2015 05 18 Tools and Services Workshop - Santa Fe Community College
Organizers | D. Bailey, L. Spangenburg, U. Hilgert, O. Frauenglass, M. Gonzales, J. Williams |
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iPlant Trainers | Uwe Hilgert, Jason Williams |
Date | May 18-19, 2015 |
Location | Santa Fe Community College 6401 Richards Avenue, Santa Fe, NM 87508 Rm. 216 (West Wing) Across from Planetarium |
| Directions: | Find directions to SFCC (.pdf) |
Map: | |
Parking: | Recommended Parking: West Wing Parking Lot
stairs to second level), you will find Room 216 across from the planetarium. |
Pre-Workshop Checklist
1. iPlant Account
- Get your free account at http://user.iplantcollaborative.org.
2. Atmosphere Access
- Once you have your account, go to https://user.iplantcollaborative.org/dashboard/ and under Available Services, request access to Atmosphere. Indicate that you are attending a workshop when you are asked for justification.
3. Laptop
Please bring a WiFi enabled laptop to the workshop. Make sure your laptop has the following:
- VNC Viewer: Download the DMG (for MAC) or exe (for PC): http://www.realvnc.com/download/viewer/
- Java: Please have JAVA installed and enabled (help)
- Browser: Please have an up-to-date web browser (Recommended Firefox or Safari )
- Windows Users: Please install PuTTY (http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html)
4. Pre-Workshop Assignment
To get the most out of the workshop, download the Pre-Workshop Packet and complete the exercises/tasks in it.
5. Office Hour
Join us online for a Pre-Workshop Q&A session (e.g. if you are experiencing problems setting up your computer or uploading data). Use the URL http://cshl.adobeconnect.com/iplant_livehelp to join us on Monday May 11th from 12:00-12:30PM (the session will close promptly at 12:30 EDT if nobody has joined by then - otherwise we'll go as long as it takes to settle all your questions.)
6. Training Materials
Download and bring the training materials, to follow along and take notes:
Etherpad
We will use an etherpad for workshop live chat/help; further info coming soon.
https://etherpad.mozilla.org/1z4hnKVoV1
Draft Workshop Program (DAY 1)
Time | Description | Toolkit | Slides | Links | Presenter |
09:00 AM | Arrive / Sign-in / Verify iPlant Accounts |
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09:30 AM | Welcome - Presenter/Participant Self-Introductions |
| slides | JW | |
09:45 AM | Overview of the iPlant Collaborative |
| slides | JW/UH | |
10:00 AM | iPlant Discovery Environment (DE) - Analyze Data | Page 16 | slides (ppt) | UH | |
10:45 AM | Coffee Break |
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11:00 AM | iPlant Data Store - Manage Data ("Big Data") | Page 8 | slides (ppt) | UH | |
11:30 AM | Workflows in the DE; Phylogenetics Example | Page 17 | slides (ppt) | JW/UH | |
12:10 PM | Lunch |
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01:00 PM | Using the DE for RNA-Seq | Page 33 | slides | JW | |
02:00 PM | Atmosphere Cloud Computing | Page 23 | slides | JW | |
03:00 PM | Coffee Break |
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03:15 PM | Tools Integration in the DE | Page 36 |
| JW | |
03:45 PM | Educational Bioinformatics - DNA Subway |
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| UH | |
04:15 PM | Workshop summary and conclusion |
| JW/UH |
Draft Workshop Program (DAY 2)
Time | Description | Slides | Links | Presenter |
|---|---|---|---|---|
| 09:00 AM | Questions/Review from Day 1 | |||
09:30 AM | Overview and demo of DNA Subway / Transcriptome assembly | UH/JW | ||
10:30 AM | Coffee Break |
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10:45 AM | Getting started with Annotation: MAKER | JW | ||
11:15 AM | Visualization of RNA-Seq results in Atmosphere | slides | JW | |
12:00 PM | Lunch (On your own) |
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01:00 PM | iCommands and other Data Store applications: | sides |
| JW |
| 01:30 PM | “What Graduate Students should Know about Cyberinfrastructure | |||
02:30 PM | Individual Consultations |
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Livestream Links from UGA Workshop
The recent UGA workshop covered a largely identical agenda to the one above. Here are the promised links to the recordings:
Day 1: https://new.livestream.com/cshl-dnalc/uga-day-I
Day 2: https://new.livestream.com/cshl-dnalc/uga-day-II
Important Pre-Workshop Travel Info
Neither the iPlant Collaborative nor Santa Fe Community College can reimburse lodging or other expenses associated with attending the workshop.
Travel
Santa Fe is served by a municipal airport (SAF). Alternatively, travelers can fly into Albuquerque (ABQ) and either use train, shuttle or rental car to get to Santa Fe.
Lodging
Santa Fe has an ample number of accommodations. Excellent hotels that are located a few driving minutes from SFCC include:
- Holiday Inn Express, 3450 Cerrillos Rd, Santa Fe, NM 85701
- Best Western Plus Inn, 3650 Cerrillos Rd, Santa Fe, NM 8570