First results

1

• First results infrastructure needs
• IST-2001-38344

2
Technology challenges in building bioGrid

• Computational complexity
• Generating protein interaction map takes ca. 1
  day.
• Analysing large sets of gene expression data can
  take up to an hour.
• Analysis of large text bodies complex.
• Semantic Complexity
• Computer does not understand data.
• DBs and systems cannot inter-operate.

3
Distributed GoPubMed-D (2/3)
BioGrid Prototype integrates with GoPubMed-D via
embedded Prova-AA JADE agent.
4
Distributed computation with Prova-AA agents

• A flexible solution for a self-managing
  self-balancing distributed computation
• Manager and Workers architecture based on
  Prova-AA agents with Java computation modules.
• Loosely synchronous interaction.
• Minimal compact coding (30 lines for Manager and
  20 lines for Worker).
• Manager does not need to keep a registry of the
  Workers that can join in at any time.
• Computation is divided in small atomic subtasks
  (4 or 5 proteins).
• Manager dispatches a new subtask asynchronously
  upon receiving a ready message from a Worker.
• Worker computes a subtask and responds with the
  results in a reply message and a new ready
  message.
• Workers compute subtasks at their own pace so
  load balancing is automatic.
• Workers extended with routing capabilities are
  available.
• Can be easily extended with failover
  capabilities.

5
Building an information system for biology is
non-trivial

• Molecular biology resources
• Are heterogeneous in content
• Genomics, proteomics, literature.
• Exist in a large number
• Public, commercial, organisational, personal.
• Variable quality Curated vs. automatic.
• Have different interfaces Web, SQL, SOAP, etc.
• Are geographically distributed w/o yellow pages.
• Store data in different formats - few standards.
• Change rapidly.
• Confidentiality IPR protection.
• Are too large to transport conveniently.

6
Social challenges in building Grid

• Technology stability reliability.
• Security.
• Usability.
• Peer-reviewed results in major biomedical
  journals
• Science, Nature, Cell, BMJ, Lancet, etc.