HPC and Grid Computing for Integrative Biomedical Research

Integrative biomedical research projects query, analyze, and integrate many different data types and make use of datasets obtained from measurements or simulations of structure and function at multiple biological scales. With the increasing availability of high-throughput and high-resolution instruments, the integrative biomedical research imposes many challenging requirements on software middleware systems. In this paper, we look at some of these requirements using example research pattern templates. We then discuss how middleware systems, which incorporate Grid and high-performance computing, could be employed to address the requirements.

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A microfluidic platform for lifelong high-resolution and high throughput imaging of subtle aging phenotypes in C. elegans

Lab on a Chip ◽

10.1039/c8lc00655e ◽

2018 ◽

Vol 18 (20) ◽

pp. 3090-3100 ◽

Cited By ~ 10

Author(s):

Sahand Saberi-Bosari ◽

Javier Huayta ◽

Adriana San-Miguel

Keyword(s):

High Resolution ◽

High Throughput ◽

Structure And Function ◽

Neuronal Structure ◽

Microfluidic Platform ◽

C Elegans ◽

And Function ◽

High Throughput Imaging

Aging produces a number of changes in the neuronal structure and function throughout a variety of organisms.

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Crystal Structures of Fragments D and Double-D from Fibrinogen and Fibrin

Thrombosis and Haemostasis ◽

10.1055/s-0037-1615842 ◽

1999 ◽

Vol 82 (08) ◽

pp. 271-276 ◽

Cited By ~ 8

Author(s):

Glen Spraggon ◽

Stephen Everse ◽

Russell Doolittle

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

Crystal Structures ◽

Structure And Function ◽

X Ray ◽

Long Period ◽

And Function

IntroductionAfter a long period of anticipation,1 the last two years have witnessed the first high-resolution x-ray structures of fragments from fibrinogen and fibrin.2-7 The results confirmed many aspects of fibrinogen structure and function that had previously been inferred from electron microscopy and biochemistry and revealed some unexpected features. Several matters have remained stubbornly unsettled, however, and much more work remains to be done. Here, we review several of the most significant findings that have accompanied the new x-ray structures and discuss some of the problems of the fibrinogen-fibrin conversion that remain unresolved. * Abbreviations: GPR—Gly-Pro-Arg-derivatives; GPRPam—Gly-Pro-Arg-Pro-amide; GHRPam—Gly-His-Arg-Pro-amide

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Ion beams as high-resolution probes of structure and function

Nuclear Instruments and Methods in Physics Research Section B Beam Interactions with Materials and Atoms ◽

10.1016/0168-583x(92)95491-9 ◽

1992 ◽

Vol 64 (1-4) ◽

pp. 342-348 ◽

Cited By ~ 2

Author(s):

G.J.F. Legge ◽

A. Saint ◽

G. Bench ◽

J. Laird ◽

M. Cholewa

Keyword(s):

High Resolution ◽

Ion Beams ◽

Structure And Function ◽

And Function

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Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers

Cold Spring Harbor Perspectives in Biology ◽

10.1101/cshperspect.a032300 ◽

2018 ◽

Vol 11 (10) ◽

pp. a032300 ◽

Cited By ~ 5

Author(s):

Sarah K. Denny ◽

William J. Greenleaf

Keyword(s):

High Throughput ◽

Structure And Function ◽

Massively Parallel ◽

Sequence Structure ◽

Rna Sequence ◽

And Function

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Detection of Small-Molecule Modulators of Actin-Myosin Structure and Function using High-Throughput Time-Resolved FRET

Biophysical Journal ◽

10.1016/j.bpj.2016.11.1297 ◽

2017 ◽

Vol 112 (3) ◽

pp. 237a

Author(s):

Piyali Guhathakurta ◽

Ewa Prochniewicz ◽

Kurt C. Peterson ◽

Benjamin D. Grant ◽

Gregory D. Gillispie ◽

...

Keyword(s):

Small Molecule ◽

High Throughput ◽

Structure And Function ◽

Throughput Time ◽

Time Resolved ◽

Small Molecule Modulators ◽

And Function

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The evolution of air-breathing respiratory faculties in craniotes

Respiratory Biology of Animals ◽

10.1093/oso/9780199238460.003.0015 ◽

2019 ◽

pp. 177-191

Author(s):

Steven F. Perry ◽

Markus Lambertz ◽

Anke Schmitz

Keyword(s):

High Performance ◽

Body Wall ◽

Structure And Function ◽

Control Of Breathing ◽

Body Wall Muscle ◽

Positive Pressure ◽

Limiting Factor ◽

Swim Bladder ◽

Body Wall Musculature ◽

And Function

The origin of lungs from a swim bladder, swim bladder from lungs, or both from a relatively undifferentiated respiratory pharynx remains unresolved. Once present, the lungs can be ventilated by a positive-pressure buccal pump, which can be easily derived from the gill ventilation sequence in a lungfish, or by negative-pressure aspiration. Although aspiration breathing is characteristic of amniotes, it has also been observed in a lungfish and body wall muscle contraction in response to respiratory stimuli has even been reported in lamprey larvae. The hypaxial body wall musculature used for aspiration breathing is also necessary for locomotion in most amniotes, just when respiratory demand is greatest. This paradox, called Carrier’s constraint, is a major limiting factor in the evolution of high-performance faculties, and the evolution of anatomical and physiological specializations that circumvent it characterize most major amniote groups. Serendipitous combinations have resulted in evolutionary cascades and high-performance groups such as birds and mammals. Complementing evolution are the capacities for acclimatization and adaptation not only in the structure and function of the gas exchanger, but also in the control of breathing and the composition of the blood.

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Facilitating and Augmenting Collaboration in the Biomedical Domain

International Journal of Systems Biology and Biomedical Technologies ◽

10.4018/ijsbbt.2012010105 ◽

2012 ◽

Vol 1 (1) ◽

pp. 52-65 ◽

Cited By ~ 2

Author(s):

Nikos Karacapilidis ◽

Manolis Tzagarakis ◽

Spyros Christodoulou ◽

Georgia Tsiliki

Keyword(s):

High Performance ◽

Large Data ◽

Biomedical Domain ◽

Data Types ◽

Processing Technologies ◽

Data Intensive ◽

Decision Points ◽

Manageable Level ◽

Performance Computing ◽

Associated Data

This paper reports on a Web 2.0 tool that aims to facilitate and augment collaboration and decision making in data-intensive and cognitively-complex biomedical settings. The proposed tool exploits prominent high-performance computing paradigms and large data processing technologies to meaningfully search, analyze and aggregate data existing in diverse, extremely large and rapidly evolving sources. It can be viewed as an innovative workbench incorporating and orchestrating a set of interoperable services that reduce the data-intensiveness and complexity overload at critical decision points to a manageable level, thus permitting stakeholders to be more productive and concentrate on creative activities. Through a particular collaboration scenario, we explore various possibilities and challenges of managing biomedical collaboration with the use of the proposed tool. Much attention is given at the increase of volume, rate of production and complexity of the associated data types.

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