Institute for Quantitative and Computational Biosciences

Using NGS Analysis Tools - Day One
2019-04-23 09:30 - 12:30 (America/Los_Angeles) | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
High-throughput sequencing technology involves a number of concepts and techniques that shape a project before application-specific processes are utilized. First, this workshop introduces the more ÒuniversalÓ aspects of high-throughput sequence analysisÑfrom experimental design to sequencing and alignment methods. Next, this workshop covers common file formats for sequence data and limitations of sequencing technologies. We will explore a hands-on exercise using the Hoffman2 cluster and will use programs designed to analyze read data, clean artifact and low-quality sequences, and align short reads to a reference genome. At the end of this workshop, students will better understand the logic behind how many of these steps work. Students who are comfortable working with the command line will find this course significantly easier than those who are inexperienced in command-line interface. While Workshop 1 is not an absolute requirement, it is highly recommended for any student who is not already experienced working in a command line environment. A student who takes this workshop at the same time as Workshop 1 should not find any problems with timing of material between these two classes.

Michael Mina, MD, PhD - "Interpreting the human antibody repertoire: Elucidating measles immune consequences & building the foundations of a Global Immunological Observatory”
2019-04-19 12:00 - 13:00 | Boyer 159
The UCLA Institute for Quantitative and Computational Biosciences and the Department of Computational Medicine is co-sponsoring an event on April 19, 2019 in Boyer Hall, Room 159 at 12:00pm. Michael Mina, MD, PhD is a resident physician from Brigham & Women’s Hospital/Harvard Medical School, and he will be visiting to speak for this research lunch event. This event is hosted by Dr. Jamie Lloyd-Smith.
*Lunch will be provided*

Introduction to Modern Statistics - Day Three
2019-04-18 13:30 - 15:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
Workshop attendees will walk away knowing when and how to run modern versions of traditional statistical analysis. First, this workshop introduces tests and underlying bioinformatical lessons about resampling which are useful to most scientific disciplines. This workshop makes no assumptions about familiarity with traditional statistics; we will simply go through relatable experimental examples and ask how to test various hypotheses, introducing the relevant methods along the way. Next, this workshop covers how to best deal with common questions in experimental analysis: What tests can be applied to small sample sizes? When can one assume linearity in the data? What to do with non-Gaussian data / residuals? How does one best detect and justify removing outliers? Which estimators are appropriate with highly non-continuous samples?

Machine Learning in Python - Day Three
2019-04-18 09:30 - 12:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
Applications of Machine Learning can be used to analyze biological data without the need of advanced programming skills. For example, Machine Learning techniques can be used to construct predictive models based on a set of training examples, to remove noise and spurious artifacts from data (e.g. photobleaching), or to help visualize trends within high dimensional datasets, etc. First, this workshop introduces the basic principles involved in the applications mentioned above, such as pattern recognition, linear and non-linear regression, and cluster analysis. This workshop will be oriented towards hands-on activities, starting from the basics of how to load and prepare biological datasets in a Python environment. By the end of this workshop, students will be able to use Scikit-Learn’s documentation (and other libraries) to build models based on their own data, assess their performance, and make new predictions. Although no advanced knowledge will be assumed, students are encouraged to attend to the Advanced Python and Modern Statistics workshops.

Introduction to Modern Statistics - Day Two
2019-04-17 13:30 - 15:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Machine Learning in Python - Day Two
2019-04-17 09:30 - 12:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Introduction to Modern Statistics - Day One
2019-04-16 13:30 - 15:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Machine Learning in Python - Day One
2019-04-16 09:30 - 12:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Introduction to MATLAB - Day Three
2019-04-11 13:30 - 15:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
MATLAB is a powerful, high-level programing language for numerical computation, visualization, and application development. First, this workshop introduces the MATLAB environment. Next, this workshop covers working with arrays and matrices, loops and conditional statements, writing your own functions, working with files, and visualizing your data. We will use MATLAB to solve differential equations and conduct basic computational systems modeling. This workshop is suitable for those with or without coding experience in other languages. No computational knowledge is assumed and no prerequisite workshops are required; however, the Unix workshop (workshop 1) may be a useful foundation.

Introduction to R - Day Three
2019-04-11 09:30 - 12:00 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
R (www.r-project.org) is a free software environment for statistical computing and graphics. First, this workshop introduces basic concepts, syntax, and usage in R programming, statistical analysis, and visualization techniques. We will conduct hands-on tutorials throughout the session, giving attendees a chance to see R in action. This workshop is geared toward those with little or no prior experience with R. Next, this workshop covers an introduction to Bioconductor (www.bioconductor.org), which provides tools for the analysis of high throughput genomic data. If you are interested in any particular R/Bioconductor topic, please contact the instructor in advance; effort will be made to cover topics of general interest.

Introduction to MATLAB - Day Two
2019-04-10 13:30 - 15:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Introduction to R - Day Two
2019-04-10 09:30 - 12:00 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Introduction to MATLAB - Day One
2019-04-09 13:30 - 15:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Introduction to R - Day One
2019-04-09 09:30 - 12:00 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Introduction to Python - Day Three
2019-04-04 13:30 - 16:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
This workshop covers the basic concepts of Python programming. The course is supplemented with many hands-on exercises with emphasis given towards computational biology use cases.

