Microarray Analysis with Bioconductor /R

The course is a general introduction to Microarrays and the use of R/Bioconductor to carry out microarray data analysis. Following introduction the workshop starts with hands-on exercise on how to install R and Bioconductor GUI packages. The course is mainly based on the use of Bioconductor open source packages for analyzing single channel and two channel data sets. R coding skill is not required since all the analysis are performed using AffylmGUI, LimmaGUI and OneChannelGUI, a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language. Students will learn how to carryout the following; Quality control, Normalization, Filtering, Statistical analysis, Differential expression and Clustering analysis of single channel and two channel data.

Perl Bioperl for Biologists

This workshop gives an overview of Perl, with a quick introduction to Bioperl. Participants will learn to read and modify Perl scripts, as well as write small scripts of their own. Special focus is given to reading, filtering, and reformatting scientific data. Because the workshop lasts only one day, we do not have time to introduce the basic concepts of programming, such as loops, conditions, and variables. Anyone who has programmed even a small amount in any programming language should be comfortable, but others are encouraged to take a more extensive class. The examples are all biology-related, but biology training is not needed for the class.

Ingenuity Pathways

Ingenuity Pathways Analysis (IPA) is a web-based application that helps researchers analyze their experimental data in the context of biological pathways and functions, search for genes, phenotypes, and diseases, and create and modify experimental models. The morning session will be an introduction to IPA and the afternoon session will deal with more advanced topics. Come for either or both sessions. Special topics, Q&A and individual usage discussions will be included in the workshop. Users are encouraged to bring their own datasets or gene lists to upload and analyze (MS Excel, or tab-delimited-text format).

Biomedical Imaging

Use of Image has significantly increased in the healthcare industry (both on clinical side and research side). Due to this increase there has been a significant increase the volume of data. The workshop/presentation will provide insight into the questions like, what is an Image (TIFF, DICOM)? How should one handle images? Focus will be on bioinformatics analysis including basic quality control requirements non-clinical as well as clinical image data. Advanced Image Analysis like segmentation concepts and registration will also be covered. Audience: Anyone interested or working in imaging, image analysis (people working with CT, MRI, PET images, histology, X-rays etc.).

Bioinformatics Education

A variety of Bioinformatics workshops are available to Harvard researchers. Please visit Countway Website to view and register for individual workshops

  • Introduction to next-generation sequencing (NGS) analysis: Orchestra and standard data processing and workflow analysis
  • mRNA-Seq analysis using JMP Genomics software
  • Introduction to JMP Statistical Discovery Software
  • Gene Expression Omnibus
  • Making the Most of the UCSC Genome Browser
  • Compound Based Pathway Analysis and System Chemical Biology using MetaDrug
  • Microarray Analysis with R & Bioconductor in a cluster environment
  • HTqPCR analysis using R/Bioconductor
  • Whole Transcript expression analysis using Gene and Exon 1.0 ST arrays
  • Introduction to CHIP-seq and data analysis using Galaxy
  • Introduction to Microarrays and Data analysis using R/Bioconductor 
  • Introduction and Fundamentals of Matlab
  • Introduction and analysis of MicroRNAs
  • Metacore Pathway Analysis
  • NCBI MapViewer and Related Resources
  • Perl and BioPerl for Biologists
  • Ingenuity Pathways Analysis 6.0 Training Workshop
  • Expression analysis using GenePattern
  • Ensembl Fundamentals
  • BLAST Tips and Tricks
  • Biomedical Imaging Analysis
  • BIOBASE ExPlain Analysis System for microarray and proteomic data
  • Fundamentals and Introduction to Bioinformatic topics
  • Relational Database design
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BIOBASE ExPlain Analysis

Harvard Libraries has an institute-wide networked license for the ExPlain Analysis System from BIOBASE. This Web-based, gene regulation-focused, systems biology tool promotes biological interpretation of high throughput experiments like microarrays and proteomic data experiments. This class will cover the basic functionality in the BIOBASE Knowledge Library and the ExPlain analysis system. Topics will include: searching for gene and protein annotations, reaction and site reports, disease and biomarker reports, using the BioKnowledge Retriever, data loading and manipulation, mapping to pathways and classification, transcription factor binding site searches, pathway discovery.

MicroRNA's

MicroRNAs (miRNAs) are a growing class of small, noncoding RNAs (22-24nt) that regulate gene expression by targeting mRNAs for translational repression, degradation, or both. These molecules are emerging as important modulators in cellular pathways such as growth and proliferation, apoptosis, and developmental timing. Mutation, dysfunction, and/or dysregulation of miRNAs may give rise to diseases such as coronary artery disease, cancer, diabetes, AIDS, hepatitis, and obesity. In this introductory course participants will learn the latest information about miRNA and the use of miRNA as a diagnostic tool. This workshop will also teach researchers about miRNA quality analysis, RT-PCR, quantification of miRNA and miRNA target prediction by bioinformatics analysis.

