Learning Bioinformatics

2023-07-18

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To prepare the syllabus and resources list, some information collected from the Harvard Informatics group and other contributors.

Table of content

Introduction

Introduction to Bioinformatics

What is Bioinformatics

  • Definition and history of bioinformatics.
  • Key areas of bioinformatics: genomics, proteomics, transcriptomics, etc.

Bioinformatics Databases

  • Introduction to key biological databases: NCBI, Ensembl, UniProt, PDB, etc.
  • Retrieving data from biological databases.

Sequence Alignment

Introduction to Sequence Alignment

  • Overview of sequence alignment (pairwise and multiple sequence alignment).
  • Local vs global alignment.

Tools for Sequence Alignment

  • Using tools like BLAST, Clustal Omega, and MUSCLE for sequence alignment.
  • Practical applications of sequence alignment in bioinformatics.

Metagenomics

Introduction to Metagenomics

  • Understanding metagenomics and its applications.
  • Difference between metagenomics and traditional genomics.

Tools for Metagenomic Analysis

  • Using tools like QIIME, Kraken, and MetaPhlAn for analyzing metagenomic data.
  • Taxonomic and functional annotation of metagenomic data.

Proteomics

Introduction to Proteomics

  • Basics of proteomics and its role in bioinformatics.
  • Techniques in proteomics: mass spectrometry, protein sequencing.

Bioinformatics Tools for Proteomics

  • Tools for analyzing protein data (e.g., MaxQuant, Skyline).
  • Protein structure prediction and modeling (e.g., AlphaFold, I-TASSER).

Protein-Protein Interaction Networks

  • Introduction to protein interaction databases and tools (e.g., STRING, Cytoscape).

Epigenomics

Introduction to Epigenomics

  • Understanding DNA methylation, histone modifications, and their roles.
  • Introduction to epigenetic regulation in diseases.

Epigenomic Data Analysis

  • Tools for analyzing epigenomic data (e.g., Bismark for bisulfite sequencing).
  • Chip-Seq data analysis.

Data Integration and Systems Biology

Introduction to Systems Biology

  • Understanding biological networks and systems biology approaches.
  • Application of network analysis in bioinformatics.

Integrative Omics Analysis

  • Combining data from multiple omics (e.g., genomics, transcriptomics, proteomics).
  • Tools for integrative omics analysis (e.g., iCluster, MultiOmics).

Population Genomics

Introduction to Population Genomics

  • Basics of population genomics and evolutionary analysis.
  • Genetic variation, SNPs, and their impact on populations.

Tools for Population Genomics

  • Using tools like PLINK, VCFtools for population-level genomic analysis.
  • Studying population structure and diversity.

Structural Bioinformatics

Protein Structure Prediction

  • Predicting 3D structures of proteins using homology modeling.
  • Introduction to tools like SWISS-MODEL, Rosetta, and Phyre2.

Structural Analysis and Visualization

  • Understanding molecular dynamics in protein function.
  • Visualization of protein structures using Chimera and PyMOL.

Network Biology and Pathway Analysis

Biological Networks

  • Basics of biological networks: metabolic, signaling, protein interaction networks.

Network Analysis Tools

  • Introduction to tools like Cytoscape for network visualization and analysis.
  • Identifying key regulators using network centrality metrics.

CRISPR and Genome Editing

Introduction to CRISPR-Cas9 Technology

  • Basics of CRISPR and its applications in bioinformatics.

CRISPR Data Analysis

  • Tools for CRISPR guide RNA design (e.g., CRISPR-Cas9).
  • Off-target analysis and optimization.

Unix for Bioinformatics

Unix Basics

  • Introduction to Unix and its role in bioinformatics.
  • Understanding the Unix file system and directory structure.
  • Basic Unix commands: ls, cd, pwd, mkdir, rm, cp, mv, etc.
  • Working with files and directories.

Working with text data

  • Using text editors in Unix (e.g., nano, vi, vim) for editing files.
  • Redirection and pipes
  • Text processing utilities: grep, awk, sed.

