2012 07 18 TSW UT Austin
Organizers: |
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Local Point of Contact: |
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Trainers: |
Matt Vaughn, John Fonner, Dan Stanzione, Christos Noutsos (assist), Young Lee (observer) |
Date: |
Wed. July 18 - Thurs. July 19, 2012 |
Location: |
Texas Advanced Computing Center (TACC), ROC 1.603 |
Online Registration: |
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Flyer: |
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Important Dates: |
Registration Opens: Tuesday, May 28 |
Section Navigation
Pre-Workshop Homework
1. Please try out your iPlant credentials to ensure you have access. You can Log-in from user.iplantcollaborative.org, click the button "iPlant Login"
- Once authenticated click the "My Services" link
- Under "My Services" please ensure you have access to: Atmosphere, Discovery Environment, iPlant Data Store. You can also request access to other services here
- If you have account problems, please email support@iplantcollaborative.org
2. Please be sure that your name is listed in the Attendee List (below) for the workshop section(s) you were accepted to. If there is a discrepancy, please email 411@iplantcollaborative.org
3. Please check your email, and this wiki prior to the workshop, as this is the way we will communicate any important changes.
4. The use of Atmosphere will require a VNC viewer which can be downloaded here.
Workshop Notes
Here are a few important links that you may wish to refer to during and after the workshop:
Account/Password Problems http://user.iplantcollaborative.org
iPlant Help and Discussion Forums
General iPlant Support Issues
iPlant Privacy (And other) policies - "Your Data is Your Data"
- www.iplantcollaborative.org/privacy
- www.iplantcollaborative.org/about/data-set-hosting
- www.iplantcollaborative.org/about/general-usage-policy
Goal
The goal of this workshop is to demonstrate some of the ways that iPlant Cyberinfrastructure can advance your scientific objectives.
As you navigate the through demonstrations and hands-on activities presented at the workshop, you will gain a sense of how to consume
and customize iPlant tools and services for your investigations.
Agenda
Please check here for the latest updates to this workshop agenda
Wednesday, July 18
Time |
Presentation |
Slides |
Links |
Instructor |
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08:30 AM - 09:00 AM |
Arrive/Sign-in/ Verify iPlant accounts |
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09:00 AM - 09:30 AM |
Welcome - Presenter/Participant Introductions |
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09:30 AM - 09:50 AM |
An Overview of the iPlant Collaborative |
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Matt Vaughn |
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09:50 AM - 10:15 AM |
Overview of the iPlant Discovery Environment (DE) |
John Fonner |
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10:15 AM - 10:30 AM |
Coffee Break |
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10:30 AM - 11:15 AM |
Building and Using Workflows Within the DE; Phylogenetics |
Matt Vaughn |
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11:15 AM - 12:00 PM |
Extending the DE: Tool Integration and Customization |
John Fonner |
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12:00 PM - 01:00 PM |
Lunch (Delivered) |
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01:00 PM - 02:15 PM |
Using the DE to Examine Differential Expression with RNA-Seq |
Matt Vaughn |
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02:15 PM - 02:45 PM |
iPlant Data Store - Managing "Big Data" using the Cloud |
(URL links below) |
John Fonner |
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02:45 PM - 03:00 PM |
Coffee Break |
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03:00 PM - 03:15 PM |
Collaborating with iPlant / What's Next? |
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Matt Vaughn |
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03:15 PM - 03:45 PM |
Atmosphere - Custom Cloud Computing |
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Matt Vaughn |
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03:45 PM - 05:00 PM |
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All |
Thursday July 19
Time |
Presentation |
Sides |
Links |
Instructor |
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08:45 AM - 09:00 AM |
Sign-in/Welcome |
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09:00 AM - 10:30 AM |
Additional RNA-seq analysis applications/ hands-on in Atmosphere |
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/wiki/spaces/eot/pages/241585220 (cont'd) |
Matt Vaughn |
10:30 AM - 10:45 AM |
Coffee Break |
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10:45 AM - 11:30 AM |
Advanced CHiP-seq - Motif Indentification |
Matt Vaughn |
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11:30 AM - Noon |
iPlant and the XSEDE National Cyberinfrastructure |
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Matt Vaughn |
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Noon - 01:00PM |
Lunch (delivered) |
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01:00 PM - 02:15 PM |
Powered by iPlant : Analysis using the iPlant API |
John Fonner |
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02:15 PM - 04:00 PM |
Data and Analysis Clinic |
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All |
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Attendee List
First |
Last |
Affiliation |
User Acct |
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|---|---|---|---|---|
Mark |
Brophy |
independent Python programmer |
mark@brophyworld.com |
X |
Charles |
Hauser |
St Edwards University |
charlesh@stedwards.edu |
X |
Xueying |
Guan |
UT Austin |
xueying107@austin.utexas.edu |
X |
Wang Kit |
Ng |
UT Austin |
dannyng@austin.utexas.edu |
X |
Vimlarani |
Chopra |
HCCS-North West |
vimlachopra@gmail.com |
needs Atmo |
Candance |
Seeve |
Baylor University |
little_seeve@hotmail.com |
needs Atmo |
Hashimul |
Ehsan |
U Houston, Victoria |
ehsan@uhv.edu |
needs Atmo |
Christy |
MacKinnon |
U Incarnate Word |
mackinno@uiwtx.edu |
X |
Juan |
Palacio |
UT Austin |
jdpalacio@utexas.edu |
CANCELLED |
Data Store "Import from URL" Test Files
1 |
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2 |
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3 |
ftp://ftp.ncbi.nlm.nih.gov/genomes/Apis_mellifera/CHR_MT/ame_ref_Amel_4.5_chrMT.fa.gz |
4 |
ftp://hgdownload.cse.ucsc.edu/goldenPath/apiMel1/database/all_mrna.sql |
Survey
iPlant is by and for the community. It is extremely important for us to hear from our colleagues about what works for them and what doesn't.
We'd also like to what computational bottlenecks in your investigations are possible challenges you think iPlant should target for developing
community-scale solutions.We want to know how you found the workshop, and what you would like to see iPlant do, so please answer the
survey you will receive by email post workshop.