Introduction to Python - Day Two
2019-04-03 13:30 - 16:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Introduction to Unix - Day Three
2019-04-03 09:30 - 12:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
Unix is a command-line-based platform that is a highly powerful and flexible tool for data management and analysis. First, this workshop introduces the basic concepts of UNIX operating system and shell scripting. We will explore essential hands-on skills to confidently use the command line interface on either a local (laptop) or a remote (hoffman2 cluster) computer running the Unix system. Next, this workshop covers how to navigate around the Unix file system from the command line and use a number of basic, common Unix commands. The course is supplemented with many hands-on examples. No prior knowledge of Unix or programming is required.

Introduction to Python - Day One
2019-04-02 13:30 - 16:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Introduction to Unix - Day Two
2019-04-02 09:30 - 12:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Introduction to Unix - Day One
2019-04-01 09:30 - 12:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

QCB Seminar: Dr. Massimo Vergassola, UCSD
2019-03-15 13:00 - 14:00 | Boyer Hall 159
Learning to Soar
MASSIMO VERGASSOLA
Professor
Department of Physics
University of California, San Diego

March 15, 2019
1:00PM to 2:00PM
BOYER HALL 159

—

FRONTIERS IN QUANTITATIVE AND SYSTEMS BIOLOGY SEMINAR SERIES

JANUARY 11 – MARCH 15, 2019

Seminars are held Fridays 1-2pm in Boyer Hall.
All seminars are free and open to the public.

A speaker series sponsored by the Department of Biomathematics and the Institute for Quantitative and Computational Biosciences (QCBio).

Galaxy for NGS Data Analysis - Day Two
2019-03-13 13:30 - 15:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
Galaxy is a web-based infrastructure for bioinformatics application. First, this workshop introduces participants to using Galaxy for analysis of Next-Generation Sequencing data. Next, this workshop covers the structure of Galaxy, data format and manipulation, obtaining and sharing data, and building and sharing workflows. We will use the tools installed on the UCLA galaxy to perform a few types of NGS analysis.

Galaxy for NGS Data Analysis - Day One
2019-03-12 13:30 - 15:30 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

QCB Seminar: Dr. Nicolas Buchler, North Carolina State University
2019-03-08 13:00 - 14:00 | Boyer Hall 159
Gene Expression Noise Accelerates the Evolution of a Biological Oscillator
NICOLAS BUCHLER
Associate Professor
Veterinary Medicine
North Carolina State University

March 8, 2019
1:00PM to 2:00PM
BOYER HALL 159

—

FRONTIERS IN QUANTITATIVE AND SYSTEMS BIOLOGY SEMINAR SERIES

JANUARY 11 – MARCH 15, 2019

Seminars are held Fridays 1-2pm in Boyer Hall.
All seminars are free and open to the public.

A speaker series sponsored by the Department of Biomathematics and the Institute for Quantitative and Computational Biosciences (QCBio).

Digital Imaging Processing in Python - Day Three
2019-03-07 09:00 - 12:00 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
Imaging datasets are becoming easier to acquire yet more difficult to analyze. First, this workshop introduces computational tools available for manipulating images and extracting quantitative information. Next, this workshop covers image conversion and handling in Python, different methods for normalizing, aligning and segmenting images, and applying these techniques to a full image processing pipeline. We will focus on cellular imaging; however, much of the techniques are broadly applicable to other data types.

Digital Imaging Processing in Python - Day Two
2019-03-06 09:00 - 12:00 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

Digital Imaging Processing in Python - Day One
2019-03-05 09:00 - 12:00 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States

QCB Seminar: Dr. Kirill Korolev, Boston University
2019-03-01 13:00 - 14:00 | Boyer Hall 159
The Role of Space in Population Dynamics
KIRILL KOROLEV
Assistant Professor
Department of Physics
Boston University

March 1, 2019
1:00PM to 2:00PM
BOYER HALL 159

—

FRONTIERS IN QUANTITATIVE AND SYSTEMS BIOLOGY SEMINAR SERIES

JANUARY 11 – MARCH 15, 2019

Seminars are held Fridays 1-2pm in Boyer Hall.
All seminars are free and open to the public.

A speaker series sponsored by the Department of Biomathematics and the Institute for Quantitative and Computational Biosciences (QCBio).

Variant Discovery with GATK - Day Three
2019-02-28 09:00 - 12:00 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
This course is designed to take researchers with no genomic experience through variant calling based on the Broad InstituteÕs best practices for GATK. This workshop will be designed to take users from raw sequence data to called variants with emphasis placed on understanding when to apply the best practices or when a particular study or system dictates that you deviate from them. WeÕll emphasize reproducibility of data processing and combining data sets with shell scripts and for-loops to minimize accidental processing errors. By the end of the course, students should feel comfortable working through their own data and have sufficient knowledge to know when and how to deviate from best practices.

Variant Discovery with GATK - Day Two
2019-02-27 09:00 - 12:00 | The Collaboratory, 610 Charles E Young Drive East - BOYER HALL ROOM 529, Los Angeles, CA, 90095, United States
