Introduction to DELSA and DEAP

Thanks to:

Gordon & Betty Moore Foundation,NIH, NSF, McMillen Foundation, andSeattle Children's Research Institute

For Tweets: please use HashTag #DELSA www.DELSAglobal.org

2

Data

Knowledge

Action

Our New Logo

Data-Enabled Life Sciences Alliance

Life Sciences & Fourth Paradigm

- Enormous increase in scale of data generation, vast data diversity and complexity

- Development, improvement and sustainability of 21st Century tools, databases, algorithms & cyberinfrastructure

- Past: 1 PI (Lab/Institute/Consortium) = 1 Problem- Future: Knowledge ecologies and New metrics to assess

scientists & outcomes (lab’s capabilities vs. ideas/impact)

- Unprecedented opportunities for scientific discovery and solutions to major world problems

Urgent Need: A Sustainable Supporting Ecosystem!(DISW1 Assignment, Sep. 2010, Seattle)

Why DELSA Now? (DISW2 Assignment, May 2011, D.C.)

- 10,000-fold improvement in sequencing vs.16-fold improvement in computing over Moore Law

- 11% Reproducibility Rate (Amgen) andup to 85% Research Waste (Chalmers)

- 27 +/-9 % of Misidentified Cancer Lines andOne of out 3 Proteins Unannotated (Unknown Function)

Urgent Need: A Community Transdisciplinary Response!

DELSA Mission and Vision (DW1/SC-11 Assignment, Nov. 2011, Seattle)DELSA Mission (<what> is our impact/deliverable/goal?):  

Accelerate the impact of data-enabled life sciences research on the pressing needs of our global society.

 

DELSA Vision (<where> will the affected community be if our mission succeeds?):

Through interdisciplinary research and transdisciplinaryengagement, the life science community will move from “one scientist—one project” to collective innovation in data-enabled science.

DELSA Expertise

• biological sciences• biodiversity• cyberinfrastructure• communication• bioenergy• environmental sciences• management• informatics• personalized medicine• (marine) microbiology• sustainability• IT• Omics

• (global) health• ecology• (meta)genomics• statistics• clinical sciences• policies• translational research• food sciences• journalism• visualization• biomedical research• evolution• computer sciences

Developing DELSA Community (DW1 Assignment)

- Advisors, NFP Status, Communications

- - Vision, Mission, Strategy, Budget

- Governance, Leadership, Business Plan

- Committees, Publications, Responses

Please, visit our new website: www.DELSAglobal.org

Next DW3 meeting: Oct. 9, 2012, Chicago

What do we need to accomplish during next 0.5-to-2 years?

DW2 Workshop, May 2012, D.C.

Who is here:- ~ 90 participants (by invitation only!)- Academia, Government, Industry, Media, NFP- 9 Countries (Belgium, Canada, China, Germany, Israel, India, Russia, U.K., and U.S.A.)

What is needed:- Help us identify Transformational Business Models- Help us identify Top (high impact/potential) Projects- Stay engaged with DELSA and support our mission

 

- Get the word out about DELSA... tweet, blog, email, talk, FB, LI, present, connect etc.- Identify your optimal role/s in DELSA and Top Projects

DW2 Outcomes

At MACRO level:

- Mapping the new modes of collective innovation and research production and utilization

- Identifying the key accelerators and metrics of success for research and its translation

- Charting the RoadMap for DELSA

DW2 Outcomes, Cont.

At PROJECT level:

- Identifying the DELSA Endorsed Projects • ‘Game-changing’ and transformative • Time at a premium: achievable in 1-2 years +

capitalizes on already existing datasets and resources

- DELSA Endorsed Projects start on July 1, 2012Now it is a perfect time to join the Project of your choice!

DELSA Endorsed Projects

Project 1: Social Networking Platform for Tool Brokering/Community Building *Goal: Open a dialog and an organizational effort to build a social networking platform to broker bioinformatics tools. This project would encourage community engagement by crowdsourcing, accelerate discovery by making tools more accessible, and through community ranking, more trustworthy. It would also build community and connect people and resources. Deliverable: Social networking platform for idea exchange, resource sharing, tool ranking and brokering.  Project 2: Data Set Accessibility Project Lead: Corinna GriesGoal: Make high quality life sciences data broadly available, traceable and usable. Deliverable: Follow-on workshop to define issues such as: Curation, Sustainability, Rapid growth in data volume, Data provider incentives, Non-trivial processing on the data in the repository, Limited bandwidth from the open Internet to clouds, and Security. Project 3: Training Data ScientistsLead: Geoffrey FoxGoal: Train new and established scientists to enable more effective use of big data and its cyberinfrastructure.Deliverable: Courses in data enabled science culminating in a certification similar to Microsoft or Cisco certification or existing scientific computing or computational science certificates/curricula. Need to evaluate existing resources such as: UW eScience classes, OGF Grid Computing certificate , and XSEDE HPC University… Possible approach is to focus on particular life science subdomains. Project 4: Global Protein AtlasLead: Jack GilbertGoal: For all the meta-genomes and genomes that are available cluster at the protein level and annotate… MG-RAST, CAMERA, MOPED, PSU, etc… The goal is to characterize all the proteins and answer the question: what protein is expressed in what organism, what disease, what tissue, what condition, what environment, and in what concentration? Deliverable: Based on current large scale projects such as Earth Microbiome Project and Human Microbiome Project, we will analyze samples from diverse communities using meta-genomics and meta-proteomics to produce a Global Protein Atlas.