File manipulation

  • Archiving and compressing files: tar, gzip, zip.
  • File permissions and ownership: chmod, chown.

Introduction to Scripting

  • Writing and executing basic shell scripts.
  • Variables, control structures, and loops.

Intermediate

Data Retrieval and Transfer

  • Downloading files from the web using wget and curl.
  • Transferring files between local and remote systems using scp and rsync.

Working with Biological Data Formats

  • Introduction to common bioinformatics data formats (FASTA, FASTQ, SAM/BAM, VCF, etc.).
  • Using tools for file format conversion (e.g., samtools, bedtools).

Text Processing and Analysis

  • Advanced text processing with regular expressions.
  • Combining Unix tools for complex data analysis.
  • Extracting relevant information from large data files.

Advanced

Shell Scripting and Automation

  • Writing more complex shell scripts for automation.
  • Using Unix tools to automate bioinformatics workflows.
  • Advanced scripting techniques and best practices.

High-Performance Computing (HPC)

  • Introduction to HPC clusters and job submission systems.
  • Writing and submitting batch scripts for bioinformatics analysis.
  • Managing resources and optimizing performance.

Advanced Data Manipulation

  • Using awk, sed, and other tools for advanced data manipulation.
  • Handling large datasets efficiently.

Bioinformatics Pipelines

  • Designing and building bioinformatics pipelines using Unix tools.
  • Integrating third-party tools into custom pipelines.

R

Introduction

Getting Started with R

  • Introduction to R and its applications in bioinformatics.
  • Installing R and RStudio (Integrated Development Environment for R).
  • Basic R syntax: variables, data types, and basic arithmetic operations.

Working with Data in R

  • Data structures in R: vectors, matrices, data frames, and lists.
  • Reading and writing data from/to files (e.g., CSV, FASTA, FASTQ).
  • Basic data manipulation: subsetting, filtering, and sorting.

Data Visualization

  • Introduction to data visualization in R.
  • Using base R graphics and ggplot2 for creating plots.
  • Customizing plots for bioinformatics data (e.g., genomics, proteomics).

Intermediate

Statistical Analysis with R

  • Introduction to statistical analysis in R.
  • Descriptive statistics: mean, median, standard deviation, etc.
  • Hypothesis testing and statistical tests for bioinformatics data.

Bioconductor and Genomic Data Analysis

  • Overview of Bioconductor, a repository of R packages for bioinformatics.
  • Analyzing gene expression data (microarrays, RNA-seq) with Bioconductor packages.
  • Working with genomic data (e.g., DNA sequencing, ChIP-seq, variant analysis).
  • Data Visualization (Advanced)

Advanced data visualization techniques in R.

  • Creating complex plots for multi-dimensional bioinformatics data.
  • Interactive data visualization using packages like Plotly and Shiny.

Advanced

Machine Learning with R

  • Introduction to machine learning in R.
  • Supervised and unsupervised learning algorithms.
  • Applying machine learning to bioinformatics data (e.g., classification, clustering).
  • Bioinformatics Workflows and Reproducibility

Building and documenting bioinformatics workflows in R.

  • Using RMarkdown for creating reproducible reports.
  • Best practices for reproducible research in bioinformatics.

Integration with Other Tools and Databases

  • Connecting R with databases (e.g., MySQL, SQLite) for data storage and retrieval.
  • Accessing and querying biological databases through R.

High-Performance Computing (HPC) with R

  • Parallel computing in R for handling large-scale bioinformatics tasks.
  • Utilizing HPC clusters for bioinformatics analysis.

Python

Introduction

Getting Started with Python

  • Introduction to Python and its applications in bioinformatics.
  • Installing Python and setting up the development environment.
  • Basic Python syntax: variables, data types, and control structures.

Working with Data in Python

  • Data structures in Python: lists, tuples, dictionaries, and sets.
  • Reading and writing data from/to files (e.g., CSV, FASTA, FASTQ).
  • Basic data manipulation: slicing, filtering, and sorting.

