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X-WR-CALNAME:Institute for Quantitative and Computational Biosciences
X-ORIGINAL-URL:https://qcb.ucla.edu
X-WR-CALDESC:Events for Institute for Quantitative and Computational Biosciences
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260929T090000
DTEND;TZID=America/Los_Angeles:20261001T120000
DTSTAMP:20260917T225752Z
CREATED:20191212T190507Z
LAST-MODIFIED:20260917T225752Z
UID:10782-1790672400-1790856000@qcb.ucla.edu
SUMMARY:W2: Using NGS Analysis Tools
DESCRIPTION: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 “universal” aspects of high-throughput sequence analysis—from experimental design to sequencing and alignment methods. Next\, this workshop covers common file formats for sequence data and limitations of sequencing technologies. \nWe 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. \nStudents 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.
URL:https://qcb.ucla.edu/event/w2-using-ngs-analysis-tools/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260929T133000
DTEND;TZID=America/Los_Angeles:20261001T163000
DTSTAMP:20260917T225814Z
CREATED:20191212T190540Z
LAST-MODIFIED:20260917T225814Z
UID:10789-1790688600-1790872200@qcb.ucla.edu
SUMMARY:W18: Advanced Python
DESCRIPTION:This workshop will cover some more advanced topics in python including an overview of object-oriented python (this will not be an in-depth course on object-oriented programming)\, use of the numpy and pandas libraries (python libraries for efficient handling of large numeric and heterogenous datasets\, and matplotlib for plotting results. At the end of this workshop\, students will better understand the python data structures for handling large datasets and will have some knowledge of how to manipulate these data and plot them for presentation.
URL:https://qcb.ucla.edu/event/w18-advanced-python/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261006T090000
DTEND;TZID=America/Los_Angeles:20261008T120000
DTSTAMP:20260917T225845Z
CREATED:20191212T190006Z
LAST-MODIFIED:20260917T225845Z
UID:10778-1791277200-1791460800@qcb.ucla.edu
SUMMARY:W9: Intro to Python
DESCRIPTION:This workshop will cover the basic concepts of Python programming. The course is supplemented with many hands-on exercises with emphasis given towards computational biology use cases.
URL:https://qcb.ucla.edu/event/w9-intro-to-python-2/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261006T133000
DTEND;TZID=America/Los_Angeles:20261008T163000
DTSTAMP:20260917T225904Z
CREATED:20191212T185111Z
LAST-MODIFIED:20260917T225904Z
UID:10775-1791293400-1791477000@qcb.ucla.edu
SUMMARY:W1a: Intro to Unix & the Hoffman2 Cluster
DESCRIPTION: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.
URL:https://qcb.ucla.edu/event/w1-intro-to-unix-command-line-2/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261013T090000
DTEND;TZID=America/Los_Angeles:20261015T120000
DTSTAMP:20260917T230238Z
CREATED:20191212T192024Z
LAST-MODIFIED:20260917T230238Z
UID:10798-1791882000-1792065600@qcb.ucla.edu
SUMMARY:W3: Intro to R and Data Visualization
DESCRIPTION: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 course is a pre-requisite for several other Collaboratory workshops. \nThis workshop is geared towards researchers who have little or no experience with R who want to get started with importing data into R and visualize it. This workshop will provide resources for data wrangling\, visualization and cover principles and best-practices for robust and reproducible data visualization. If you are interested in any particular R/Data Visualization tool\, please contact the instructor in advance and effort will be made to cover topics of community interest.
URL:https://qcb.ucla.edu/event/w3-intro-to-r-2/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261013T090000
DTEND;TZID=America/Los_Angeles:20261015T120000
DTSTAMP:20260917T230220Z
CREATED:20230831T231651Z
LAST-MODIFIED:20260917T230220Z
UID:25316-1791882000-1792065600@qcb.ucla.edu
SUMMARY:W21: Image Processing for Microscopy
DESCRIPTION:The analysis of imaging datasets is both exciting and challenging. New and increasingly powerful techniques try to maximize the information derived from multi-dimensional imaging datasets. Yet\, every dataset can be a unique analysis challenge\, and packages may not always work out-of-the-box. In this workshop\, we will explore some popular computational tools to extract quantitative information from imaging data. Our focus will be to first grasp the principles underlying image analysis\, and see how they can be logically applied to different kinds of imaging datasets. We will cover image generation\, filtering\, object identification\, measurement of object properties\, and the basics of object tracking. Through a series of stepwise hands-on exercises for each concept\, we will build up to the goal of designing a full image analysis pipeline. Some programming experience in Python is highly recommended (but optional). Participants are also welcome to bring their own images and videos for discussion.
