2014 06 23 Understanding GWAS, iPlant TSW- Univ.of Nebraska-Lincoln

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. Uploaded Data (Optional)

If you are bringing data to the workshop, please follow the instructions below. It is recommended to upload your data before attending the workshop. You should upload from the best possible internet connection, and if you have any issues email support@iplantcollaborative.

Depending on your level of comfort and the size of the data, you may want to try one of two methods.

1)   iDrop – a desktop drag/drop utility

2)   iCommands – command line interface 

For iDrop, you can download the utility here: http://www.iplantcollaborative.org/learning-center/get-started/import-data

• You can read documentation here: bit.ly/PuWXPP
• You can see a video explanation here: http://youtu.be/0YiMG3OMbhM

For iCommands, you can download the scripts here: bit.ly/1kNdDyR

• You can read documentation here: bit.ly/1frB8W1
• You can see a video explanation here: http://youtu.be/C8tLzBdNG8Y

When uploading via iCommands (using iput) it is recommended that you use the T option to renew the connection socket, especially for single large (>30GB) files. The documentation also discusses the options to display progress and to create a restart file. 

4. Laptop

Please bring your own 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 )

Agenda

This agenda is an outline of the activities we will present at the clinic. We will make every effort to make adjustments as needed based upon the needs and interests of the participants.

Handout

At this Link

Day 1

Day 2

Parking and Hotel Accommodations

Parking

Passes are available at the Union for $5 daily. There is parking close to Keim hall, and the union staff can advise you where you can find legal spots.

Below are lodging options for extended stays of visiting scientists. If you would like one of these options, you may make direct contact with the facility. Mention that you will be working with the University of Nebraska, Agronomy and Horticulture Department for any of these rates.

 

The Chase Suite Hotel (70th & O Sts). PH: 402-483-4900. Quoted UNL rate is $79/night for studio suite, $95 for two bedroom suite, or $89 for suite with side-by-side queen beds. Patrons pay personally. Website tour at:  www.chasehotellincoln.com. Contact name for booking is: Richard Zierke, email at:  rzierke@chasesuitehotels.com

The Staybridge Suites, 2701 Fletcher Ave. (on North 27th St.) PH: 402-438-7829. Quoted UNL rate: $79/night. They will not go any lower because of services offered (listed below). Patrons pay personally. Website tour at:  www.staybridge.com/welcome  On-site contact name is:  Rosann Kevil for more information:  402-323-5007 or email at:    rosannk@sbs-lincoln.com  The StarTran city bus comes to hotel corner (27^th & Fletcher) every 30 minutes starting at 5:45 am, and takes 30 minutes to get to downtown. Once downtown, transfer to another bus to get to East Campus would be necessary. The Staybridge Suites does not provide a shuttle to East Campus, but they do provide shuttle between their site and Cornhusker Hwy so patrons can get to Walmart or grocery stores. Other Suite sizes are available and the price increases accordingly. Staybridge is a beautiful facility, completely renovated in 2010. Guest amenities include:  Free full breakfast, Free Complimentary laundry, Free Wireless internet, Free Socials on Tues, Wed, & Thurs evenings which are catered meals in from different restaurants.

Candlewood Suites (4100 Pioneer Woods Dr.)  PH: 402-420-0330. Nathan Walden at ext. 151 is the contact. For long-term stays a month or longer, rates are as follows:  2-queen beds with kitchenette for $45 a night, 1-bedroom suite with kitchenette with pull-out couch for $50, and a 2-bedroom suite for $59.99. Patrons pay personally. Reservations held with credit card. Mention University of Nebraska for these rates. Amenities include: Free high-speed, wireless Internet access, 24-hour fitness center, coin-operated laundry. Rooms available with kitchenette. Wednesday night socials. There is a shuttle weekdays from 7-11 a.m. and 3-7 p.m.

 

Value Place Extended Hotel, 2050 Fletcher Ave., 402-438-7000. No university rate as rates are already low -  usually $26 a day for shorter term stays. They have a 28-day rate (not quite a month) for $679.99 which divides out to $24.285 per day for a standard studio with a full-sized bed. This includes a kitchenette with 2-burner stove, microwave, refrigerator/freezer, table with 2 chairs, and a sink. They have satellite TV with high Speed Internet (will need an Ethernet cord). They charge tax for the 1^st 30 days and starting on day 31, there is no tax. There is an on-site laundry room. For the standard studio suite layout, see: http://www.valueplace.com/rooms-and-features/room-choices/rooms/. There is no shuttle to and from campus so taking a taxi or renting a car are options.

 

Town House Extended Stay Hotel Downtown, 1744 M Street, PH: 402-475-3000, Quoted UNL rate of $35 per night for stay of 1 month or longer. Rate of $50/day for shorter stay. Website tour at: www.hotels.com/ho262507/town-house-extended-stay-hotel-downtown-lincoln-united-states/  Contact name for booking is:  Amrish Patel at: townhouse.lincoln@gmail.com  Patrons pay personally. No airport shuttle or van service. Would need to take Star Tran city bus to City Campus & transfer to East Campus. Rate is for a one or 2 bedroom (queen beds) suite with guest amenities including: Free Wireless internet, coin operated laundry, a carpeted living area with 2 TV, recliner, desk, dresser & closet, iron/ironing board. Bedroom area is carpeted. The bath and kitchen area is tile and is located between the living and bedroom area, with full size refrigerator, stove, sink, coffee maker, pots, pans, dishes, silverware, and toaster. Facility was renovated in 2009.

Victorian Suites. 225 N. 50^th St., Lincoln (402) 464-4400. http://newvictorianinn.com/locations/ . These suites don’t actually have a kitchenette, just a refrigerator & microwave. Costs are $64.99 for a king bed or $74.99 for two queen beds. Free breakfast.
Commercial Investment Properties. Apartment-style. Property Manager’s name given by post doc, “Bee”, Karen Heinzle, (402) 436-3420), karenh@rentcip.com.