Biosciences Working Group Update Wilfred W. Li, Ph.D., UCSD, USA Habibah Wahab, Ph.D., USM, Malaysia Hosted by CNIC, CAS Beijing, China Oct 16-18, 2013

Cloud based solutions for Biosciences Data as a Service (DaaS) Software as a Service (SaaS) Platform as a Service (PaaS) Infrastructure as a Service (IaaS) Network as a Service (NaaS) Data Sets, Public Records, Biological Databases Computational Pipelines, Specialized tools Execution Platforms, Programming Environments Virtual Machines, Virtual Clusters Network Resources, Programmable Networks

Rocks BioApp Utilizing Rocks Cluster Distribution IaaS: Virtual Machines SaaS: Utilizing the Opal toolkit Applications: AutoDock AutoDock Vina PDB2PQR MEME … PRAGMA Cloud: Using Gfarm for VM storage and sharing Contact: Nadya Williams 2013 Google Science Fair Grand Prize Winner, Eric Chen, a high school student in the UCSD BioChemCore program. New antivirals against Influenza endonuclease using virtual screening tools.

CNIC – Duckling Collaboration Library CLB - Collaboration Library – A component of Duckling, an open-source toolkit developed by the CNIC, Chinese Academy of Sciences (CAS) – Used by all Duckling applications as the Data Repository – Extended to support data cloud service (CLB+) Duckling Portal Resource Document Collaboration Tool (DCT) Collaboration Library (CLB) User Management Tool (UMT) Virtual Organization Tool (VMT) Duckling Application Integration Framework Resource Application Plug-ins Application Plug-ins Dong et al, IEEE e-science 2013, in press.

UCSD – Private Cloud Data service UCSD Research Cyberinfrastructur e Program Campus funded initiative to support big data applications Interviewed 50 groups on campus Li et al, IEEE e-science 2013, in press.

Mashup of Typical Research Data Flows Many research groups follow similar data flows Utilize a subset of the components on a routine basis Number of storage/replica nodes, computing nodes and instruments vary among the groups but the data flow and usage patterns are quite similar. NFS NFS/CIFSFTP ReplicateNFS/CIFS LustreArchive Share Network Attached Storage Nodes Network Attached Storage Nodes Replicated Storage Nodes Replicated Storage Nodes Compute nodes Laptop/Desktop On Campus External Servers Instruments High Performance File System Cloud storage nodes Cloud storage nodes

Update from Konkuk University Prepared a proposal for a government grant – Development of novel technologies for studying metagenomics based on cloud computing (Institutes: CBRU and BDRC at Konkuk University, SDSC and Calit2 at UCSD) Workshop proposal for PRAGMA26 – Theme: NGS, Metagenomics, HPC, Clouds and Collaboration, CFP out early next year. 7 Jaebum Kim Ph.D.

Update from Konkuk University Plan for an international consortium – Time: Jan (tentative) – Place: Konkuk University, Korea – Topic: Environment- and toxicity-related microorganism and bioinformatics – Institutes: UW-METC (Dr. Yu), Konkuk University, and more (tentative) – More information will be out soon – If you are interested let us know. We can invite you 8

Active Folder: Integrating All Activities of Simulation on File System Congratulation! Dr. Daeyoung Heo – He got the PhD degree in the last summer! Two posters & a Demo in WG – Active Folder: Integrating All Activities of Simulation on File System - NAS Version – Predicting and Forecasting System of Urban Ecology on Meteorological Changing Active Folder – good for case comparative study – Tasks Described as regular folders and files – Product Input or output of simulation Can be handled like regular file by using legacy software Contains provenance information (meta data, task info, etc) Can be reproduced by the task which is extracted from the provenance information – Resource Computing server(Local, Grid, Cloud, what ever, …) is registered as regular folders and files To submit a Job(task), just Drag&Drop the task folder to the folder which represents computing server Daeyoung Heo ( ) Suntae Hwang ( )

Active Folder: Integrating All Activities of Simulation on File System ⊙ Active Folder on DropBox+EC2 – Cost & Performance Problem with very large files ⊙ Active Folder on NAS ⊙ NAS(Network Attached Storage) ● Large Volume Storage ● Network File System ( NFS, SMB/CIFS, AFP … ) ● Most vendors support Cloud solution like DropBox at PRAGMA 25 at PRAGMA 24

Case Study : Volcano Eruption Simulation using Active Folder

Breakout Sessions Presentations (Today, 2:40 – 4:15 pm, Rm 514) – Kevin Dong, CNIC – Jaebum Kim, Konkuk University – Wilfred Li, UCSD – Daeyoung Heo, Kookmin University – Others, please let me know. Planning (Tomorrow, 11:10 am – 12:30 pm) Join Sessions (Tomorrow, 3:50 – 4:30 pm, Resources and Data, Cyber Learning) Conferences – IEEE e-Science 2013, 10/23-25/2013 (National Convention Center, Beijing)