URL:https://qcb.ucla.edu/event/w21-image-processing-for-microscopy/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261020T090000
DTEND;TZID=America/Los_Angeles:20261022T120000
DTSTAMP:20260917T230702Z
CREATED:20191212T192359Z
LAST-MODIFIED:20260917T230702Z
UID:10805-1792486800-1792670400@qcb.ucla.edu
SUMMARY:W14: Intro to Modern Statistics with R
DESCRIPTION:Through this seminar\, attendees will walk away knowing when and how to run modern versions of traditional statistical analysis. These tests and the underlying bioinformatical lesson about resampling will be of use to most scientific disciplines. The course 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. There will be homework assignments each night to solidify the concepts from class. These are short and optional\, but will allow advanced students to gain more of the class.
URL:https://qcb.ucla.edu/event/w14-intro-to-modern-statistics-2/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261020T133000
DTEND;TZID=America/Los_Angeles:20261022T163000
DTSTAMP:20260917T230706Z
CREATED:20191212T191445Z
LAST-MODIFIED:20260917T230706Z
UID:10795-1792503000-1792686600@qcb.ucla.edu
SUMMARY:W16: Library Prep for NGS
DESCRIPTION:This workshop will cover the basis of Next-Gen Sequencing Library Preparation for Illumina Sequencers. Different Library Preparation Techniques (DNA-seq\, ChIP-seq\, RNA-seq\, Methyl-seq) are explained the first and second day in class. The third day\, Quality Control steps of the starting input material and final libraries are performed in the Lab (TapeStation). Purification from Primer Dimers (using AMPure beads) and Library Submission is also performed on the same day. The third day is optional\, sign-up is required.
URL:https://qcb.ucla.edu/event/w16-library-prep-for-ngs-2/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261027T090000
DTEND;TZID=America/Los_Angeles:20261028T120000
DTSTAMP:20260917T232607Z
CREATED:20230831T232341Z
LAST-MODIFIED:20260917T232607Z
UID:25320-1793091600-1793188800@qcb.ucla.edu
SUMMARY:W31: Spatial Transcriptomics
DESCRIPTION:Spatial transcriptomics is an emerging field that bridges molecular biology and anatomy. Over the last decade\, a battery of assays have been developed that profile gene expression in-situ\, i.e\, measuring the abundances of mRNA molecules in cells and tissues while retaining information about their spatial locations. This workshop will introduce the basic concepts\, major techniques\, and typical analysis workflows in spatial transcriptomics. It will also offer guided hands-on coding exercises for the analysis of public spatial transcriptomic datasets.  \nGiven the field’s rapid development\, this workshop will try not to position itself as an authoritative guide of the subject. Rather\, it will serve as a means of encouragement and support. It aims to help people jump into the field\, plan experiments\, play with data analysis\, and contemplate about the future potential of this powerful technology.
URL:https://qcb.ucla.edu/event/w31-spatial-transcriptomics/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261027T133000
DTEND;TZID=America/Los_Angeles:20261029T163000
DTSTAMP:20260917T232604Z
CREATED:20191212T194026Z
LAST-MODIFIED:20260917T232604Z
UID:10814-1793107800-1793291400@qcb.ucla.edu
SUMMARY:W20: Single-Cell RNA-Seq Analysis with R
DESCRIPTION:This workshop aims to introduce the basic concepts and algorithms for single-cell RNA-seq analysis. It will help participants obtain a better idea of how to use scRNA-seq technology\, from considerations in experimental design to data analysis and interpretation. This workshop can serve researchers who are interested in designing an scRNA-seq study or who have acquired scRNA-seq data and would like to learn about different analytical approaches. \n\n\n 
URL:https://qcb.ucla.edu/event/w20-single-cell-rna-seq-analysis-2/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261103T133000
DTEND;TZID=America/Los_Angeles:20261105T163000
DTSTAMP:20260917T233335Z
CREATED:20191212T193559Z
LAST-MODIFIED:20260917T233335Z
UID:10811-1793712600-1793896200@qcb.ucla.edu
SUMMARY:W22: Intro to Cytoscape
DESCRIPTION:The workshop introduces Cytoscape (https://cytoscape.org/) – an open source platform for retrieval and visualization of complex biological interactions that are available from public interaction resources: The IMEx Consortium (https://www.imexconsortium.org/)\, STRING (https://string-db.org/) and BioGIRD (https://thebiogrid.org/). It covers querying for interactions data using built-in search interface\, interaction data cleanup and visualization as well as overlying of the in-house generated data (eg. gene expression levels) on top of the imported reference interaction network. The workshop will also provide an overview of the experimental methods of interaction determination and of the information available from the interaction resources\, both necessary to critically evaluate imported interaction networks. \n 
