AToL Workshop Breakout

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Social Networking and Collaborative Tools

• AToL Workshop Breakout

William Barnett Research Technologies, Indiana
University March 8, 2008
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What is a Social Network Service?

• Wikipedia definition
• A social network service focuses on the building
  and verifying of online social networks for
  communities of people who share interests and
  activities, or who are interested in exploring
  the interests and activities of others, and which
  necessitates the use of software. Most services
  are primarily web based and provide a collection
  of various ways for users to interact, such as
• chat,
• messaging,
• email,
• video,
• voice chat,
• file sharing,
• blogging,
• discussion groups, and so on.

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NSFs Goals for Virtual Organizations(Cyberinfras
tructure Vision for 21st Century Discovery)

• To catalyze the development, implementation and
  evolution of a functionally complete national
  cyberinfrastructure that integrates both physical
  and cyberinfrastructure assets and services to
  support VOs
• To promote and support the establishment of
  world-class VOs that are secure, efficient,
  reliable, accessible, usable, pervasive,
  persistent and interoperable, and that are able
  to exploit the full range of research and
  education tools available at any given time.
• To support the development of common
  cyberinfrastructure resources, services, and
  tools enabling the effective, efficient creation
  and operation of end-to-end cyberinfrastructure
  systems for and across all science and
  engineering fields, nationally and
  internationally.

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NSF Building Effective Virtual Organizations

• 2008 BEVO Workshop
• http//www.ci.uchicago.edu/events/VirtOrg2008/inde
  x.php?pgmain
• Best Practices and Success Stories
• Infrastructures and Technologies
• Project Management and Organization
• Fostering Ongoing Collaboration
• NSF Virtual Organization Funding
• Cyber-Enabled Discovery and Innovation (CDI)
• Sustainable Digital Data Preservation and Access
  Network Partners (DataNet)

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Research Virtual Organizations Phase 1EXAMPLE
NEESGrid Cyberinfrastructure to facilitate
simultaneous multi-site earthquake engineering
experimentation/simulation (B.F. Spencer, U. of
Illinois)

• Tele-control Tele-observation
• Electronic Notebook
• Advanced Data Metadata
• Remote Collaboration
• Core Grid Services
• Security
• Simulation

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Research Virtual Organizations Phase 2EXAMPLE
TeraGrid high end compute, data and
visualization resources to the nations academic
researchers (JP Navarro, U. of Chicago)

• Make science more productive through an
  integrated set of very-high capability resources
  (ASTA Projects)
• Bring TeraGrid capabilities to the broad science
  community (Science Gateways)
• Provide a coordinated, general purpose, reliable
  set of services and resources (Grid
  interoperability working group)
• 9 resource providers of supercomputers, high end
  storage systems, visualization hardware, very
  high speed backbones
• Coordinated authorization and allocation process
  (Globus)
• Science Gateways (20) of Web portals or
  applications that serve specific communities or
  projects
• Management model as single, integrated facility

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Research Virtual Organizations Next Gen Human
Cyberinfrastructure (HCI) of Web 2.0
technologies, user-defined mashups, Semantic Web,
(aka e-Science in Europe)

• Self-published scientific workflows (eg.
  MyExperiment)
• Cloud Computing (temporary virtual machines or
  storage)
• Organizational Hubs (eg. NanoHUB)
• Grid Computing Environments
• others?
• The Goal is to transform science and lead to
  discoveries that otherwise would not happen.

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Community SitesReinforces weak social linkages
use existing or build your own?

