SPV: a JavaScript Signaling Pathway Visualizer

Calderone, Alberto

doi:10.1093/bioinformatics/bty188

Cited by 9 publications

(4 citation statements)

References 17 publications

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“…Cell–cell interaction graphs are laid out with cytoscape.js (Franz et al, 2016), a graph library written in JavaScript that allows the assembly of graphs based on entity nodes (cells and proteins) and edges (interactions among entities), including annotations for nodes and edges. Molecular interactions are displayed via the SIGNOR graph viewer (Calderone and Cesareni, 2018), which allows a compartmental visualization of molecular entities as a signed directed graph.…”

Section: Methodsmentioning

confidence: 99%

Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration

et al. 2019

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Muscle regeneration is a complex process governed by the interplay between several muscle-resident mononuclear cell populations. Following acute or chronic damage these cell populations are activated, communicate via cell-cell interactions and/or paracrine signals, influencing fate decisions via the activation or repression of internal signaling cascades. These are highly dynamic processes, occurring with distinct temporal and spatial kinetics. The main challenge toward a system level description of the muscle regeneration process is the integration of this plethora of inter-and intracellular interactions. We integrated the information on muscle regeneration in a web portal. The scientific content annotated in this portal is organized into two information layers representing relationships between different cell types and intracellular signalinginteractions, respectively. The annotation of the pathways governing the response of each cell type to a variety of stimuli/perturbations occurring during muscle regeneration takes advantage of the information stored in the SIGNOR database. Additional curation efforts have been carried out to increase the coverage of molecular interactions underlying muscle regeneration and to annotate cell-cell interactions. To facilitate the access to information on cell and molecular interactions in the context of muscle regeneration, we have developed Myo-REG, a web portal that captures and integrates published information on skeletal muscle regeneration. The muscle-centered resource we provide is one of a kind in the myology field. A friendly interface allows users to explore, approximately 100 cell interactions or to analyze intracellular pathways related to muscle regeneration. Finally, we discuss how data can be extracted from this portal to support in silico modeling experiments.

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Section: Methodsmentioning

confidence: 99%

Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration

et al. 2019

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“…D3.js (data-driven documents) is a JavaScript library (Bostock et al 2011), which is also called an interactive and dynamic data visualization tool library and can be visualized with great flexibility through programming. Based on D3.js, CellWhere showing the local interaction network organized into subcellular locations (Heberle et al 2017), SPV simplifies biological signaling pathways visualization (Calderone and Cesareni 2018).…”

Section: Path Visualizationmentioning

confidence: 99%

Mapping the technology evolution path: a novel model for dynamic topic detection and tracking

et al. 2020

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Identifying the evolution path of a research field is essential to scientific and technological innovation. There have been many attempts to identify the technology evolution path based on the topic model or social networks analysis, but many of them had deficiencies in methodology. First, many studies have only considered a single type of information (text or citation information) in scientific literature, which may lead to incomplete technology path mapping. Second, the number of topics in each period cannot be determined automatically, making dynamic topic tracking difficult. Third, data mining methods fail to be effectively combined with visual analysis, which will affect the efficiency and flexibility of mapping. In this study, we developed a method for mapping the technology evolution path using a novel non-parametric topic model, the citation involved Hierarchical Dirichlet Process (CIHDP), to achieve better topic detection and tracking of scientific literature. To better present and analyze the path, D3.js is used to visualize the splitting and fusion of the evolutionary path. We used this novel model to mapping the artificial intelligence research domain, through a successful mapping of the evolution path, the proposed method’s validity and merits are shown. After incorporating the citation information, we found that the CIHDP can be mapping a complete path evolution process and had better performance than the Hierarchical Dirichlet Process and LDA. This method can be helpful for understanding and analyzing the development of technical topics. Moreover, it can be well used to map the science or technology of the innovation ecosystem. It may also arouse the interest of technology evolution path researchers or policymakers.

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“…Every searching method (Basic Protocol 1) returns, on the result page, the "Interaction list" and the "Interaction Network." The Interaction Network allows users to explore, through a graphic visualizer (Calderone & Cesareni, 2018), the interaction network of the performed search (Fig. 7).…”

Section: Mint Visualizermentioning

confidence: 99%

Using the MINT Database to Search Protein Interactions

Calderone

Iannuccelli

Peluso

et al. 2020

CP in Bioinformatics

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The Molecular INTeractions Database (MINT) is a public database designed to store information about protein interactions. Protein interactions are extracted from scientific literature and annotated in the database by expert curators. Currently (October 2019), MINT contains information on more than 26,000 proteins and more than 131,600 interactions in over 30 model organisms. This article provides protocols for searching MINT over the Internet, using the new MINT Web Page. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Searching MINT over the internet Alternate Protocol: MINT visualizer Basic Protocol 2: Submitting interaction data

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SPV: a JavaScript Signaling Pathway Visualizer

Cited by 9 publications

References 17 publications

Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration

Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration

Mapping the technology evolution path: a novel model for dynamic topic detection and tracking

Using the MINT Database to Search Protein Interactions

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