[ FROM REDDY GALI ]
We are pleased to announce the following [bioinformatics] workshops. To sign up
visit this URL or just click on the Sign UP icon below the individual workshop.
https://www.countway.harvard.edu/classes#bioinfo
Expression analysis using 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.
2009-10-21 09:30:00 (duration: 7 hours, available seats: 19) -
Countway Library, Room 403
BLAST Tips and Tricks
(Brownbag)
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.
Microarray Data Analysis of Illumina Data Using
R/Bioconductor
Illumina microarrays are becoming a
popular microarray platform. This workshop will demonstrate lumi package that
provides an integrated solution for the bead-level Illumina microarray data
analysis. The hands-on workshop covers data input, quality control, variance
stabilization, normalization, differential expression and gene annotation.
2009-11-03 13:00:00 ((duration: 3
hours, available seats: 23) - Countway Library, Room 403
2009-12-01 12:30:00 (registration not required) - Countway
Library, Ballard Room, 5th Floor
Expression analysis using 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.
2009-10-21 09:30:00 (duration: 7 hours, available seats: 19) -
Countway Library, Room 403
Browsing Genes and Genomes with Ensembl
With Ensembl trainer Bert Overduin of the European Bioinformatics
Institute. This day long workshop will include an introduction to Ensembl, a
tour of the most important Ensembl views, and an overview of how Ensemble gene
and transcripts predictions are made. Participants will learn about comparative
genomics and proteomics tools (orthologues, protein families, alignments) or
variation tools (SNPs, haplotypes, linkage disquilibrium). The workshop also
covers data mining and large data set retrieval with BioMart. Participants are
encouraged to bring problems and questions about their research to try to
tackle during the workshop. Requires a general knowledge of molecular biology
and genomics.
2009-11-16 09:00:00 (duration: 7 hours, available seats: 20) -
Countway Library, Lower Level 2, 025
Ensembl Genome Browser Workshop
Ensemble provides unified access to genomic information and annotation for more
than 50 eukaryotic species. Learn how to find what you need, from splice sites
to regulatory regions to SNPs. We'll also explore the BioMart tool to select
and export Ensembl data. With hands-on exercises.
2009-10-01 15:30:00 (duration: 2 hours, available seats: 5) -
Countway Library, Lower Level 2, 025
MetaCore: Getting the most from your "omics"
analysis
The ability to generate massive amounts of
data with "omics" analysis begs the need for a tool to analyze and
prioritize the biological relevance of this information. GeneGo provides a
solution for using "omics" gene lists to generate and prioritize
hypotheses with MetaCore. This tutorial highlights how to work with different
types of data (genomics, proteomics, metabolomics and interaction data)
beginning with how to upload gene lists and expression data (if available).
Here we demonstrate data manager capabilities including how to upload, batch
upload, store, share and check data properties and signal distribution. We then
focus on how MetaCore uses your gene list to extract functional relevance by
determining the most enriched processes across several ontologies. This entails
a detailed lesson on how to prioritize your hypothesis using the statistically
significance enrichment histograms and associate highly interactive GeneGo Maps
and pre-built networks. We further emphasize the role of expression data in
your analysis and the ability to visually predict experimental results,
associated disease and possible drug targets. Lastly we highlight the benefits
of using MetaCore workflows to compare data sets and work with experiment
intersections.
2009-10-28 13:00:00 (duration: 3 hours, available seats: 23) -
Countway Library, Room 403
Microarray Data Analysis of Illumina Data Using
R/Bioconductor
Illumina microarrays are becoming a
popular microarray platform. This workshop will demonstrate lumi package that
provides an integrated solution for the bead-level Illumina microarray data
analysis. The hands-on workshop covers data input, quality control, variance
stabilization, normalization, differential expression and gene annotation.
2009-11-03 13:00:00 ((duration: 3
hours, available seats: 23) - Countway Library, Room 403
BIOBASE ExPlain Analysis System for microarray and proteomic
data
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.
[Coming December
1st week]
Biomedical Imaging Analysis
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.).
[Will be
schedule soon for Nov]
Reddy Gali, Ph.D.
Countway /CBMI -407
10 Shattuck Street
Boston,
MA
Email: rgali@hms.harvard.edu
