2014 03 26 Mission Critical Bioinformatics

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: bit.ly/1i7wm4s

• 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. 

Once you have uploaded the data, please fill out this survey (https://docs.google.com/forms/d/1DdQMjk_ri9L4eEma5AOLiRsGMOPRwOB0mVezThF_W2o/viewform ) so that we can have a clearer idea of what data you will be bringing.

4. Laptop (Optional)

You may wish to bring your own WiFi enabled laptop to the workshop. We will be working from the computer lab, but you may choose to use your own laptop either during the course, or for homework. Please be 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 over the 2 days of the workshop. We will make every effort to make adjustments as needed based upon the needs and interests of the participants.

Downloads:

Handout

March 26th

March 27th

Workshop Evaluation: Please click here!

Command Line Resources

Software Carpentry - Great slides and comprehensive instructions for command line, python, etc. (See: the UNIX shell section)

Westwind - MAC specific, but very well explained and most of the commands work on any Linux system

ss64 - Comprehensive glossary and help