iPlant Tools and Services Workshop @ Purdue University
Date and Time
Please Note: This workshop is CLOSED as of 5/4/12. New applicants will be automatically waitlisted.
|May 21 2012||09:00am - 5:00pm (NLSN 1195)|
|May 22 2012||09:00am - 5:00pm (NLSN 1195)|
Biological research depends increasingly on computational analysis of large and complex data sets. This two-day workshop provides a comprehensive look at tools and services for large-scale data analysis provided by the iPlant Collaborative, a major computer infrastructure project of the National Science Foundation (www.iplantcollaborative.org). Workshop topics build progressively to cater to the needs of general and advanced audiences. Computational thinking is applied to two “large-data” challenges in plant biology: analyzing high-throughput genotype and constructing large phylogenetic trees.
Day 1: Participants are introduced to iPlant’s tools to manage, analyze, and share data – then apply them to structured use cases on analyzing differential gene expression in an RNA-seq dataset, and creating workflows for phylogenetics. The Discovery Environment is a customizable workspace for a variety of applications. Data Store offers free, secure storage that co-localizes user data with iPlant analysis tools. Atmosphere is a personal,computing cloud in which to run analyses and share projects. Learn to integrate tools to further customize workflows.
Day 2: Participants transition to advanced work on challenging informatics problems. Use advanced workflows to analyze protein-binding sites in a CHIP-seq dataset and to merge trait and phylogenetic data for continuous ancestral character estimation (CACE). Participants can also work from the command line to increase flexibility. The Data Clinic is an opportunity to consult with experts on specific analysis and support problems – such as implementing the Data Store for your data, interacting with the iPlant API, and using supercomputing resources (XSEDE) for bioinformatics.
We have additional travel funds for individuals who are US citizens/permanent residents; participants from minority groups under-represented in the life-sciences are especially encouraged to apply.
Monday, May 21st, 2012
|08:30 AM - 09:00 AM|| Arrive
/ Sign-in / Verify iPlant Accounts
|09:00 AM - 09:30 AM||Welcome - Presenter/Participant Self-Introductions|
|09:30 AM - 09:50 AM||An Overview of the iPlant Collaborative|
|09:50 AM - 10:15 AM||Overview of the iPlant Discovery Environment (DE)|
|10:15 AM - 10:30 AM||Break|
|10:30 AM - 11:15 AM||iPlant Data Store - Managing "Big Data"|
|11:15 AM - 12:00 AM||Atmosphere - Custom Cloud Computing|
|12:00 PM - 01:00 PM||Lunch|
|01:00 PM - 01:30 PM||Building and Using Workflows Within the DE; Phylogenetics|
|01:30 PM - 02:45 PM||Using the DE to Examine Differential Expression Within an RNA-seq Dataset|
|02:45 PM - 03:00 PM||Break|
|03:00 PM - 04:30 PM||Extending the DE for Your Research: Tool Integration and Customization|
|04:30 PM - 05:00 PM||Collaborating with iPlant: Future Projects and Workshop Summary|
Tuesday, May 22nd, 2012
|08:45 AM - 09:00 AM||Sign-in/ Welcome|
|09:00 AM - 10:30 AM||Advanced CHiP-seq in the iPlant Cyberinfrastructure|
|10:30 AM - 10:45 AM||Break|
|10:45 AM - 11"30 AM||Advanced CHiP-seq in the iPlant Cyberinfrastructure (cont'd)|
|11:30 AM - 12:00 PM||Comparative Phylogenetic Methods in the iPlant Cyberinfrastructure|
|12:00 PM - 12:30 PM||Lunch|
|Data Clinic Appointments|
|12:30 PM - 01:30 PM||Powered by iPlant - Consuming iPlant Services in Your Portals, iPlant API|
|01:30 PM - 02:30 PM||Using XSEDE for Bioinformatics|
|02:30 PM - 03:30 PM||Additional RNA-seq analysis applications/ hands-on|
|03:30 PM - END||User determined topics / appointments (TBD)|