Workshops

Differential Gene Expression using RNA-Seq: Hands-on Workshop

Apr,2015

This workshop provides a hands-on introduction to differential gene expression analysis using Illumina reads. Target audience: Those completely unfamiliar with RNA-Seq analysis using high throughput NGS data.

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Phylogenomics: Hands-on Workshop

Nov 08,2013

This workshop will provide a workflow for large scale phylogenomic analyses on High Performance Computing nodes. We will provide a logical workflow, starting from downloading the whole genomes, identifying the orthologs, multiple sequence alignments, trimming and merging alignments, and constructing Maximum Likeli-hood Bayesian phylogenetic tree.

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Differential Gene Expression using RNA-Seq: Hands-on Workshop

Oct 10,2013

This workshop provides a hands-on introduction to differential gene expression analysis using Illumina reads. Target audience: Those completely unfamiliar with RNA-Seq analysis using high throughput NGS data.

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Basic UNIX for Biologists: Hands-on Workshop

Aug 29,2013

Understanding the UNIX environment and interface is criti-cal to using bioinformatics programs. This hands-on work-shop will cover some of the basics of using UNIX, including basic UNIX commands, file manipulation techniques, and running programs on RCAC clusters.

The workshop comprises three sections, each of which ad-dresses different levels of UNIX computing. The first sec-tion concentrates on teaching basic skills necessary to use the UNIX environment; the second section teaches necessary skills to perform routine file manipulations and the third section will serve as an introduction to the serv-ers and computational resources available at RCAC/ITaP at Purdue as well as utilizing them to run some simple next generation sequence analysis programs.

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Differential Gene Expression using RNA-Seq: Hands-on Workshop

Jul 18,2013

This workshop provides a hands-on introduction to differential gene expression analysis using Illumina reads. Target audience: Those completely unfamiliar with RNA-Seq analysis using high throughput NGS data.

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FAQs of Differential Gene Expression using RNA-Seq: Seminar

Jul 18,2013

This seminar summarizes and discusses about some of questions related to RNA-Seq - experimental design and data analysis.

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Introduction to Galaxy: Hands-on Workshop

Oct 22,2012

Galaxy is an open, web-based platform for data intensive biological research that enables nonbioinformaticians to create, run, tune,and share their own bioinformatic analyses. This hands-on workshop will teach participants how to integrate data,and perform simple and complex analysis within Galaxy. They will also cover data visualization and visual analytics, and how to share and reuse your bioinformatic analyses, all from within Galaxy.

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Introduction to Unix for Biologists: Hands-on Workshop

Aug 30,2012 & Sept 6,2012

Understanding the UNIX environment and interface is criti-cal to using bioinformatics programs. This hands-on work-shop will cover some of the basics of using UNIX, including basic UNIX commands, file manipulation techniques, and running programs on RCAC clusters.

The workshop comprises three sections, each of which ad-dresses different levels of UNIX computing. The first sec-tion concentrates on teaching basic skills necessary to use the UNIX environment; the second section teaches necessary skills to perform routine file manipulations and the third section will serve as an introduction to the serv-ers and computational resources available at RCAC/ITaP at Purdue as well as utilizing them to run some simple next generation sequence analysis programs.

Some references and suggested reading:
UNIX and perl for biologists: http://korflab.ucdavis.edu/Unix_and_Perl
Gibas, Cynthia and Per Jambeck. "Developing bioinfor-matics computer skills" O'Reilly Media, Inc., 2001.
http://www.ee.surrey.ac.uk/Teaching/Unix/

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Beginning Unix for Bioinformatics: Hands-on Workshop

May 10, 2012

Beginning Unix for Bioinformatics : Seminar

April 12, 2012

We will discuss how to get started using computational resources from the ITaP Rosen Center and the Purdue Bioinformatics Core. These computers use Linux and other Unix-like Operating Systems. Practical advice and background for using these Unix servers is the focus of this talk. About 20 common Unix commands for managing, cre-ating, viewing and extracting information from data files will be discussed and demonstrated. Simple exam-ples using genomic sequencing will be used to illustrate some commands. Tips for working with Unix servers using software run-ning on Windows workstations will be discussed. The intended audience for this presentation are scien-tists and students who want to start using bioinfor-matics tools at Purdue but who have little or no experi-ence working with Unix servers at the command line. Some references and suggested reading: [1] Gibas, Cynthia and Per Jambeck. "Developing bioin-formatics computer skills" O'Reilly Media, Inc., 2001. [2] http://heather.cs.ucdavis.edu/~matloff/UnixAndC/Unix/UnixBareMn.pdf [3] http://www.ee.surrey.ac.uk/Teaching/Unix/

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An Introduction to Next Generation Sequencing – Chemistry, Data Files and Applications

Feb 29, 2012

This is the first in a series of seminars to be con-ducted by the Bioinformatics Core during the year. This seminar is to serve as an introduction to Roche GS-FLX (454) and Illumina sequencing sample types and chemistries, output data file formats, measures of quality, and a very brief overview of applications. The file formats dis-cussed will be FASTA, FASTQ, SAM, GTF/GFF, BED and Wig. This seminar will set the stage for subsequent seminars and hands-on workshops and application specific in-depth analysis. Target audience: Those completely unfamiliar with high throughput sequencing and NGS data.Please note that this is not a hands-on workshop on how to use any specific software package(s).

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Contact

Bioinformatics Core
Young Hall 1022
155 South Grant Street
West Lafayette, Indiana 47907

bioinformatics@purdue.edu
Phone: 765.496.6252
jyothit@purdue.edu

Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, (765) 494-4600

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