• LinkedIn (http//linkedin.com) professional
  networking, contact management, information
  resource, job seeking
• Facebook (http//www.facebook.com) personal
  social utility gossip, chit-chat, social
  coordination, fun toys
• MySpace (http//www.myspace.com) personal
  communication personal self expression, gossip,
  social coordination
• MyExperiment (http//myexperiment.org) scientist
  created shared workflows, research collaboration
• Ning (http//www.ning.com) tools to create social
  networks
• Club Penguin (http//clubpenguin.com) for the
  next next gen

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MyExperiment Self-Published Workflowsa
community social network, a market place, a
platform for launching workflows and a gateway to
other publishing environments

• Scientists create workflows, hence have
  intellectual control
• Coordinates services and links resources
• Build once, use many times. Allows sharing,
  re-using, re-purposing
• A repository of experimental workflows

Generic protein sequence analysis performs an
homology search followed by multiple sequence
alignment and phylogenetic analysis. By M.B.
Monteiro
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Content SharingLow barriers to contributed
content, community enforcement

• Flickr (http//flikr.com) post, comment, tag,
  rate, and organize photos
• YouTube (http//www.youtube.com) post, comment
  (blog), tag, rate, video clips
• Googledocs (http//docs.google.com) create and
  share documents, including web-based word
  processor and spreadsheet
• SciVee (http//www.scivee.tv) science
  pubcasts, blogs, and discussions (part of PLoS)
  
• Scribd (http//scribd.com) library of
  self-published documents
• Wikipedia (http//wikipedia.org) self-authored
  encyclopedia driven by self-professed authorities
  (and Colbert. For example, see
  http//seek.ecoinformatics.org

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Real Time CollaborationVideo, Audio, and data
conferencing

• Skype (http//skype.com) network-based voice and
  video calling
• Polycom (http//www.polycom.com) high-end
  multipoint videoconferencing, including HD
• Office Live (http//www.officelive.com)
  Microsoft shared personal productivity
  applications and files
• WebEx (http//webex.com) Internet-based
  multi-point collaborations, including application
  sharing
• Adobe Acrobat Connect Professional
  (http//adobe.com) web-based collaboration and
  document sharing, Flash-based

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ToolsContainers for content Management and
Productivity

• Drupal (http//drupal.org) collaborative content
  management
• Joomla (http//www.joomla.org) open source
  content management system for website
  construction (used by NanoHUB)
• Moveable Type (http//moveabletype.org)
  user-based content editing of web sites using
  blogging tools
• Programmable Web (http//www.programmableweb.com)
  APIs that allow users to integrate multiple
  functions
• Doodle (http//www.doodle.ch) online polling
  utility to coordinate meeting times
• SurveyMonkey (http//www.surveymonkey.com) online
  surveys

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Tag SharingUser-based content characterization
and grouping (contra librarian based
metatagging)

• Del.icio.us (http//del.icio.us) a social
  bookmarking web service for storing, sharing, and
  discovering web bookmarks
• Digg (http//digg.com) tagging and voting for web
  content
• Connotea (http//www.connotea.org) online
  reference management and sharing for scientists,
  researchers, and clinicians
• Citeulike (http//www.citeulike.org) online
  service that organizes and shares academic papers
  through tagging

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Cloud Computing Backend computational resources
for research communities

• Server virtualization permits the ability to
  create temporary, task specific resources.
• Allows personal infrastructures.
• Amazons elastic compute cloud (EC2) and Google
• Amazons simple storage service (S3), Google, and
  now Microsofts Skydrive
• Can be configured as a data or compute back end
  to community sites.
• cf. the Google-IBM Academic (NSF) Cluster
  Computing Initiative at
• http//www.google.com/intl/en/press/pressrel/20071
  008_ibm_univ.html

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Cloud Computing

• Hadoop EC2 S3 Super alternatives for
  researchers ( real people too!)I recently
  discovered and have been inspired by a real-world
  and non-trivial (in space and in time)
  application of Hadoop (Open Source implementation
  of Google's MapReduce) combined with the Amazon
  Simple Storage Service (Amazon S3) and the Amazon
  Elastic Compute Cloud (Amazon EC2). The project
  was to convert pre-1922 New York Times
  articles-as-scanned-TIFF-images into PDFs of the
  articles 
• Recipe    4 TB of data loaded to S3 (TIFF
  images)     Hadoop ( Java Advanced Imaging and
  various glue)     100 EC2 instances     24
  hours
  11M PDFs, 1.5 TB on S3
• Unfortunately, the developer (Derek Gottfrid) did
  not say how much this cost the NYT. But here is
  my back-of-the-envelope calculation (using the
  Amazon S3/EC2 FAQ)    EC2 0.10 per
  instance-hour x 100 instances x 24hrs
  240    S3 0.15 per GB-Month x 4500 GB x
  1.5/31 months 33     0.10 per GB of data
  transferred in x 4000 GB 400     0.13 per
  GB of data transferred out x 1500 GB
  195     Total 868
• Glenn Newton (2/27/2008) _at_ http//zzzoot.blogspot.
  com/2008/02/hadoop-ec2-s3-super-alternatives-for.h
  tml

