Cloud Computing Considerations for Biomedical Applications

Author(s):  
Richard Rauscher
Author(s):  
Nicoletta Dessì ◽  
Barbara Pes

Bioinformatics traditionally concerns applying computational approaches for the management and the exploitation of large volumes of biomedical data that continues to expand in size and in distribution. Although the application of cloud computing in biomedical areas is still preliminary, an increasing number of biomedical applications rely on the Cloud for processing large datasets. This chapter investigates the extent to which cloud technology offers a viable platform for developing and deploying applications that support users in searching and integrating information offered by bioinformatics resources. The chapter outlines the basic features that such computing applications should exhibit and the challenging issues they deal with. The architecture and the functionality of the cloud-based environments are presented to stress how cloud platforms could offer added-value service components and flexibility that make their adoption attractive for bioinformatics.


Author(s):  
Nicoletta Dessì ◽  
Barbara Pes

Bioinformatics traditionally concerns applying computational approaches for the management and the exploitation of large volumes of biomedical data that continues to expand in size and in distribution. Although the application of cloud computing in biomedical areas is still preliminary, an increasing number of biomedical applications rely on the Cloud for processing large datasets. This chapter aims investigating the extent to which cloud technology offers a viable platform for developing and deploying applications that support users in searching and integrating information offered by bioinformatics resources. The chapter outlines the basic features that such computing applications should exhibit and the challenging issues they deal with. The architecture and the functionality of the cloud-based environments are presented to stress how cloud platforms could offer added-value service components and flexibility that make their adoption attractive for bioinformatics.


2018 ◽  
Vol 2018 ◽  
pp. 1-17
Author(s):  
Ahmed Abdulhakim Al-Absi ◽  
Najeeb Abbas Al-Sammarraie ◽  
Wael Mohamed Shaher Yafooz ◽  
Dae-Ki Kang

MapReduce is the preferred cloud computing framework used in large data analysis and application processing. MapReduce frameworks currently in place suffer performance degradation due to the adoption of sequential processing approaches with little modification and thus exhibit underutilization of cloud resources. To overcome this drawback and reduce costs, we introduce a Parallel MapReduce (PMR) framework in this paper. We design a novel parallel execution strategy of Map and Reduce worker nodes. Our strategy enables further performance improvement and efficient utilization of cloud resources execution of Map and Reduce functions to utilize multicore environments available with computing nodes. We explain in detail makespan modeling and working principle of the PMR framework in the paper. Performance of PMR is compared with Hadoop through experiments considering three biomedical applications. Experiments conducted for BLAST, CAP3, and DeepBind biomedical applications report makespan time reduction of 38.92%, 18.00%, and 34.62% considering the PMR framework against Hadoop framework. Experiments' results prove that the PMR cloud computing platform proposed is robust, cost-effective, and scalable, which sufficiently supports diverse applications on public and private cloud platforms. Consequently, overall presentation and results indicate that there is good matching between theoretical makespan modeling presented and experimental values investigated.


2011 ◽  
Vol 23 (17) ◽  
pp. 2338-2354 ◽  
Author(s):  
Thilina Gunarathne ◽  
Tak-Lon Wu ◽  
Jong Youl Choi ◽  
Seung-Hee Bae ◽  
Judy Qiu

Author(s):  
T. L. Hayes

Biomedical applications of the scanning electron microscope (SEM) have increased in number quite rapidly over the last several years. Studies have been made of cells, whole mount tissue, sectioned tissue, particles, human chromosomes, microorganisms, dental enamel and skeletal material. Many of the advantages of using this instrument for such investigations come from its ability to produce images that are high in information content. Information about the chemical make-up of the specimen, its electrical properties and its three dimensional architecture all may be represented in such images. Since the biological system is distinctive in its chemistry and often spatially scaled to the resolving power of the SEM, these images are particularly useful in biomedical research.In any form of microscopy there are two parameters that together determine the usefulness of the image. One parameter is the size of the volume being studied or resolving power of the instrument and the other is the amount of information about this volume that is displayed in the image. Both parameters are important in describing the performance of a microscope. The light microscope image, for example, is rich in information content (chemical, spatial, living specimen, etc.) but is very limited in resolving power.


