2017 11 29 Half-day workshop on bioinformatics tools for Plant Genomics
| Date and Time | Wednesday November 29, 2017 12PM-5PM (US Eastern Time) |
|---|---|
Organizers: | Liya Wang, Kapeel Chougule, Josh Stein, Jason Williams (CyVerse) Marcela Karey Tello-Ruiz (Gramene) Cristina Fernandez-Marco (MaizeCode) |
Local Point of Contact: | Marcela Karey Tello-Ruiz, Cristina Fernandez-Marco |
Location | Bush Lecture Hall, Cold Spring Harbor Laboratory (Building 4 on Campus Map) |
| LiveStream Link | https://livestream.com/cshl-dnalc/bioinformatics-for-plant-genomics |
Workshop Prep
1. CyVerse Account
- Get your free account at http://user.cyverse.org/. Please register with an institutional email account.
2. Atmosphere Access
- Go to http://user.cyverse.org/. In the Services Menu under ‘MY SERVICES’ you should see Atmosphere listed as an option you can launch. If not, look under the Available menu, and click the ‘REQUEST ACCESS’ link. You will receive an email requesting additional information. To qualify for an Atmosphere account, your CyVerse account must be associated with an institutional email address (e.g. .edu/.org/.gov).
3. Laptop
Please bring your own Wi-Fi enabled laptop to the workshop. Make sure your laptop has the following:
- Internet Browser: Please have an up-to-date web browser (We strongly recommend Firefox, Safari, or Chrome and others have significant issues.)
- Download Cyberduck: Using Cyberduck for Uploading and Downloading to the Data Store
- If you want command line access to the CyVerse Data Store (Mac/Linux) download iCommands (see: Prerequisites)
Agenda
Time | Topic/Activity | Presenter | Slides | Guides | Notes/Links |
|---|---|---|---|---|---|
| 12:00 PM | Boxed-Lunch / Sign-in / Verify CyVerse Accounts | ||||
12:15 PM | Speaker/Project Intros and Overview of CyVerse | All, Kapeel (CyVerse Intro) | slides | ||
12:30 PM | Data uploading and sharing with CyVerse | Kapeel | slides | guide |
|
| 01:00 PM | Overview of sequencing and assembly technologies | Josh | slides | ||
01:30 PM | Intro to MAKER annotation pipeline | Josh |
| ||
| 01:45 PM | Break | ||||
02:00 PM | Annotation with SciApps | Liya | tutorial | ||
02:45 PM | Intro to Gramene and Data wrangling | Marcela | |||
03:30 PM | Community-Driven Genome Curation | Monica | |||
| 04:15 PM | Additional resources: KBase | Vivek | |||
| 04:30 PM | Wrap up and questions | All |
Speakers and Affiliations
Cold Spring Harbor Laboratory
CyVerse, Gramene
Cold Spring Harbor Laboratory
Gramene
Cold Spring Harbor Laboratory
KBase
Cold Spring Harbor Laboratory DNA Learning Center
MaizeCode
Cold Spring Harbor Laboratory
Gramene, CyVerse
Cold Spring Harbor Laboratory
CyVerse, MaizeCode