Open source tools and standardized data in cancer systems biology

Macklin, Paul; Friedman, Samuel H.

doi:10.1101/244319

Cited by 6 publications

(16 citation statements)

References 30 publications

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“…Single-cell systems biology has already shown the enabling role of stable data standards [29]: once SBML crystallized as a stable data language, a rich and growing ecosystem of data-compatible simulation and analysis software emerged. Multicellular systems biology has not yet reached this point: most computational models have custom configuration and output formats, sometimes with customized extensions of SBML to represent single-cell systems biology [18].…”

Section: Key Challengesmentioning

confidence: 99%

Key challenges facing data-driven multicellular systems biology

Macklin

2019

GigaScience

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Increasingly sophisticated experiments, coupled with large-scale computational models, have the potential to systematically test biological hypotheses to drive our understanding of multicellular systems. In this short review, we explore key challenges that must be overcome to achieve robust, repeatable data-driven multicellular systems biology. If these challenges can be solved, we can grow beyond the current state of isolated tools and datasets to a community-driven ecosystem of interoperable data, software utilities, and computational modeling platforms. Progress is within our grasp, but it will take community (and nancial) commitment.

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Section: Key Challengesmentioning

confidence: 99%

Key challenges facing data-driven multicellular systems biology

Macklin

2019

GigaScience

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“…X-Ray reconstruction of Moving Morphology is one of the advancement in biomechanical software that utilizes static bone shape data from CT scan along with motion data that are obtained from X-ray videos. XROMM software are not only limited for studying motion within human systems [15]. They have been applied to study morphological and mechanical movements within reptiles, fishes and even arthropods.…”

Section: Development Of Motion Analysis Softwarementioning

confidence: 99%

“…Marker based XROMM requires additional software that are required for correction of distortions created by fluoroscopic image intensifier and calibrating cameras [15]. In addition, tracking of radio markers and calculation of rigid body motion poses to be problematic for the researchers.…”

Section: Development Of Motion Analysis Softwarementioning

confidence: 99%

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Optimization of the Application Software in Biomechanics and Their Contribution to The Biological Field

Daoud¹,

Ghadi²,

Almimi³

2019

JESTR

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Biomechanics refers to study of movement within dynamic biological systems. Advancement of computer software technologies such as JAVA language leads to combine stimuli and signals by biological systems and utilize them for research purposes. The main aim of this research is to analyse various biomechanical software and advancements that have been made in the field of mechanical software. Secondary research analysis has been utilized within this research paper. A Number of computational software such as OpenSim and ABAQUS have been proven to be very beneficial in this aspect. Advancement in biomechanical software has led to better research in cancer and cytoskeletal studies. Thus, Biomechanical software enables us to study kinetics of body without invasive procedures and does not cause any hindrance to ethical issues.

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“…, 2018 ), using their minimal reporting requirements ( Rigano and De Castillia, 2017 ). Efforts have been also made in the arena of mathematical modeling ( Macklin and Friedman, 2018 ), for example, Multi Cellular Data Standard, a new data format for multicellular data ( Friedman et al. , 2016 ).…”

Section: Barriers and Solutions Toward Open Cell Image Datamentioning

confidence: 99%

Sharing and reusing cell image data

Zaritsky

2018

MBoC

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The rapid growth in content and complexity of cell image data creates an opportunity for synergy between experimental and computational scientists. Sharing microscopy data enables computational scientists to develop algorithms and tools for data analysis, integration, and mining. These tools can be applied by experimentalists to promote hypothesis-generation and discovery. We are now at the dawn of this revolution: infrastructure is being developed for data standardization, deposition, sharing, and analysis; some journals and funding agencies mandate data deposition; data journals publish high-content microscopy data sets; quantification becomes standard in scientific publications; new analytic tools are being developed and dispatched to the community; and huge data sets are being generated by individual labs and philanthropic initiatives. In this Perspective, I reflect on sharing and reusing cell image data and the opportunities that will come along with it.

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Open source tools and standardized data in cancer systems biology

Cited by 6 publications

References 30 publications

Key challenges facing data-driven multicellular systems biology

Key challenges facing data-driven multicellular systems biology

Optimization of the Application Software in Biomechanics and Their Contribution to The Biological Field

Sharing and reusing cell image data

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