Author(s):  
Philippe Fragu

The identification, localization and quantification of intracellular chemical elements is an area of scientific endeavour which has not ceased to develop over the past 30 years. Secondary Ion Mass Spectrometry (SIMS) microscopy is widely used for elemental localization problems in geochemistry, metallurgy and electronics. Although the first commercial instruments were available in 1968, biological applications have been gradual as investigators have systematically examined the potential source of artefacts inherent in the method and sought to develop strategies for the analysis of soft biological material with a lateral resolution equivalent to that of the light microscope. In 1992, the prospects offered by this technique are even more encouraging as prototypes of new ion probes appear capable of achieving the ultimate goal, namely the quantitative analysis of micron and submicron regions. The purpose of this review is to underline the requirements for biomedical applications of SIMS microscopy.Sample preparation methodology should preserve both the structural and the chemical integrity of the tissue.


Author(s):  
J. D. Shelburne ◽  
Peter Ingram ◽  
Victor L. Roggli ◽  
Ann LeFurgey

At present most medical microprobe analysis is conducted on insoluble particulates such as asbestos fibers in lung tissue. Cryotechniques are not necessary for this type of specimen. Insoluble particulates can be processed conventionally. Nevertheless, it is important to emphasize that conventional processing is unacceptable for specimens in which electrolyte distributions in tissues are sought. It is necessary to flash-freeze in order to preserve the integrity of electrolyte distributions at the subcellular and cellular level. Ideally, biopsies should be flash-frozen in the operating room rather than being frozen several minutes later in a histology laboratory. Electrolytes will move during such a long delay. While flammable cryogens such as propane obviously cannot be used in an operating room, liquid nitrogen-cooled slam-freezing devices or guns may be permitted, and are the best way to achieve an artifact-free, accurate tissue sample which truly reflects the in vivo state. Unfortunately, the importance of cryofixation is often not understood. Investigators bring tissue samples fixed in glutaraldehyde to a microprobe laboratory with a request for microprobe analysis for electrolytes.


Author(s):  
Yasushi P. Kato ◽  
Michael G. Dunn ◽  
Frederick H. Silver ◽  
Arthur J. Wasserman

Collagenous biomaterials have been used for growing cells in vitro as well as for augmentation and replacement of hard and soft tissues. The substratum used for culturing cells is implicated in the modulation of phenotypic cellular expression, cellular orientation and adhesion. Collagen may have a strong influence on these cellular parameters when used as a substrate in vitro. Clinically, collagen has many applications to wound healing including, skin and bone substitution, tendon, ligament, and nerve replacement. In this report we demonstrate two uses of collagen. First as a fiber to support fibroblast growth in vitro, and second as a demineralized bone/collagen sponge for radial bone defect repair in vivo.For the in vitro study, collagen fibers were prepared as described previously. Primary rat tendon fibroblasts (1° RTF) were isolated and cultured for 5 days on 1 X 15 mm sterile cover slips. Six to seven collagen fibers, were glued parallel to each other onto a circular cover slip (D=18mm) and the 1 X 15mm cover slip populated with 1° RTF was placed at the center perpendicular to the collagen fibers. Fibroblast migration from the 1 x 15mm cover slip onto and along the collagen fibers was measured daily using a phase contrast microscope (Olympus CK-2) with a calibrated eyepiece. Migratory rates for fibroblasts were determined from 36 fibers over 4 days.


2021 ◽  
Author(s):  
Jintong Liu ◽  
Jing Huang ◽  
Lei Zhang ◽  
Jianping Lei

We review the general principle of the design and functional modulation of nanoscaled MOF heterostructures, and biomedical applications in enhanced therapy.


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