# Presentation: 591915

## Architecture Workspace

- R. Michael Townsend, Ph.D.
- Director of Information Technology
- Cold Spring Harbor Laboratory

## Architecture Workspace

- How to establish a common cross-institutional data and analysis sharing architecture?

-  What do we NEED to share?
-  What do we WANT to share?
-  CAN we share?
-  WILL we share?
-  What is the SCOPE OF THINGS to share?

## Architecture Workspace

-  What do we NEED to share?
- Common semantics, data representations, access and transport mechanisms
-  What do we WANT to share?
- Locally developed databases, applications, bioinformatics portal, communications, preliminary data, ...

## Architecture Workspace

- CAN we share?
- With some translation and/or faith, currently:  “sometimes yes”.
- WILL we share?
- YES, tempered with bandwidth (both machine and human) and written/unwritten rules.
-  What is the SCOPE OF THINGS to share?
- The sum of what we NEED and WANT to share.

## Architecture Workspace

- 		How to proceed?
- Interoperate among existing architectures
- Build a simplified architecture that everyone uses
- Do both

## Architecture Workspace

- Comparison IT @ CSHL:
-  Hardware environment:
- Sun, Dell, IBM, Apple,VA-Linux, PSSC Labs, Compaq, Rackable Systems, Penguin, Aberdeen, Overland, etc.
-  Operating environment:
- Windows, MacOS, Linux, Solaris, Irix
-  Software environment:
- commercial, open source, and home grown

## Architecture Workspace

-  Computing paradigms:
- client only, client-server, server (batch); scalar & parallel
-  Network:
- Cisco, BayNetworks, Coyote, Kentrox, NetGear, SynOptics, 3Com, Lucent, Adtran, etc.
- LAN– fiber, T1, microwave, mostly Gbit inter-building, 100Mbit to desktop
- WAN– 18Mbit

## Architecture Workspace

-  Requirements:
- increase/improve everything, and of course keep costs down 
-  In progress:
- Shift to blade based environments (e.g. IBM w/ Linux and Windows)
- Increase bandwidth to both LAN and WAN

## Architecture Workspace

- Excerpts from CSHL researchers

## Architecture Workspace

- The goal of making data and the results of the analyses of data available to a network of cancer centers would require common or at least compatible formats and database structures.

## Architecture Workspace

- It would be nice if NCI can support a network of computational facilities among different institutions and establish a virtual database/analysis tool resource linked/contributed from these cancer centers. It would need a common interface and protocol specifications so that a user would not have to care about where and how to get each individual dataset/tool. It would also allow each institution to make their unique contribution under this unified framework. And each institution's website would have one part that's open to the world and another that's open to the intranet.

## Architecture Workspace

- I believe that providing incentives for researchers to share their data and analysis is critical to the success of such an undertaking. This is because, in free societies, it is really impossible to implement something without some kind of motivation. The business community is a good place to look at how to provide incentives, as people will only purchase a product if it’s in their own interest to do so. A business thus needs to come up with a workable strategy on how to create a viable product and to get people to buy into that product of their own free will. As the main government agency promoting cancer research, I believe that it's the NCI's responsibility to set up a viable model for data and analysis sharing in such a way as to provide strong incentives for researchers to buy into this agenda.  Three primary incentives for researchers are, of course, funding, publications, and (in my view most importantly) biomedical discoveries. Right now sharing data and results prematurely may only hurt one's chances of publishing them or of getting credit for one's discoveries.  I might suggest that the NCI set up a prepublication site where one's results could be deposited pending peer review and formal journal publication. This would allow a research group to stake a claim on a specific discovery before it is formally published so that they might feel freer about releasing their data and results in a public database earlier rather than later. This sort of prepublication of technical reports is common in the CS, math and physics communities, but is pretty much unheard of among biologists. This would clearly involve IT issues. Similarly, NCI might try to foster more collaboration between centers, as collaborators (unlike competitors) are more willing to share information with each other. If two groups are working on nearly the same problem, however, such collaborations are probably impossible.

## Architecture Workspace

- The future will depend heavily on semantic representations of biological data, and will be characterized by data-heavy messages that are exchanged in a many-to-many fashion.  We will need to develop a set of shared representations of biological data including, but not limited to genome coordinates, genome assemblies, protein identifiers, sequence identifiers, descriptions of macromolecular complexes, descriptions of pathways, cell anatomy, tissue anatomy, developmental stages, and physiological states.  These representations must not be static, but must be flexible to allow for ad hoc extensions by groups that wish to play with, extend, and modify the protocols without violating the integrity of the semantic core.  I think we are talking about a semantic web here, perhaps one based on RDF, OWL, or one of the other semantic languages.  Possibly we are talking about web services, but I like the dominant form of web services, SOAP, less and less as I work with it.

## Architecture Workspace

- So where does this lead us?

## Architecture Workspace

- Key architectural features:
-  Web based
- semantic?  XML, RDF, OWL, SOAP, ...
-  Data normalization
- disparity in vocabulary, scales, and categorizations
-  Extensibility
- technology or the quest for knowledge will drive change; revisit charter

## Architecture Workspace

- Key architectural features:
-  Interoperability
- browsers, operating and programming environments, mode (e.g. accommodate batch?)
-  Scalability
- usage and  data size
-  Communication
- monitored, adjustable, efficient, I2, NLR, ‘local’ network consortia

## Architecture Workspace

- Key architectural features:
-  Security
- authorization, authentication, access
-  Topology
- CONSTRAINTS?
-  “Business Continuity”
-  Promotion
- consultation, support, and documentation; incentives?

## Architecture Workspace

- Possible solution?
- Semantic Web, based on Resource Description Framework (RDF), using XML as an interchange syntax and URIs for naming.

## THANK YOU

- Architecture Workspace

- THANK YOU