Biology As A Data Science
The objective of the OmicsLogic program is to provide training via online materials and easy-to-use analytical tools that demonstrate the use of and explain the conceptual framework of data analysis in the context of biological research and discovery. Training materials are delivered online in courses that highlight key data types, biomedical and biotech topics as well as statistical concepts. Practical assign- ments provide specific guidelines on how to plan and prepare for anal- ysis in integrated settings (online and in-person workshops). These are developed based on published datasets that are hosted on NCBI.
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COMPREHENSIVE HANDS-ON CURRICULUM
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Introduction to Bioinformatics
This module is an introduction to the field of bioinformatics, or the intersection of informatics and biology. It speaks about the opportunities that come with the available big data and methods for its analysis for research and industry, including health care, agriculture, environmental sciences, public health, and more. Important aspects of big data bioinformatics are highlighted:
- Data-driven discovery using big data in life sciences
- Examples of bioinformatics playing an impact in healthcare and industry
- Available resources for bioinformatics: databases, methods and platforms
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Genomics
This module discusses DNA as the code of life and its variation - from single nucleotide variation to copy number variation. We cover the basics about Genes and chromosomes and then talk about how to study Genomic variation using Next Generation Sequencing. The practical modules offer sample projects to the analysis of NGS whole-exome sequencing (WGS), various variant calling algorithms and challenges in interpretation. We also discuss GWAS studies and copy number variation projects.
- Identification of somatic and germline mutations
- Statistical analysis of variants like differentiation based on mutation frequency
- Mutability of single variants and global analysis of genomic variation (GWAS studies)
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Transcriptomics
This module talks about real-world applications of RNA-seq. We will review methods of quantitative and qualitative analysis of RNA in a sample, how data is generated using Next Generation Sequencing and use several projects to practice generating a table of expression from raw FASTQ files and the subsequent analysis of this table of gene and isoform expression. Subsequent modules explore how standard tools like differential gene expression profiling and regression-based approaches can be used to explore RNA-seq data.
- Processing NGS data for gene and isoform expression profiling
- Exploratory analysis and hypothesis testing
- Conventional Machine Learning tools (clustering and classification)
- Single Cell RNA-seq techniques
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Epigenomics & Epigenetics
DNA Methylation, Chromatin Immunoprecipitation and non-coding RNA
This module talks about regulation of gene expression with regulatory RNAs. These in- clude long non coding RNAs, microRNAs and other non-coding elements. We will also discuss Chromatin Immunoprecipitation or CHiP-Seq to study histone modification. Histone modification can make some regions of the genome more open or closed for transcription. Each course explores a relevant project that comes with public-domain datasets and a detailed tutorial that helps start the analysis and validate that your re- sults are consistent with the reference publications.
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Metagenomics
The Metagenomics module covers the conceptual and practical aspects of microbiome studies. We discuss the metagenomics sequencing approaches and Data analysis tools. For practical exercises, we review the significance of the microbiome for human health and ecology. You will learn about multiple types of sequencing methods, 16S rRNA and DNA, and then practice analysis of 16s sequencing data, including several public-domain methods for processing, analysis and visualization of microbiome data.
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Machine Learning for High-throughout Biomedical Data
The module on Machine Learning will allow participants to explore various machine learning methods and their application to various types of high-throughput biomedical datasets. As a hot topic, the terminology and uses of machine learning across various domains have been widely discussed. Using examples in precision medicine, we will learn to apply methods and combine them together to solve real-world challenges.
- Machine Learning for High-throughput data in research and biomedical applications
- Conventional tools that are used: clustering, dimensionality reduction, classification and feature selection
- General Linear models and Network Analysis
- Application and Tuning of Machine Learning to solve real-world challenges
SUPPORTED BY REGULAR WORKSHOPS & HACKATHONS
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05November
Introduction to Bioinformatics
Introduce bioinformatics to your students as a data science approach to biology. Learn about the important progress in basic and translational research afforded by data technologies and discoveries in precision medicine, drug discovery and crop improvement.
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09November
Introduction to RNA Seq
RNA-seq is a standard way to analyze gene expression using Next Generation Sequencing data. This introductory meeting is designed to cover the basics of Next Generation Sequencing process, library prep techniques and the resulting data qualities to be considered when performing the analysis.
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03December
Introduction to Epigenomics
Epigenetics is the study of variation in gene expression that is the result of changes not related to changes in DNA code. Epigenetics is a recent field of study gaining popularity as technologies like chromatin immunoprecipitation and bisulfite sequencing reveal the important role chromatin packaging and DNA methylation play in cell development and differentiation. We also discuss the role of non-coding RNAs in these processes.
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10December
RNA Seq Workshop
Workshops are longer sessions that provide hands-on training and a deep dive into analysis methods and process. RNA-seq conceptually seems like a straight-forward approach, but the understanding of each step with practical considerations around various methods of pre-processing, mapping and quantification play a major role in clear and reliable results.
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17December
Introduction to Genomics
Genomics deals with the DNA sequence and analysis of variants. Introduction to the structure and role of DNA, chromosomes and genomic elements like genes, base pairs and codons prepares participants of the program to perform analysis in an informed and logical way.
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18January
Bioinformatics Workshop
A general workshop on bioinformatics can be scheduled mid-way through the program to make this experience open to others, like faculty and administration - to demonstrate the way the OmicsLogic program can be used by biology students, clinicians and others. One of the projects or a mix of introductory topics can be combined to offer a comprehensive overview of the program or a deep dive into its practical impact.
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04February
Genomics Workshop
A deep dive into single nucleotide variation and the ways statistical analysis of variance can lead to exciting discoveries of differences between two samples (for example tumor vs. normal in oncology studies), groups of samples (heterozygosity or mutability at the single nucleotide level to discriminate between groups of samples) and even Genome-Wide Association Studies (GWAS).
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25February
Machine Learning Workshop
Machine Learning is an emerging topic for data scientists working with a variety of data types. When it comes to high-throughput biomedical data, machine learning methods are used for every aspect of analysis: variance, clustering, feature selection, dimensionality reduction and association. In this hands-on sessions, students get exposure to the methods in application to cancer classification and treatment selection for oncology patients.
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08March
Introduction to MetaGenomics
LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.
DESIGNED FOR STUDENT ACHIEVEMENT
When it comes to data, everyone moves at their own pace. Make sure no one is left behind!
AND FACULTY PEACE OF MIND
Student activity for your class and for each individual is at your fingertips.
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