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Introduction to DELSA and DEAP Thanks to: Gordon & Betty Moore Foundation, NIH, NSF, Mc. Millen Foundation, and Seattle Children's Research Institute For Tweets: please use Hash. Tag #DELSA www. DELSAglobal. org
Our New Logo Data Knowledge Action Data-Enabled Life Sciences Alliance 2
Life Sciences & Fourth Paradigm - Enormous increase in scale of data generation, vast data diversity and complexity - Development, improvement and sustainability of 21 st 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! (DISW 1 Assignment, Sep. 2010, Seattle)
Why DELSA Now? (DISW 2 Assignment, May 2011, D. C. ) - 10, 000 -fold improvement in sequencing vs. 16 -fold improvement in computing over Moore Law - 11% Reproducibility Rate (Amgen) and up to 85% Research Waste (Chalmers) - 27 +/-9 % of Misidentified Cancer Lines and One of out 3 Proteins Unannotated (Unknown Function) Urgent Need: A Community Transdisciplinary Response!
DELSA Mission and Vision (DW 1/SC-11 Assignment, Nov. 2011, Seattle) DELSA Mission (
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 (DW 1 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 DW 3 meeting: Oct. 9, 2012, Chicago What do we need to accomplish during next 0. 5 -to-2 years?
DW 2 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
DW 2 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 Road. Map for DELSA
DW 2 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, 2012 Now 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 Gries Goal: 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 Scientists Lead: Geoffrey Fox Goal: 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 e. Science classes, OGF Grid Computing certificate , and XSEDE HPC University… Possible approach is to focus on particular life science subdomains. Project 4: Global Protein Atlas Lead: Jack Gilbert Goal: 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: Internet 2 Application Lead: Michael Sullivan Background: Internet 2 is an advanced not-for-profit networking consortium developing revolutionary Internet technologies and leveraging a high-performance network (http: //www. internet 2. edu/). It is currently being adopted by NLM. It has three components: 1) connect pilot place to Internet 2; 2) Deploy Science DMZ at the pilot place; and 3) Perform routine exchange of Big. Data. 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 Internet 2. 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 Kemnitz Goal: 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: Para. MEDIC Use Case Lead: Wu Feng Background: 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 Para. MEDIC: Parallel Metadata Environment for Distributed I/O & Computing) on a Suggested Big. Data challenge to show what can be done if the system was widely available. Deliverable: Big. Data life sciences challenging project successfully accomplished.
(Sample) Project 5: Internet 2 Vision and Goals Internet 2 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 Internet 2 propose a collaborative project with the following initial goals: 1. Connect SCRI to the Internet 2 Network to enable high-performance wide area connectivity with U. S. and international research centers. 2. Deploy a Science DMZ 1 at SCRI’s enterprise network perimeter to enable a highspeed 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 Internet 2 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 Internet 2 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 Stanberry Courtney Mac. Nealy-Koch Chris Moss Randy Salomon Peter Arzberger Geoffrey Fox Neo Martinez Rob Arnold Daniel Atkins Corinna Gries Evelyne Kolker Christian Burks Jack Faris Vural Ozdemir Laurie Meyer Deborah Elvins Support: Gordon & Betty Moore Foundation Join DELSA! Please, contact eugene. [email protected] org
DELSA 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 disciplinaryspecific approaches to address common problem.
DELSA Strategy (DW 1 Assignment;