PEARC17 Gateway Users Tutorial

• Introduce the team, the Gateway concept, and the audience members

• Slides (URL)

• Any necessary downloads and installations

• Tutorial Notes (URL)

1.40 pm - 2.30 p-

CIPRES Gateway/NeuroScience Gateway

• Introduction (12 min)

• Hands-on Browser interface (28 min)

• Create Account/Login

• Sequence Alignment

• Tree Inference

•  Brief demo of sharing service

•  Feedback/Questions (5 min)

• Useful links:
• http://www.phylo.org/portal2 CIPRES Gateway
• http://www.phylo.org/tools/tool_tests/mafft_input.txt  Input for sequence alignment
• http://etetoolkit.org/treeview/: Second Party Tree Viewer
• http://www.phylo.org/demo/ Sharing service demo 
• Slides (URL)
  

NeuroScience Gateway

• Overview: What does NSG do?

• Hands on: Download Jones model from ModelDB site, and run on Comet using the NEURON tool.

• How to use NSG - presentation

• Feedback/Questions

SEAGrid Gateway

• Overview

• Hands on

• Create accounts

• Simple file upload and submit jobs for Gamess and Gaussian

• CSD (crystal structure DB search) to create an input and use Nanocad and Gaussian GUI for further manipulation and submit a job.

• Use Jamberoo to edit structures and Gamess GUI and submit jobs.

• Use Jamberoo for Post Processing and Data Grid for automated post-processed data and web interface for sharing collaboratory.

• Feedback

• Useful links:

  • SEAGrid.org

  • Clients: Download - Mac, Linux and Windows clients available

  • Mac Users: Use control-click-open to open the SEAGrid desktop client the first time.

  • Inputs: Tutorial Application Input Files and Parameters

  • Post Processing: https://sourceforge.net/projects/avogadro/files/latest/download

• Slides (URL)

Lightning Round: dREG, ChemCompute, and Campus Gateways

Suresh Marru 

Marlon Pierce

Closing remarks