Table 6. Computing Roadmap: Facility for Characterization and Imaging of Molecular Machines

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Table 6. Computing Roadmap: Facility for Characterization and Imaging
of Molecular Machines (acronyms)

Topic	Research, Design, and Development	Demonstration: Pilots and Modular Deployment	Integration and Production Deployment
LIMS and Workflow Management Participate in GTL cross-facility LIMS working group	Available LIMS technologies Process description for LIMS system Crosscutting research into global workflow management systems Approaches to guiding experiment-based production protocols to optimize protein production	Prototype molecular machine characterization LIMS system* Characterization design strategy Workflow management for identification and characterization Workflow process simulation	Molecular machines LIMS and workflow system Workflow integrated with other GTL facilities and experimental strategy system
Data Capture and Archiving Participate in GTL cross-facility working group for data representation and standards	Data-type models* Technologies for large-scale storage and retrieval Preliminary designs for databases	Prototype storage archives Prototype user-access environments	Archives for key large-scale data types* Archives linked to community databases and other GTL data resources GTL Knowledgebase feedback
Data Analysis and Reduction Participate in GTL cross-facility working group for data analysis and reduction	Algorithmic methods for various modalities* Grid and high-performance algorithm codes Design for tools library Approaches for automated image interpretation in confocal light microscopy and FRET	Prototype visualization methods and characterization tools library* Prototype grid for data analysis, with partners Prototypes for automated image interpretation in confocal light microscopy/FRET Analysis tools linked to data archives	Production-analysis pipeline for various modalities* on grid and HP platforms Automated image interpretation in confocal light microscopy, FRET Repository production-analysis codes Analysis tools pipeline linked to end-user problem-solving environments
Modeling and Simulation Participate in GTL cross-facility working group for modeling and simulation	Technologies for: Fixed and flexible docking and constrained molecular dynamics Low-resolution cryoEM data modeling and reconstruction Reconstruction of protein interaction and regulatory networks Multiscale stochastic and differential equation network models	Automated production pipeline (experimentally guided molecular docking and machine dynamics; efficient modeling methods for 3D CryoEM data reconstruction) Mature methods for reconstructing protein-interaction and regulatory networks	Production pipeline and end-user interfaces for genome-scale fold prediction Production codes for scattering-data modeling
Community Data Resource Participate in GTL cross-facility working group for serving community data	Data-modeling representations and design for databases: Protein machine catalog, protein machines models and simulations, interaction network models and simulations, protein machine methods and protocols	Prototype database End-user query and visualization environments Integration of databases with other GTL resources	Production databases and mature end-user environments Integration with other GTL resources and community protein-data resources
Computing Infrastructure Participate in GTL crosscutting working group for computing infrastructure	Analysis, storage, and networking requirements for Molecular Machines Facility Grid and high-performance approaches for large-scale data analysis for MS and image data; requirements established	Hardware solutions for large-scale archival storage Networking requirements for large-scale grid-based MS and image data analysis	Production-scale computational analysis systems Web server network for data archives and workflow systems Servers for community data archive databases

Topic

Research, Design,
and Development

Demonstration:
Pilots and Modular Deployment

Integration and Production Deployment

LIMS and Workflow Management

Participate in GTL cross-facility LIMS working group

Available LIMS technologies

Process description for LIMS system

Crosscutting research into global workflow management systems

Approaches to guiding experiment-based production protocols to optimize protein production

Prototype molecular machine characterization LIMS system*

Characterization design strategy

Workflow management for identification and characterization

Workflow process simulation

Molecular machines LIMS and workflow system

Workflow integrated with other GTL facilities and experimental strategy system

Data Capture and Archiving

Participate in GTL cross-facility working group for data representation and standards

Data-type models*

Technologies for large-scale storage and retrieval

Preliminary designs for databases

Prototype storage archives

Prototype user-access environments

Archives for key large-scale data types*

Archives linked to community databases and other GTL data resources

GTL Knowledgebase feedback

Data Analysis and Reduction

Participate in GTL cross-facility working group for data analysis and reduction

Algorithmic methods for various modalities*

Grid and high-performance algorithm codes

Design for tools library

Approaches for automated image interpretation in confocal light microscopy and FRET

Prototype visualization methods and characterization tools library*

Prototype grid for data analysis, with partners

Prototypes for automated image interpretation in confocal light microscopy/FRET

Analysis tools linked to data archives

Production-analysis pipeline for various modalities* on grid and HP platforms

Automated image interpretation in confocal light microscopy, FRET

Repository production-analysis codes

Analysis tools pipeline linked to end-user problem-solving environments

Modeling and Simulation

Participate in GTL cross-facility working group for modeling and simulation

Technologies for:

Fixed and flexible docking and constrained molecular dynamics

Low-resolution cryoEM data modeling and reconstruction

Reconstruction of protein interaction and regulatory networks

Multiscale stochastic and differential equation network models

Automated production pipeline (experimentally guided molecular docking and machine dynamics; efficient modeling methods for 3D CryoEM data reconstruction)

Mature methods for reconstructing protein-interaction and regulatory networks

Production pipeline and end-user interfaces for genome-scale fold prediction

Production codes for scattering-data modeling

Community Data Resource

Participate in GTL cross-facility working group for serving community data

Data-modeling representations and design for databases: Protein machine catalog, protein machines models and simulations, interaction network models and simulations, protein machine methods and protocols

Prototype database

End-user query and visualization environments

Integration of databases with other GTL resources

Production databases and mature end-user environments

Integration with other GTL resources and community protein-data resources

Computing Infrastructure

Participate in GTL crosscutting working group for computing infrastructure

Analysis, storage, and networking requirements for Molecular Machines Facility

Grid and high-performance approaches for large-scale data analysis for MS and image data; requirements established

Hardware solutions for large-scale archival storage

Networking requirements for large-scale grid-based MS and image data analysis

Production-scale computational analysis systems

Web server network for data archives and workflow systems

Servers for community data archive databases

* Data types and modalities include MS, NMR, neutron scattering, X-ray, confocal microscopy, cryoEM, and process metadata. Large-scale experimental data results are linked with genome data, and feedback is provided to GTL Knowledgebase.

U.S. Department of Energy Office of Science

Genomics:GTL