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Date: May 15th, 2018
Time: 1:00 pm to 4:00 pm (CST)
Location: 1110 S 67th St, Omaha, NE 68182
Conventional Machine Learning Workflows for Transcriptomics with Data Exploration and Visualization Workflows – 1 day workshop at the University of Nebraska at Omaha.
“Machine Learning for Biomedical Data – Workflows in Next Generation Sequencing Transcriptomics”
Part 1: Conventional Machine Learning Approaches for Next Generation Sequencing
Using a public-domain dataset that models multi-omics integration in Precision Medicine (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-10-r110), we will review rapid RNA-seq processing for expression quantification applying logical pipeline construction and pre-processing considerations. In hands-on exercises, participants will explore the expression table using conventional unsupervised machine learning methods and build supervised classifiers with and without feature extraction. The session will be conducted in a non-coding environment to accommodate all levels of users
Using the T-BioInfo platform, participants will learn about the logic and considerations of applying such methods and be prepared for independent downstream analysis and visualization of data using the downloaded R scripts produced by the system. The produced/downloaded code will be reviewed, customized and used in subsequent sessions.
Part 2: Combining custom software with R to streamline analysis workflows and visualize ‘Omics data insights.
The second session will build on the same topics and utilize the same dataset to focus on basic data exploration and visualization in R. Once processed, expression values from huge Next Generation Sequencing datasets are hard to work with and need to be reduced to provide meaningful insights. Once key genes or isoforms are selected, the produced tables can be used This session will strengthen the participants ability to transition to script-based workflows in RNA-seq downstream analysis and visualization. Participants will learn the basics of loading, transforming and manipulation of tables and subsequent visualization of produced tables to represent meaningful findings.
Session led by Stepan Nersisyan (Tauber Bioinformatics Research Center)
Team: The workshops are designed by the researchers at the Tauber Bioinformatics Research Center at University of Haifa, Israel in collaboration with academic centers across the US. Technical support for the workshops is provided by the Pine Biotech team.
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Technical requirements: Participants must have a laptop/desktop computer with internet access. Spreadsheet analysis software is used for simple analyses of pipeline results in most of the exercises. A working version of Excel or other spreadsheet analysis software is necessary to follow these examples. Most of the analysis steps will be done using the t-bio.info platform. No coding or statistics background is required to participate in the workshop, however basic cell biology and biostatistics will be beneficial. In preparation for the workshop, everyone is encouraged to complete the online course material available at edu.t-bio.info.
Certification: Workshop participants will receive a certificate of participation from the Tauber Bioinformatics Research Center and Pine Biotech. The certificate will be emailed after the workshop.
Expected outcomes: Participants will have hands-on experience processing and analyzing Next Generation Sequencing data. After practical exercises and discussion of examples, we will open the discussion to address real-life challenges faced by participants with their own data or workflows for critical review.