2015 09 21 iPlant Workshops at UC Davis

Workshop Checklist and Software Downloads

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 your own WiFi enabled laptop to the workshop.

4. Workshop Specific Instructions

Depending on which workshop you are attending, please see the following notes on pre-workshop prep and software installation:

iPlant Intro Workshop (9/21)

 Software:

• 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 )

Pre-workshop Homework:

It is suggested you try the excises in the Pre-Workshop Guide

iPlant Intermediate Workshop (9/22)

Software:

• 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 )

Mac:

• Install R (if you have not previously installed it): Download the .pkg file for R.3.2.1 appropriate for your version of MAC OS: https://cran.r-project.org/bin/macosx/

• Install R Studio (If you have not previously not installed it): Install R Studio from this link: https://www.rstudio.com/products/rstudio/download/

PC:

• Install R (if you have not previously installed it): Download R.3.2.1 here: https://cran.r-project.org/bin/windows/base/R-3.2.1-win.exe (Tip: For additional help see: https://cran.r-project.org/bin/windows/base/ )
• Install R Studio (If you have not previously not installed it) Install R Studio from this link: https://www.rstudio.com/products/rstudio/download/

Data Carpentry Workshop (9/22-23)

See detailed instructions here: http://www.datacarpentry.org/2015-09-22-UCDavis/install.html

iPlant Advanced Workshop (9/23)

• • Docker
    • Macintosh and Windows users please install Docker Toolbox
    • Linux users please install Docker 1.8

Etherpad/Chatroom

We will use the following etherpad for workshop live chat/help:

• https://etherpad.mozilla.org/iplant-ucdavis-sep2015

Livestream

You can watch the Livestream of this event.

Instructions for virtual attendees:

While it is not possible to have the exact in-person experience, you can follow along to a good extent, please observe the following suggestions:

1. Use the instructions in the PRE-WORKSHOP PACKET to request access to Atmosphere. Launch the following Image (at default tiny1 size) at least one day before the workshop: TSW Workshop Williams 1.2
2. Please use the etherpad chat ( https://etherpad.mozilla.org/iplant-ucdavis-sep2015) to ask questions. Livestream chat will not be monitored. if any question is not followed up on, please post to ask.iplantcollaborative.org
3. Download the Workshop Packet ( Download) to follow along
4. Please complete the post-survey

Livestream URLS:

Day 1: https://livestream.com/cshl-dnalc/ucdavis2015-1   (9:30 PDT)

Day 2: https://livestream.com/cshl-dnalc/ucdavis2015-2   (9:15 PDT)

Instructional Materials

You can download a copy of the workshop packet to follow along:

Getting Started with iPlant Toolkit (Required for Intro iPlant)

Intro iPlant Workshop Program (Sep 21)

Intermediate Workshop Program (Sep 22)

Data Carpentry Workshop Program (Sep 22-23)

See the Data Carpentry Website Here:

http://www.datacarpentry.org/2015-09-22-UCDavis/

Advanced iPlant Workshop Program (Sep 23)

Github Repo: https://github.com/iPlantCollaborativeOpenSource/Advanced_iPlant

Travel and Campus Map and Parking

All of the workshops will be in Gladys Valley Hall (Valley Hall).

• Campus map linked to Valley Hall: http://campusmap.ucdavis.edu/?b=178 (if you click "Click here to view" next to Campus Parking in the lower left hand corner, you can see where parking is available on campus).
• Map of the Vet-Med area: http://www.vetmed.ucdavis.edu/Academic_Programs/map/General/  Of interest is Valley Hall, and the nearby Scrubs cafe, which has coffee and sandwiches.
• Floor plan of Valley Hall (and another map of the surrounding area): http://www.vetmed.ucdavis.edu/Academic_Programs/map/ValleyHall/default.html 

The first floor will have Intro to iPlant (1010), Intermediate iPlant (1041), and Data Carpentry (1043). The second floor will have Advanced iPlant (2020).

Visitors can purchased a Daily Visitor Permit ($9.00/day) to park, which are available for purchase the entrance of some parking lots. The closest lots to which sell the permit at their entrance are lots 50 and 55

http://taps.ucdavis.edu/parking/information/visitor