Towards high-throughput structure determination at SSRL

Ashley DeaconStanford Synchrotron Radiation Laboratory

Motivation for high-throughput structure determination

BL 11-1 Stanford/TSRI/SSRL Monochromatic

BL 9-2 Multi-wavelength BL 7-1

Monochromatic

BL 1-5 Multi-wavelength

BL 9-1 Monochromatic

Five macromolecularcrystallography beamlines in

operation (including 11-1).

SPEAR 3 upgrade of storage ring to 3rd generation capabilities

by 2003

SMB user program Structural genomics

Solve hundreds of structure per year without relying on many

crystallographers

High-throughput goals

• Automate the crystallography experiment New hardware (e.g. crystal mounting robot) Rapid crystal characterization Optimal data collection from best crystals

• Automate crystallographic computations Include latest crystallographic techniques Route data through an analysis pipeline Evaluate progress of structure determination

• Integrate the experiment and the analysis Feedback to the diffraction experiment. Feedback to the other core groups.

• Develop the Automated Structural Analysis of Proteins (ASAP) system Integrate SDC with the SMB program. Staged delivery of useful components.

Paul Phizackerley P34, Ana Gonzalez P30, Aina Cohen P27

Aina Cohen P27, Hsiu-Ju Chiu P33Thomas Eriksson P29, Scott McPhillips P32

Paul Ellis P12

The world of crystallography according to Ashley (pre-JCSG) I

Data Collection

LocateHeavyAtoms

SolveStructure

ModelBuilding

Model Refinement

SSRL Mosflm SnB Mlphare warpNtrace XPLOR ???

What do I do if this approach fails?

What if that fails?

Re-run programs with modified parameters

Slow trial-and-error process

Not very systematic

DataProcessing

The world of crystallography according to Ashley (pre-JCSG) II

Energy Barrier

• Consult the literature Discover the “Golden Bullet”. Learn new applications.

• Consult colleagues Borrow scripts. Try out suggestions.

• Problems and bottlenecks… Slow learning process. Cannot systematically try all applications / possibilities. Rely on hearsay.

The world of crystallography according to Ashley (pre-JCSG) III

Data Collection

DataProcessing

LocateHeavyAtoms

SolveStructure

ModelBuilding

Model Refinement

SSRL

Mosflm

SnB

Mlphare warpNtrace XPLOR

DataProcessing

LocateHeavyAtoms

SolveStructure

DENZO SHELX SHARP

LocateHeavyAtoms

SnB

• Still have problems Limited experience Not systematic.

Ashley Frank

Tassos

Duncan

Gerard

Glen

The world of crystallography according to ASAP I

The world of crystallography according to ASAP II

OperationManager

Operations

• The Operation Managerallows Single-click execution of

Operations. Standardized file input and

output to all Operations. A common communication

protocol to Operations for developers via an API and Library.

JCSG staff

The world of crystallography according to ASAP III

SchedulerMarket-based resource allocation

Operation

Manager

JCSG Staff and Scripted Operations

Operation

Manager

• The Scheduler supports Multiple Operation

Managers. Distribution of resources

to multiple projects. Efficient use of all

resources.

The world of crystallography according to ASAP IV

SchedulerMarket-based resource allocation

Operation

Manager

Operation

Manager

SolverRules-based execution

of a project

• Dynamic rules-based Solver Modify rules on the fly to

reflect knowledge accumulated from all projects.

Take all characteristics of the current project into account when interpreting rules.

• Static rules-based Solver An “if…then…else…”

approach. All decisions must be

preprogrammed. Hard to take all factors

into account. Nothing learnt from

past operations.

The world of crystallography according to ASAP V

Inputs Outputs

InputAttributes

OutputAttributes

• Operations Can be connected together as

defined by the inputs they require and the outputs they produce.

Can incorporate some internal feedback and intelligence to make them smart.

An ASAP Operation

• Attributes Describe the inputs and outputs

of an operation.

Correlations between the attributes can be used to generate rules, which can guide the Solvers.

The world of crystallography according to ASAP VI

• Build a graph of Operations

• Traverse the graph by the most efficient route or try many routes and choose the best results

The world of crystallography according to ASAP VII

SchedulerMarket-based resource allocation

Operation

Manager

SolverRules-based execution of a project

Data MinerDerives rules for the Solver

Feedback to Solver

A production ASAP system

SchedulerMarket-based resource allocation

Operation

Manager

SolverRules-based execution of a project Data Miner

Derives rules for the Solver

System State DatabaseStores past operations

• System State Database will Store file locations and all

Attributes derived from past operations for Data Miner.

Track progress of all crystals relating to each target protein.

ASAP – Summary

• The ASAP architecture is

Capable of parallel operation on multiple samples within a project Capable of parallel operation on multiple projects Flexible and modular in design Scalable in both hardware and software Maintainable Testable

• The ASAP staged-delivery will

Provide a series of useful systems that gradually improve throughput. Ultimately lead to a fully automated production system.

Acknowledgements

• The entire SMB group at SSRL Fred Bertsch Tim McPhillips Peter Kuhn

• GNF Glen Spraggon

• The Scripps Research Institute Frank von Delft

• Syrrx Duncan McRee

SSRL is funded by:SSRL is funded by:

Department of Energy, Office of Basic Energy Department of Energy, Office of Basic Energy Sciences,Sciences,

The Structural Molecular Biology Program is supported The Structural Molecular Biology Program is supported by:by:

National Institutes of Health, National Center for National Institutes of Health, National Center for Research Resources, Biomedical Technology Program Research Resources, Biomedical Technology Program

and Department of Energy, Office of Biological and and Department of Energy, Office of Biological and Environmental Research.Environmental Research.