library

UCSF Clinical Data Colloquium

Have you ever wondered what clinical data resources exist at UCSF to support your research?  Are you confused about what our data exploration tools can do or how to access them?  Not sure about all of the options for storing, analyzing and sharing data sets? Want to know more about the process to gain approvals?

If you’ve asked yourself any of these questions then don’t miss the UCSF Clinical Data Colloquium on May 10^th! 

            CLICK HERE TO REGISTER

 A number of recent improvements have been made to our clinical data resources and access processes.  Reserve your seat today! See here for more info.

TIME: 9:00 am – 12:30 pm
LOCATION: Mission Bay Conference Center, Robertson Auditorium
SPONSORED BY: Center for Digital Health Innovation (CDHI), Clinical & Translational Science Institute (CTSI), the Institute for Computational Health Sciences (ICHS), UCSF Information Technology and the UCSF Library

7th Annual Academic Senate Faculty Research Lecture in Translational Science

The Academic Senate is pleased to announce the selection of Sarah Nelson, PhD, as the recipient of the seventh annual Faculty Research Lecture in Translational Science.  The lecture titled “Precision Imaging of Brain Tumors,” will take place on Wednesday, May 10, 2017, at 3:30 p.m. in Byers Auditorium at the Mission Bay Campus. The event will be simulcast and a reception will follow.

 A world leader in metabolic assessment of the brain, Professor Nelson has had a career leveraging multi-disciplinary fields to achieve the ultimate goal of improving patient care. Dr. Nelson’s career exemplifies the concept of translational research. As a trained mathematician, she has drawn upon her understanding of mathematical concepts in applications to brain imaging. Her collaborative efforts in using magnetic resonance spectroscopy to obtain metabolic information about brain tumors have made an important contribution to how UCSF approaches surgery and treatment planning. Dr. Nelson’s publications are dedicated to improving patient care and management using advances in quantitative imaging techniques.

 She has over 250 peer-reviewed publications. A recent seminal paper on the first in vivo human application of hyperpolarized carbon-13 MRI garnered over 260 citations by the end of 2013 when it was published.

 Colleagues praise Professor Nelson’s contribution towards nurturing and mentoring junior faculty.  Over 25 years of teaching clinicians and scientists about brain imaging, her mentorship has guided hundreds of trainees from countries around the world. Many of these trainees are now leaders of their perspective fields and carrying on the tradition of translating new technologies into clinical practice.

 Dr. Nelson is a Professor in the Department of Radiology and Biomedical Imaging, with secondary appointments in the Department of Bioengineering and Therapeutic Sciences and in the Department of Neurology. She is the Director of the Surbeck Laboratory of Advanced Imaging and the Director of the Precision Imaging of Cancer and Therapy program in the Helen Diller Family Comprehensive Cancer Center. Dr. Nelson received her PhD from University of Heidelberg in 1982.  She joined UCSF in 1990.

 Again, the Academic Senate Faculty Research Lecture – Translational Science will be held in Byers Auditorium at the Mission Bay Campus on Wednesday, May 10, 2017, at 3:30 p.m.  The event will also be available to view via live simulcast.  A link to the live simulcast will be available and disseminated the day before the event.

The lecture will be open to the campus community and the general public. Following the lecture will be a reception in the atrium of Genentech Hall. Refreshments will be provided.

TIME: 3:30 pm
LOCATION: Byers Auditorium, Genentech Hall, Mission Bay Campus
SPONSORED BY: UCSF Academic Senate

Scaled computation & inferential methods in biomedicine: Machine learning for biomedical applications

Jure Leskovec

Associate Professor of Computer Science, Stanford University
Chief Scientist, Pinterest 

A link to the talk can be found here
If viewing remotely, you may submit your questions at Slido.com , Event Code: UCSF-Leskovec

RSVP here

TIME: 10-11:00am Lecture, 11-11:30am Reception (light refreshments served)
LOCATION: Mission Hall 1400
SPONSORED BY: ICHS

R/Python Programming Workshop – Software Carpentry

Are you looking for an introduction to programming in R or Python? Then this workshop is for you! This event, brought to you by the UCSF Library Data Science Initiative and the UCSF Institute for Computational Health Sciences, is a hands-on two-day workshop that will introduce you to the basics of programming in either R or Python as well as Git/GitHub and the Unix Shell.

This two-day workshop will run May 20 & 21, 9am-5pm each day.  We will be running two concurrent bootcamps meaning both workshops are happening at the same time and you should register for either the R workshop or the Python workshop.

The fee for the workshop is $25. For more info, and to register, click here

CONTACT:ariel.deardorff@ucsf.edu for details
TIME: 9am-5pm, May 20 & 21
LOCATION: Mission Hall rooms 1406 & 1407
SPONSORED BY: ICHS & UCSF Library

Hail Software Presentation

Hail is a Spark-based parallel computing architecture designed for extremely large genetics datasets with VCFs on the order of terabytes that can make computation tractable by massively parallel processing, usually in the cloud.

