Introduction to iplant Collaborative Jinyu Yang Bioinformatics and Mathematical Biosciences Lab

Transcription

1 Introduction to iplant Collaborative Jinyu Yang Bioinformatics and Mathematical Biosciences Lab May/27 th /2016

2 About iplant What is iplant Collaborative? 1. A virtual organization 2. Created by a cooperative agreement 3. Funded by the US National Science Foundation(NSF) 3. Aiming to create cyberinfrastructure for the plant sciences.

3 About iplant iplant at-a-glance Developing cyberinfrastructure for life sciences research Developing the national cyberinfrastructure for data-intensive biology Providing powerful extensible platforms Making broadly applicable cyberinfrastructure resources

4 Tools and Services analysis tools and workflows educational resources visualization and image analysis data storage high performance computing computational expertise

5 Get Stated 1. Set up your Account CyVerse portal( 2. Accessing to your account Two important sections: My Services Available Services

6 My Services

7 Available Services

8 Request Access E.g. Request Access to Atmosphere You must have a valid institutional (academic or governmental) address, else your request may be denied.

9 Import Data All iplant platforms interact with the Data Store Two quick ways to upload even very large (>2GB) datasets. 1. drag-and-drop graphical interface: Download Cyberduck (for Windows, Mac) Downoload iplantcyberduck Profile (Required) Documentation Download idrop Desktop (for Windows, Windowsx64, Mac, Linux) Documentation 2. command line: Download icommands (Mac, Linux - 32bit, Linux - 64bit) Documentation

10 Import Data How much and what type of data can I upload? Each iplant user has a 100GB allocation by default Any kind of data (sequence reads, documents, images, etc.) Terabytes of data? Support first Need more storage? request an increase in your storage allocation. iplant Data Store Automatic data backup Easy upload /download and sharing Move files seamlessly between iplant platforms Automate file transfers Share files with lab members, collaborators, and communities

11 Atmosphere A cloud service Can launch your own virtual working environment and software Get computing resources A gateway to access the iplant's core infrastructure resources, including high performance computing (HPC), grid computing environments, and the iplant Data Store.

12 Bisque Image Analysis Environment A web-based system provides secure image storage, sharing, management and analysis.

13 Discovery Environment A primary web interface and platform to access the powerful computing, storage, and analysis application resources analytical tools seamless access to the iplant Data Store share with collaborators or with the community

14 Data Discovery Environment

15 Apps Discovery Environment

16 Discovery Environment Analyses: You can found the status, parameters and results of your executed apps

17 DNA Subway Makes high-level genome analysis available to students and educators Provides easy access to the types of data and informatics Organizes bioinformatics analysis tools into logical workflows

18 DNA Subway Users can: Predict and annotate genes in up to 150,000 base pairs of DNA sequence Prospect entire plant genomes for related genes and sequences Determine sequence relationships, view phylogenetic trees and analyze "DNA barcodes" Analyze RNA-Seq data for differential expression

19 DNA Subway

20 Data Store Cloud-based Can store all the data related to your research Provides reliable and redundant storage Accessible from anywhere on iplant's platform 100GB for each user by default, with increase up to 1TB or more possible.

21 Data Store

22 Taxonomic Name Resolution Service (TNRS) A tool for the computer-assisted standardization of plant scientific names corrects spelling errors and alternative spellings to a standard list of names converts out-of-date names to the currently accepted name.

23 Thanks!