2015 12 17-18 iPlant Workshop at Univ of Chile Santiago
Organizers | Alejando Mass, Roberto Neira, Herman Silva |
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iPlant Trainers | Eric Lyons, Nirav Merchant |
Helpers and Guest Instructors | TBD |
Date | Dec 17-18 2015 |
Locations | Univ of Chile, Santiago |
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 (12/17)
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 Advanced Workshop (12/18)
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://public.etherpad-mozilla.org/p/iplantchile
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 (Dec 17 Thu)
Time | Description | Slides | Links | Packet | Presenter |
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08:30 | Arrive / Sign-in / Verify iPlant Accounts |
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09:00 | Welcome - Presenter/Participant Self-Introductions/Interests | slides (full) | Nirav | ||
10:00 | Overview of the iPlant Collaborative | Eric | |||
10:30 | Overview of the iPlant Discovery Environment (DE) | p.17-18 | Nirav | ||
11:00 | Coffee Break |
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11:15 | iPlant Data Store - Managing "Big Data" |
| p.10-14 | Eric | |
12:00 | Workflows and HT Batch Jobs |
| p.18-20 | Nirav | |
13:00 | Lunch | ||||
14:00 | Using the DE for NGS Data | slides | p.32-34 | Nirav | |
14:30 | Atmosphere Cloud Computing | slides | p.24-25 | Nirav | |
15:00 | Coffee Break |
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15:15 | Tools Integration in the DE | Nirav | |||
16:15 | Workshop summary and conclusion |
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iPlant Workshop Day 2 (Dec 18)
Time | Description | Slides | Links | Presenter |
|---|---|---|---|---|
| 9:00-10:00 | Review topics; question and answers from previous day | Nirav Merchant | ||
| 10:00 - 12:00 | Part I: Genome management, visualization, and analysis: RNASeq, variant calling, comparative genomics with CoGe | Keynote, PDF, and PPT in link | Eric Lyons | |
| 10:00 - 12:00 | Computational virtualization: intermediate level (Virtual Machines and Docker) | Nirav Merchant | ||
| 12:00 - 13:00 | Lunch | |||
| 13:00-15:00 | Part II: Genome management, visualization, and analysis: RNASeq, variant calling, comparative genomics | Keynote, PDF, and PPT in link | Eric Lyons | |
| 13:00-15:00 | Computational virtualization: advanced level (Virtual Machines and Docker) | Nirav Merchant | ||
| 15:00-16:00 | ||||
| Other topics | Description | Slides | Links | |
Algorithms for RNA seq- from raw reads to differential expression analysis | slides | |||
| Demo of using Kallisto with test data | Hand on demo | |||
| Visualization of RNA-Seq results in Atmosphere (Sleuth & CummeRbund) | |||
| Overview and demo of iPlant Transcriptome assembly |
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| Trinotate RNA seq annotation pipeline | Hands on demo | |||
| MAKER-P Genome annotation pipeline using cctools and Atmosphere |
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| GWAS: Genome-Wide Association Studies | Tutorial | |||
Individual Consultations |
| Please posts your requests for 10-15 min consultations to the Etherpad (from 2:30-3 or so) |
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