Data Visualization in Python

  • Introduction to data visualization in Python.
  • Using matplotlib and seaborn libraries to create plots.
  • Customizing plots for bioinformatics data (e.g., genomics, proteomics).

Intermediate

Bioinformatics Algorithms in Python

  • Implementing common bioinformatics algorithms (e.g., sequence alignment, motif finding).
  • Utilizing Python libraries for bioinformatics tasks (e.g., pairwise2 for sequence alignment).
  • Analyzing biological sequences and structures.

Biological Data Analysis with Pandas

  • Introduction to Pandas library for data manipulation and analysis.
  • Handling and processing bioinformatics data using Pandas DataFrames.
  • Data cleaning and preprocessing techniques.

Bioinformatics Libraries in Python

  • Exploring Biopython: installation and basic usage.
  • Working with biological sequences, structures, and annotations.
  • Retrieving data from biological databases using Biopython.

Advanced

Machine Learning for Bioinformatics

  • Introduction to machine learning in Python.
  • Supervised and unsupervised learning algorithms for bioinformatics data.
  • Applying machine learning to tasks like gene expression analysis, variant calling, etc.

Bioinformatics Workflows and Automation

  • Building bioinformatics pipelines in Python.
  • Utilizing workflow management tools like Snakemake.
  • Automating repetitive tasks and batch processing.

Data Visualization (Advanced)

  • Advanced data visualization in Python using Plotly, Bokeh, or Dash.
  • Creating interactive visualizations for complex bioinformatics data.

Structural Bioinformatics with PyMOL

  • Introduction to PyMOL for visualization and analysis of molecular structures.
  • Structural alignment, superimposition, and visualization.

Git and Version Control

Introduction

Understanding Version Control

  • What is version control and why it is important for researchers?
  • The benefits of using version control in research projects.
  • Overview of Git as a distributed version control system.

Installing Git and Basic Configuration

  • Installing Git on your computer (Windows, macOS, Linux).
  • Configuring your Git identity (name, email).
  • Setting up a global .gitignore file to exclude unnecessary files.

Creating and Cloning Repositories

  • Initializing a new Git repository for a research project.
  • Cloning an existing repository from a remote source (e.g., GitHub, GitLab).
  • Understanding the local and remote repository relationship.

Working with Git for Researchers

Basic Version Control Operations

  • Staging and committing changes to the repository.
  • Viewing the commit history and understanding commit messages.
  • Checking out previous versions of files and repositories.

Collaborating with Others

  • Adding collaborators to your repository.
  • Handling merge conflicts and resolving them.
  • Pulling changes from a remote repository and pushing your changes.

Branching and Merging

  • Creating and managing branches for different research tasks.
  • Merging branches and resolving conflicts during merges.
  • Utilizing feature branches for experimental work.

Advanced Git Techniques for Researchers

Managing Large Files and Data

  • Using Git LFS (Large File Storage) for handling large files.
  • Handling datasets and large research files with Git.

Tagging and Releases

  • Creating tags to mark important milestones in your research.
  • Creating releases for specific versions of your research project.

Git Best Practices for Research

  • Organizing your research project repository effectively.
  • Writing meaningful commit messages and documentation.
  • Using branching strategies that suit research workflows.

Integrating Git into Research Workflows

Version Control with Data Analysis

  • Using Git to version control scripts and notebooks.
  • Incorporating Git into data analysis workflows.

Collaborative Writing with Git

  • Using Git for collaborative writing (e.g., research papers, documentation).
  • Integrating Git with LaTeX, Markdown, or other writing formats.

Automating Workflows with Git Hooks

  • Setting up Git hooks to automate tasks (e.g., running tests, code formatting).
  • Customizing pre-commit and post-commit hooks for your research needs.

Molecular Drug Designing

Introduction

Introduction to Molecular Drug Design

  • Overview of molecular drug design and its importance in pharmaceutical research.
  • Understanding the process of drug discovery and development.

Proteins as Drug Targets

  • Identifying and selecting protein targets for drug design.
  • Understanding the importance of protein structure in drug design.