URL:https://qcb.ucla.edu/event/w22-intro-to-cytoscape/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261109T090000
DTEND;TZID=America/Los_Angeles:20261112T120000
DTSTAMP:20260917T234320Z
CREATED:20260917T234320Z
LAST-MODIFIED:20260917T234320Z
UID:29327-1794214800-1794484800@qcb.ucla.edu
SUMMARY:W19: AI Agents
DESCRIPTION:This 3-day workshop (3 hours per day) introduces participants to the foundations and practical implementation of AI agents using large language models (LLMs) and LangChain. The course covers how LLMs reason\, how retrieval-augmented generation (RAG) works\, and how to extend models with tool use to automate tasks \n 
URL:https://qcb.ucla.edu/event/w19-ai-agents/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261109T133000
DTEND;TZID=America/Los_Angeles:20261112T163000
DTSTAMP:20260917T234642Z
CREATED:20240214T162259Z
LAST-MODIFIED:20260917T234642Z
UID:26326-1794231000-1794501000@qcb.ucla.edu
SUMMARY:W37: Applications of Large Language Models
DESCRIPTION:This 3-day interactive workshop introduces the overarching principles guiding generative modeling and specifically Large-Scale Language Models (LLM)\, their application in Python for inference\, and specific use-cases in Genomics. Experience with Python is necessary\, and basic knowledge about ML workflows is preferred. \nAt the end of this workshop\, you WILL be comfortable with loading\, inferencing and experimenting with state-of-the-art LLMs in Python\, and making small changes to suit your research interests in Genomics. You WILL NOT be exposed to the internal architecture of LLMs and training your own models.
URL:https://qcb.ucla.edu/event/w33-analysis-of-electronic-health-records-2/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261117T090000
DTEND;TZID=America/Los_Angeles:20261119T120000
DTSTAMP:20260917T234808Z
CREATED:20191212T195402Z
LAST-MODIFIED:20260917T234808Z
UID:10831-1794906000-1795089600@qcb.ucla.edu
SUMMARY:W5a: RNA-seq I Analysis
DESCRIPTION:RNA-seq I aims to provide an introduction and the basics tools to process raw RNA-seq data on a cluster machine (Hoffman2). The workshop can serve also as a starting point to develop a gene expression project. This workshop is divided in three days that will cover major steps of processing RNA-seq. \nTo facilitate learning\, the workshop will be centered on hands-on tutorial that will guide students in processing the data from raw reads through read counts using a real case study based approach appropriate for Illumina read data.
URL:https://qcb.ucla.edu/event/w5a-rna-seq-i-analysis-2/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261117T133000
DTEND;TZID=America/Los_Angeles:20261119T163000
DTSTAMP:20260917T234830Z
CREATED:20230831T232626Z
LAST-MODIFIED:20260917T234830Z
UID:25323-1794922200-1795105800@qcb.ucla.edu
SUMMARY:W28: Advanced Data Visualization w/ ggplot2
DESCRIPTION:
URL:https://qcb.ucla.edu/event/w28-advanced-data-visualization-w-ggplot2/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261201T090000
DTEND;TZID=America/Los_Angeles:20261202T110000
DTSTAMP:20260917T234910Z
CREATED:20191212T195940Z
LAST-MODIFIED:20260917T234910Z
UID:10840-1796115600-1796209200@qcb.ucla.edu
SUMMARY:W5b: RNA-Seq II Analysis
DESCRIPTION:RNA-seq II aims to provide tools for analysis of gene expression data from read counts to biology using R. To facilitate learning\, the workshop will use a real case study based approach appropriate for Illumina read data (same as RNA-seq I).
URL:https://qcb.ucla.edu/event/w5b-rna-seq-ii-analysis-2/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20261201T133000
DTEND;TZID=America/Los_Angeles:20261203T163000
DTSTAMP:20260917T234934Z
CREATED:20210908T213207Z
LAST-MODIFIED:20260917T234934Z
UID:18777-1796131800-1796315400@qcb.ucla.edu
SUMMARY:W17: Machine Learning with Python
DESCRIPTION:This workshop will cover the basic principles involved in the applications mentioned above\, such as pattern recognition\, linear and non-linear regression and cluster analysis. The workshop will be oriented towards hands-on activities\, starting from the basics of how to load and prepare biological datasets in a Python environment.
URL:https://qcb.ucla.edu/event/w17-machine-learning-with-python/
LOCATION:529 Boyer Hall\, 611 Charles E Young Dr E\,\, Los Angeles\, CA\, 90095\, United States
CATEGORIES:Workshops,Interactive Workshop
ATTACH;FMTTYPE=image/png:https://qcb.ucla.edu/wp-content/uploads/sites/14/2020/02/1dNLbh0n_400x400.png
ORGANIZER;CN="QCB Collaboratory":MAILTO:collaboratory@ucla.edu
END:VEVENT
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