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Organizational HubsEducational analysis and
collaboration tools (eg., NanoHUB)

• A structured compendium of educational resources,
  particularly simulations
• Online presentations, courses, learning modules,
  podcasts, animations, teaching materials, etc
• Infrastructure is transparent to users
• HUBZero software (Purdue) to be released in 2008
  built on Joomla, using Rappture for applications

Molecular dynamics simulation using the BioMOCA
simulation program at NanoHUB.org
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Grid Computing EnvironmentsWeb portal interfaces
and user-centric services to the Grid

• May be moving away from high barrier resourcing
  and authorization schemes such as Globus although
  there is still a focus on a limited number of
  transformative or big science programs.
• Evolution would be to social networking models
  for access to resources either through community
  created portals (eg., Joomla) or the use of
  commodity portals like Facebook.
• Back end computational resources may coalesce
  into a national cloud structure or disassociate
  into multiple, independent clouds.

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Opportunities and Challenges of Social
NetworksHow do you create and sustain momentum?
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Organizational Behaviors of Virtual
OrganizationsWilliam B. Rouse (Health Care as a
Complex Adaptive System)

• Roles based on Leadership rather than Management
• Management through Incentives and Inhibitions
  rather than Command and Control
• Measurement by Outcomes rather than Activities
• Focus on Agility rather than Efficiency
• Relationships based on Personal Commitment rather
  than Contracts
• Organization structure is non-heirarchical
• The design is based on self-organization

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AToL Social Networking Goals?

• Goals of AToL Digital Library of Biodiversity
  Information Grant (Maddison, PI)
• Improve core scientific content of the ToL
  collection
• Implement new technical features focusing on
  needs of users from the education and research
  communities.
• Initiate collection of content specifically aimed
  at K-16 learners
• Develop and implement robust policies pertaining
  to the administrative structure of the ToL

I still have not found the details of the first
page after 1 hour rummaging through your web
site. It needs to be simplified before it will be
widely used. I am a retired researcher who has
time to search but even I had to give up because
of difficulties. I could have added to your data
base if I could have found out how to do it. A.
A. Berryman Comment on First chapter of book of
life goes live, Nature.com 26 Feb, 2008
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Broader AToL Collaborative Goals?

• Share Sequences hot off the sequencers data
  (note impact of high throughput sequencers and
  data management needs)
• Bridge gaps for AToL projects that do not have
  Informatics components
• Communications challenges data sharing,
  day-to-day communications, sharing among
  different projects
• Information Repositories
• Interoperability standards, workflows, and
  architectures
• Extending results and outcomes to greater science
  and educational communities

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Broader Impact Goals

• Transformative science (lead to new discoveries)
• Democratization of science (lower barriers of
  entry)
• Build for the next generation of scientists
• Expand roles as scientific authorities and
  authentic science

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Making this breakout productive

• What are the goals of and tools needed by AToL?
• Activity Map significant activities and
  organizational processes of the AToL community
  onto existing offerings (eg., a requirements
  traceability matrix)
• Goal To come out with workshop or other
  proposals to advance AToL collaboration

• Thanks to the following people for help with this
  presentation
• Reed Beaman, Florida Museum of Natural History
• Geoffrey Fox, Pervasive Technology Labs, Indiana
  University
• Rick McMullin, Pervasive Technology Labs, Indiana
  University
• Mark Notess, Digital Library Program, Indiana
  University
• Marlon Pierce, Pervasive Technology Labs, Indiana
  University