Molecular Docking

Principles of Molecular Docking

  • Understanding the basic principles of molecular docking.
  • Different types of molecular docking algorithms and scoring functions.

Bioinformatics Tools for Molecular Docking

  • Introduction to molecular docking software (e.g., AutoDock, AutoDock Vina).
  • Preparing protein and ligand structures for docking.

Performing Molecular Docking

  • Conducting protein-ligand docking simulations.
  • Analyzing docking results and interpreting binding interactions.

Molecular Dynamics Simulation

Introduction to Molecular Dynamics (MD)

  • Understanding the principles of molecular dynamics simulations.
  • Applications of MD in drug design and biomolecular studies.

Bioinformatics Tools for Molecular Dynamics

  • Introduction to MD simulation software (e.g., Schrodinger, GROMACS, AMBER, NAMD).
  • Preparing biomolecular systems for MD simulations.

Running Molecular Dynamics Simulations

  • Setting up and running MD simulations.
  • Analyzing MD trajectories and extracting relevant data.

Integration of Docking and Dynamics in Drug Design

Virtual Screening and Hit Identification

  • Using molecular docking for virtual screening of compound libraries.
  • Filtering and prioritizing potential drug candidates.

Free Energy Calculations

  • Introduction to free energy calculation methods.
  • Enhancing accuracy with binding free energy calculations.

Advanced Topics in Molecular Drug Design

Personalized Medicine and Drug Design

  • Exploring the concept of personalized medicine.
  • Customizing drug design approaches for individual patients.

RNA-seq

Introduction to RNA-Seq Analysis

Introduction to RNA-Seq

  • Understanding RNA-Seq technology and its applications in genomics.
  • Differences between RNA-Seq and other sequencing methods (e.g., DNA-Seq).

RNA-Seq Experimental Design

  • Design considerations for RNA-Seq experiments.
  • Sample preparation, library construction, and sequencing platforms.

Preprocessing and Quality Control

Raw Data Quality Assessment

  • Understanding the raw sequencing data formats (FASTQ).
  • Performing quality control (QC) checks using tools like FastQC.

Preprocessing of RNA-Seq Data

  • Trimming adapters and low-quality bases with tools like Trimmomatic.
  • Quality filtering and read preprocessing.

Mapping and Alignment

Reference Genome and Transcriptome

  • Selecting an appropriate reference genome or transcriptome for mapping.
  • Building custom references if needed.

RNA-Seq Read Alignment

  • Aligning preprocessed reads to the reference using tools like STAR or HISAT2.
  • Dealing with splice junctions and novel transcripts.

Quantification of Gene Expression

Gene Expression Estimation

  • Counting aligned reads at the gene level using tools like featureCounts or HTSeq.
  • Generating count matrices for downstream analysis.

Differential Gene Expression Analysis

  • Introduction to differential expression analysis.
  • Using tools like DESeq2 or edgeR to identify differentially expressed genes.

Functional Analysis and Visualization

Gene Ontology (GO) Enrichment Analysis

  • Understanding GO terms and their significance in functional analysis.
  • Using tools like GOseq or topGO for GO enrichment analysis.

Pathway Analysis

  • Introduction to pathway analysis and its importance in understanding gene functions.
  • Performing pathway analysis using tools like KEGG, Reactome, or GSEA.

Data Visualization

  • Creating various plots for RNA-Seq data visualization (e.g., heatmaps, volcano plots).
  • Utilizing tools like R and Python libraries for data visualization.

Advanced Topics in RNA-Seq Analysis

Isoform-level Analysis

  • Quantifying gene isoforms using tools like Salmon or Kallisto.
  • Analyzing alternative splicing events.

Long Non-Coding RNA (lncRNA) Analysis

  • Identifying and characterizing long non-coding RNAs in RNA-Seq data.
  • Special considerations for lncRNA analysis.

Integration with other Omics Data

  • Integrating RNA-Seq data with other genomics data (e.g., DNA-Seq, ChIP-Seq) for comprehensive analysis.