Metacore Pathways

How to choose the right network building algorithm to test and expand your hypothesis. One aspect of systems biology is to integrate complex interactions of biological systems. GeneGo provides a highly annotated and dense interaction database with over ten different network building algorithms. Here we demonstrate the strength of these tools in the ability to visualize signaling interaction networks and expand on your hypotheses outside of the realm of your core research areas. This tutorial describes each network building algorithm and modeling workflows including building with canonical pathway interactions, with examples of when to use each. In this session we also highlight how to optimize the visualization of your interactions of interest on a network we will build. We will show tools such as how to add/ hide/show objects and how to manipulate visualizations of pathways using post-filters such as disease, tissue, orthologs or gene ontology processes.

GenePattern

GenePattern is a powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis workflows that enable reproducible in silico research. Through lectures and hands-on exercises, this workshop introduces GenePattern and the methods behind the GenePattern modules for Gene Expression Analysis, including: Running analyses using the GenePattern web interface; Differential gene expression analysis; Classification/prediction methods; Clustering; Using pipelines to chain modules together to create and share methodologies.

Database Design and Normalization

Fundamentals of Database design and Normalization is presented.  Normalization is the process of applying a set of rules to your database design and ensuring data dependencies make sense (only storing related data in a table) mostly to achieve minimum redundancy in the data.  Entity- Relationship model to design the database will also be discussed.

 

Fundamentals and Introduction to Bioinformatics

This workshop will give overview of  basic concepts and fundamentals underlying modern bioinformatics.  Topics presented include sequence databases, sequence comparisons, database searches, phylogenetic analysis, protein structure, proteomics, RNA structure prediction, gene prediction and identification, genetic analysis of disease, and microarray-based studies of gene expression.

Blast Tips and Tricks

Learn how to use BLAST as an experimental tool. We will cover the use of filters as BLAST tools and contrast them with the use of PHI-BLAST. We will learn about substitution matrices and how the PSSM relates to PSI-BLAST. We will discuss how to avoid doing a BLAST search and still obtain the relevant information.

NCBI MapViewer and Related Resources

Learn to use the NCBI MapViewer to generate useful analytical views of genomes, expression data, variation resources, and more. Discover how MapViewer can serve as an entry point for other NCBI resources such as the Sequence Viewer and the Evidence Viewer.

Ensembl Fundamentals

Ensembl provides access to over 50 genomes and to genome-linked information on expression, variation, and conservation. In this session, learn how to search and navigate and make the most of this rich source of data. We'll also cover BioMart, Ensembl's flexible and easy to use tool for retrieving bulk data.

Functional Analysis of Genomic data using Metacore Pathway Suite

Functional Analysis of Genomic data using Metacore 

How to choose the right network building algorithm to test and expand your hypothesis. One aspect of systems biology is to integrate complex interactions of biological systems. GeneGo provides a highly annotated and dense interaction database with over ten different network building algorithms. Here we demonstrate the strength of these tools in the ability to visualize signaling interaction networks and expand on your hypotheses outside of the realm of your core research areas. This tutorial describes each network building algorithm and modeling workflows including building with canonical pathway interactions, with examples of when to use each. In this session we also highlight how to optimize the visualization of your interactions of interest on a network we will build. We will show tools such as how to add/ hide/show objects and how to manipulate visualizations of pathways using post-filters such as disease, tissue, orthologs or gene ontology processes.

Biobase Transcription factor analysis

Biobase Transcription factor analysis (Explain) and human inherited disease mutations (HGMD + Genome Trax) analysis

Explain: Interested in microarray, ChIP-chip or ChIP-seq analysis? Biobase's ExPlain™ is a unique upstream data analysis system that combines promoter and pathway analysis tools and enables you to identify transcription factors affecting gene expression in your microarray and RNA-Seq experiments, as well as predict how they, in combination, can induce observed gene expression patterns. Come learn how to take your analysis further and gain insight into the key upstream signaling regulators influencing the activity of these transcription factors. HGMD + Genome Trax: Got mutations? HGMD® Professional is a unique resource providing comprehensive data on human inherited disease mutations. Its compilation of structured, manually curated data from the peer-reviewed literature enables quick access to both single mutation queries and advanced search applications. HGMD® is widely used in human genetics research, diagnostics, and personal genomics applications. Genome Trax™ is a data analysis tool which works with HGMD® and other data sources to enable scientists to identify human genome variations of functional significance by mapping their NGS data to known elements such as disease mutations and regulatory