AFRICAhome: Volunteer computing for health

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AFRICA_at_homeVolunteer computing for health

• Ben Segal, IT Department, CERN

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Volunteer computinga worldwide movement

• What is volunteer computing?
• Volunteer computing is a global grassroots
  movement to harness the computing power of
  privately owned PCs.
• Millions of people are donating spare time on
  their computers for scientific projects. Anyone
  with a computer can join.
• SETI_at_home downloaded by gt 5 million people, gt 1
  million years of compute time, rated at gt 60
  Teraflop (worlds fastest computer!)
• There are dozens of projects available to
  download. Some of these tackle global
  health-related issues such as drug design.
• Examples ProteinFolding_at_home, FightAids_at_home,
  Compute Against Cancer,World Community Grid...
• There is a general purpose platform for volunteer
  computing which many projects use, called
  Berkeley Open Infrastructure for Network
  Computing, BOINC.

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Volunteer computing vs. Grid computing

• Similarities
• Both enable distributed computing on a global
  scale
• Both adapted to massively parallel computing
  (trivial parallelism)
• Differences
• Grids federate dedicated resources, VC relies on
  public participation.
• Grid clients are active, and can submit jobs, VC
  clients are passive.
• Grids exploits high-speed networks, VC minimises
  bandwidth use.
• Grids used for distributed data storage, VC (so
  far) for computing.

Volunteer computing relies on central server
Grid computing has complex topology
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AFRICA_at_homeVolunteer computing for Africa

• What is AFRICA_at_home?
• Huge potential for volunteer computing to
  contribute to solving pressing health and
  environmental issues facing developing world.
• AFRICA_at_home tackles such issues by providing a
  common framework for volunteer computing projects
  that address African needs.
• An important goal of AFRICA_at_home is to involve
  African students, scientists and institutions in
  the development and running of these volunteer
  computing projects.
• The first application running in the AFRICA_at_home
  framework concerns computer simulations of
  malaria epidemiology.

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Volunteer computing and malaria epidemiology

• Why use computer simulations?
• Simulation models of transmission dynamics and
  health effects of malaria are an important tool
  for malaria control.
• Models help develop optimal strategies for
  delivering mosquito nets, chemotherapy, or new
  vaccines currently under development and testing.
• Such modelling is computer intensive, requiring
  simulations of large human populations with
  diverse parameters related to biological and
  social factors that influence disease
  distribution.
• .

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Volunteer computing and malaria epidemiology

• Why use volunteer computing?
• At Swiss Tropical Institute, a computer model for
  malaria epidemiology called MalariaControl.net
  had been developed and tested on an institutional
  PC network of about 40 machines.
• The model uses an individual-based approach to
  simulate complex patterns of malaria
  epidemiology. Some outcomes of interest are rare
  events (death). The model involves fitting
  parameters to more than 60 data sets from field
  studies for a wide range of scenarios.
• To validate models and simulate the full range of
  interventions and transmission patterns requires
  many millions of simulation runs, each in the
  order of hours, totalling thousands of years of
  CPU time. STI cannot afford a computer centre!

Data set for age-prevalence of parasitemia
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AFRICA_at_homefirst project

• Porting of MalariaControl.net to BOINC platform
• Project team involves 3 students from Geneva,
  Bamako and Yaoundé
• Funded by Geneva International Academic Network,
  hosted at CERN
• Port takes 3 months, beta-test February 2006,
  open to public July 2006
• Server at University Geneva, African students
  recruited by ICVolunteers

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AFRICA_at_homefirst results for MalariaControl.net

• Volunteers 7000 total, 4500 active
• Sign up rate up to 400 new users per day
• Currently 50-60 per day
• Host PCs 20,000 total, 15,000 active,
• 80 Windows, 20 Linux

• CPU power 3.0 Teraflops
• equivalent to 1,000 CPU years/yr (midrange PCs)
• delivered to date 1,800 CPU years (Apr 07)
• Simulations per day 35,000
• huge public/press interest!

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AFRICA_at_homefuture plans

• Volunteer computing for Africa
• Involve African scientists, institutions in
  hosting, porting and developing volunteer
  computing projects for African humanitarian
  needs.
• Port two more applications. STDSIM with Erasmus
  Medical Centre, Rotterdam already underway.
• Establish BOINC servers in two African
  institutions (candidates in Mali, Senegal, South
  Africa).
• Volunteer computing workshop for African
  scientists, in Africa. Workshop at AIMS (African
  Institute for Mathematical Sciences) planned for
  16-22 July 2007 call for participants closes 15
  May.
• It is expected that further volunteer computing
  applications will be contributed to AFRICA_at_home
  by other groups in future.
• Please contact us with your suggestions!

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AFRICA_at_homethe partners

• Core Partners
• European Organization for Nuclear Research (CERN)
• International Conference Volunteers (ICV)
• Informaticiens sans Frontières (ISF)
• Swiss Tropical Institute (STI)
• University of Geneva, Computer Science Dept.
• World Health Organisation (WHO)
• Associated Partners
• Agence Universitaire de la Francophonie (AUF)
• Erasmus University Medical Center, The
  Netherlands
• SACEMA, Stellenbosch University, South Africa
• African Institute for Mathematical Sciences,
  Muisenberg, South Africa
• University of Bamako, Mali
• University of Dakar, Senegal
• University of Yaoundé, Cameroon
• Sponsor
• Geneva International Academic Network (GIAN)