DELSA Endorsed Projects, Cont.

Project 5: Internet2 ApplicationLead: Michael SullivanBackground: Internet2 is an advanced not-for-profit networking consortium developing revolutionary Internet technologies and leveraging a high-performance network (http://www.internet2.edu/). It is currently being adopted by NLM. It has three components: 1) connect pilot place to Internet2; 2) Deploy Science DMZ at the pilot place; and 3) Perform routine exchange of BigData. It is a dedicated data transfer mode to enable fast data transfer mode. Goal: Create scalable process to connect entities (Research institutes, Universities, and Global Governments) to Internet2.  

Project 6: DELSA Matchmaking Website *Goal: Help scientists connect to each other, tools, publications, industry as a way to facilitate more effective science. Possible examples are VIVO and Linkedin. Could develop matchmaking 20 questions to determine individuals’ skills, interests, tools, review favorites. Could point to publications, tools or resources.Deliverable: A web-based platform for connecting scientists to other scientists as well as research resources. 

Project 7: Pregnancy Atlas Use Case Lead: Joseph KemnitzGoal: Utilize DELSA and its members and connections for resources that would help the Pregnancy Atlas….The Pregnancy Atlas Consortium has an Integrative Discovery Platform that could be expanded. Help with metrics to assess Platform success.Deliverable: Additional information for the Pregnancy Atlas such as potential collaborators, CI tools, data formats and funding opportunities. Provide files in a format that could be integrated by the Platform.  

Project 8: ParaMEDIC Use CaseLead: Wu FengBackground: Frequent Pain Points experienced by DELSA members include ease of use issues with analysis tools and compute resources, as well as performance issues which may be due to compute problems, data management problems or data representation problems. Goal: Use the automated, easy to use and integrated high-performance Biocomputing system (including ParaMEDIC: Parallel Metadata Environment for Distributed I/O & Computing) on a Suggested BigData challenge to show what can be done if the system was widely available. Deliverable: BigData life sciences challenging project successfully accomplished.

(Sample) Project 5: Internet2

Vision and GoalsInternet2 and SCRI envision the routine, ultra high-speed transport of Big Data between life sciences research centers. Gigabit speeds require a clean data path with no choke points in either local or wide area networks. SCRI and Internet2 propose a collaborative project with the following initial goals:

1. Connect SCRI to the Internet2 Network to enable high-performance wide area connectivity with U.S. and international research centers.

2. Deploy a Science DMZ1 at SCRI’s enterprise network perimeter to enable a high-speed local path, performance monitoring, and problem resolution.

3. Exchange large datasets at 1 Gigabit per second between SCRI and at least two other research centers, for example, UW, PNNL, ANL, and NCBI.

Once SCRI and Internet2 have accomplished these initial goals, we plan to use lessons learned to create a reproducible process that can be applied at other data-enabled life sciences research centers. We also plan to collaborate in tailoring the Science DMZ architecture to accommodate more sensitive data, e.g. protected health information.

Dissemination Internet2 and SCRI can report on the progress of their collaboration at a number of meetings in the months ahead. For example, Mike Sullivan is scheduled to speak about “Strategies and Tools for Big Data Transport Across Wide Area Networks at Hundred-Gigabit Speeds” at the Bio-IT Cloud Summit, and he can highlight a SCRI Science DMZ deployment.

Thanks to:Team:

Beth Stewart Natali Kolker Bill Broomall Roger Higdon Winn Haynes Greg Yandl

Maggie Lackey Andrew Lowe Larissa StanberryCourtney MacNealy-Koch Chris Moss Randy

Salomon Peter Arzberger Daniel Atkins Jack Faris

Geoffrey Fox Corinna Gries Vural OzdemirNeo Martinez Evelyne Kolker Laurie MeyerRob Arnold Christian Burks Deborah Elvins

Support:Gordon & Betty Moore Foundation

Join DELSA! Please, contact eugene.kolker@delsaglobal.org

DELSA Definitions

Definitions are modified from original work by Rosenfield, 1992:  

Level one: Multidisciplinary - Researchers work in parallel or sequentially from disciplinary-specific base to address common problem.

 Level two: Interdisciplinary - Researchers work jointly but still

from disciplinary–specific basis to address common problem.  Level three: Transdisciplinary - Researchers work jointly using

shared conceptual framework and combined disciplinary-specific approaches to address common problem.

 

DELSA Strategy (DW1 Assignment;<how> will we pursue our mission?):

- Identifying, inspiring and supporting new transformational modes of business and innovation

- Providing a leading voice and coordinating framework for collective innovation in data-enabled science for the life sciences community- Promoting sustainable and shared access to data, knowledge, tools, and services - Facilitating information exchange through workshop development,

community involvement and publications - Identifying and cultivating opportunities to create essential solutions

by implementing interdisciplinary and transdisciplinary approaches - Coordinating and monitoring individual initiatives focused on translational impact.