Hail’s creators, from the Broad Institute, are coming to give a talk at Stanford on June  5th, 1-2:30pm at Alway 106 Auditorium. This talk presents an opportunity to get a sense of best practices for using the system and provide input on desired features for future versions.

Remote viewing will be offered, please click here to attend the talk remotely. The remote viewing session will require you to install the zoom client on your computer, so plan accordingly. The link will be live 10-15 min in advance of the talk.

TIME: Monday, June 5th, 1:00-2:30 pm
LOCATION: Stanford University, Alway 106 Auditorium
SPONSORED BY:Wall Lab

Computational Immunology Seminar Series

We would like to invite you to join us for a Computational Immunology Seminar Series as part of the BMS 270 Computational Immunology Mini-Course. The seminars will be hosted at the Mission Bay Campus. We have an array of exciting speakers lined up and hope you will join us! 

See flyer for details, including speakers: Computational Immunology Course May 2017

TIME: Tuesdays & Thursdays, 3-4pm
LOCATION: Mission Hall 1401 (except on 5/18 & 5/23 in HD-160, Bakar Auditorium)
SPONSORED BY: Biomedical Sciences Graduate Program, Precision Medicine in Rheumatology, and ICHS

InSpire 2017: Developing the Health Informatics Workforce of the Future Conference

DATE: June 6-8
LOCATION: Hyat Regency, La Jolla, CA
SPONSORED BY: AMIA

Programming & Pizza: Python/R Work Session

Learning Python or R? Need dedicated practice time where you can ask questions? Like pizza? This 2-hour work session is designed to give people a chance to work on their Python/R projects alongside other beginners, and receive support from other users and our in-house experts.

Bring your laptop, questions, and anything you are working on. Brought to you by the UCSF Library Data Science Initiative and the Institute for Computational Health Sciences.

Register here for the June 8th session
Register here for the June 15th session

TIME: 12:00 pm – 2:00 pm (6/8/17); 5:00 pm – 6:30 pm (6/15/17)
LOCATION: UCSF Parnassus campus, Kalmanovitz Library CL211 (6/8/17); UCSF Mission Bay campus, 1407 Mission Hall (6/15/17)
SPONSORED BY: UCSF Library, ICHS

SQL for Beginners

This class will introduce you to SQL and relational databases, two closely related tools for storing, searching, and analyzing data.  We will cover the major features of SQL, including querying, filtering, and aggregating result sets. You’ll learn how to join and merge data, and how to our organize your own data to make best use of a relational database.

Prerequisites: To follow along with class exercises, you’ll need to be able to run basic UNIX commands and execute Python statements through Jupyter notebook or CLI.

Do you need help with any of these prerequisites? Register for “Programming & Pizza” on June 8th

Please bring your own laptop.

Register here

TIME: 1:00 pm – 3:00 pm
LOCATION: UCSF Parnassus campus, Kalmanovitz Library CL221/222
SPONSORED BY: UCSF Library, ICHS

Delivering Precision Medicine at UCSF

Clinical Exome Sequencing Goes Live

Tuesday, June 27, 2017
1 – 5 pm, Reception to follow
GENENTECH HALL
Byers Auditorium & Atrium, 600 16th Street
Clinical Exome Sequencing is now available at UCSF! Come learn about how our in-house service can serve your patients’ needs and advance precision medicine.

FEATURING

“Moving the Genome to the Clinic”

Gail P. Jarvik, MD, PhD
Charles J. and Lois B. Epstein Visiting Professor
Head, Division of Medical Genetics
Arno G. Motulsky Endowed Chair in Medicine
Professor of Genome Sciences
University of Washington Medical Center

TOPICS
UCSF’s New Exome Sequencing Service
Laboratory Aspects, Bioinformatics, Variant Annotation, CLIA Certification
Clinical Perspectives on Whole Exome Sequencing
Patients, Triage for Sequencing, Referral instructions
Ethical, Legal, & Social Implications
Patient Perspective & Expert Panel Discussion

Register

gmi.ucsf.edu
#UCSFexome

Leveraging molecular and clinical data to transform cancer drug discovery in the era of precision medicine

Bin Chen, PhD

Assistant Professor, Pediatrics, Institute for Computational Health Sciences
University of California, San Francisco

TIME: 9:00 -10:00 am
LOCATION: UCSF Mission Bay campus, 1407 Mission Hall
SPONSORED BY: ICHS

Leveraging Omics and Computational Approaches to Understand Immune Tolerance Across the Lifespan

Marina Sirota, PhD

Assistant Professor, Pediatrics, Institute for Computational Health Sciences
University of California, San Francisco

TIME: 10:00 -11:00 am
LOCATION: UCSF Mission Bay campus, 1401 Mission Hall
SPONSORED BY: ICHS