2012 03 12 TSW UC Davis
Organizers |
Jason Williams (mailto: williams@cshl.edu), Sheldon McKay, (mailto: mckays@cshl.edu)Siobhan Brady |
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Local Point of Contact |
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Trainers |
Jason Williams, Sheldon McKay, Naim Matasci, Nirav Merchant |
Date |
March 12: 8 AM - 3 PM; March 13: 9:30 - 4 PM |
Location |
March 12: SciLab 2060; March 13: Genome Center 4202 |
Description |
This is a tools and services workshop for UC Davis. |
Other Links |
Training Modules under consideration: |
Catering Contact |
Barbara Dallas, UC Davis Catering, (530) 754-5865 |
Connecting to the workshop via WebEx
Please click on the links below for instructions on connecting to the workshop.
WebEx Info: Day 1: 8:30 AM - Noon
WebEx Info: Day 1: Noon - 2:30 PM
WebEx Info: Day 2: 9:30 AM - Noon
WebEx Info: Day 2: 1:30 PM - 4:00 PM
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.
5. If you are attending any sessions on day 2 (Genome Center Conference Room 4202) please bring your own laptop!
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
Monday March 12th: SciLab 2060
Time |
Presentation |
Slides |
Links |
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08:00 AM - 08:30 AM |
Arrive/Sign-in |
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08:30 AM - 09:00 AM |
Welcome - Presenter/Participant Introductions |
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09:00 AM - 09:20 AM |
An Overview of the iPlant Collaborative |
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09:20 AM - 09:45 AM |
Overview of the iPlant Discovery Environment (DE) |
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09:45 AM - 10:00 AM |
Coffee Break (next to BioBrew) |
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10:00 AM - 10:30 AM |
iPlant Data Store - Managing "Big Data" |
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10:30 AM - 11:30 AM |
Using the DE to Examine Differential Expression Within an RNA-seq Dataset |
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11:30 AM - 12:00 PM |
Atmosphere - Custom Cloud Computing |
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12:00 PM - 12:30 PM |
Lunch (delivered, next to BioBrew) |
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12:30 PM - 01:00 PM |
Building and Using Workflows Within the DE; Phylogenetics |
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01:00 PM - 01:45 PM |
Extending the DE for Your Research: Tool Integration and Customization |
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01:45 PM - 02:30 PM |
Collaborating with iPlant: Future Projects and Workshop Summary |
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Tuesday March 13th: Genome Center Conference Room 4202
Time |
Presentation |
Sides |
Links |
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09:30 AM - 11:30 PM |
Advanced CHiP-seq in the iPlant Cyberinfrastructure |
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11:30 AM - 12:00 PM |
Comparative Phylogenetic Methods in the iPlant Cyberinfrastructure |
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Tuesday March 13th: Genome Center Conference Room 4202
Time |
Presentation |
Slides |
Links |
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01:30 PM - 02:00 PM |
Powered by iPlant - Consuming iPlant Services in Your Portals |
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02:00 PM - 03:00 PM |
Using XSEDE for Bioinformatics |
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03:00 PM - 03:30 PM |
Using the iPlant Data Store as a Reliable Repository for Your Lab |
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03:30 PM - 04:00 PM |
TBD |
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Attendee List
Day 1: Introduction to iPlant |
User |
Day 2: Session 1 - Advanced CHiP-seq |
User |
Day 2: Session 2 - Comparative Phylogenetic |
User |
Day 2: Data Clinic |
User |
|---|---|---|---|---|---|---|---|
Shajahan Anver |
X |
Shajahan Anver |
X |
Shajahan Anver |
X |
Shajahan Anver |
X |
Timothy Butterfield |
X |
Monica Britton |
X |
Monica Britton |
X |
Monica Britton |
X |
Dario Cantu |
X |
Jason Corwin |
X |
Vince Buffalo |
X |
Vince Buffalo |
X |
Phillip Conklin |
X |
Michael Dorrity |
X |
Dario Cantu |
X |
Phillip Conklin |
X |
Joe Edwards |
1970 |
Daniel Fulop |
X |
Daniel Fulop |
X |
Jason Corwin |
X |
Daniel Fulop |
X |
Gregory Gambetta |
X |
Andrew Groover |
X |
Daniel Fulop |
X |
Gregory Gambetta |
X |
Andrew Groover |
X |
Yansunori Ichihashi |
X |
Gregory Gambetta |
X |
Andrew Groover |
X |
Yansunori Ichihashi |
X |
Bindu Joseph |
X |
Rosa Gil |
X |
Sanjiv Gupta |
X |
Ryan Kim |
X |
Ryan Kim |
X |
Sanjiv Gupta |
X |
Xueqin He |
X |
Ksenia Krasileva |
X |
Venkat Kolla |
X |
Xueqin He |
X |
Yansunori Ichihashi |
X |
Andrew Latimer |
X |
Shisong Ma |
X |
Polly Hsu |
X |
Bindu Joseph |
X |
John Leichty |
X |
Mohan Prem Andand Marimuthu |
X |
Venkat Kolla |
X |
Ryan Kim |
X |
Mohan Prem Andand Marimuthu |
X |
Kathie Ngo |
X |
Lijun Liu |
X |
Venkat Kolla |
X |
Kathie Ngo |
X |
Guogui Ning |
X |
Ciera Martinez |
X |
Ksenia Krasileva |
X |
Kazunari Nozue |
X |
Sharman Diane O'Neill |
X |
Guogui Ning |
X |
Andrew Latimer |
X |
Aashish Ranjan |
X |
Aashish Ranjan |
X |
Kazunari Nozue |
X |
John Liechty |
X |
Davide Scaglione |
X |
Davide Scaglione |
X |
Natraj Kumar Podishetty |
X |
Shisong Ma |
X |
Anandkuma Surendrarao |
X |
Anandkuma Surendrarao |
X |
Aashish Ranjan |
X |
Mohan Prem Andand Marimuthu |
X |
Carl Vangestel |
X |
Alejandra Vazquez Lobo Yuren |
X |
Anandkumar Surendrarao |
X |
Pedro Jose Martinez Garcia |
X |
Yanmei Xiao |
X |
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Hans Vasquez-Gross |
X |
Ravi Maruthachalam |
X |
Phillip Conklin |
X |
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John Yu |
X |
Ugrappa Nagalakshmi |
X |
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Kathie Ngo |
X |
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Guogui Ning |
X |
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Kazunari Nozue |
X |
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Sharman Diane O'Neill |
X |
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Aashish Ranjan |
X |
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Mily Ron |
X |
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Davide Scaglione |
X |
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Li Tian |
X |
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Carl Vangestel |
X |
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Hans Vasquez-Gross |
X |
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Yanmei Xiao |
X |
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John Yu |
X |
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Yaniv Brandvain |
X |
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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.