SynLethDB 2.0: A web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery

Two genes are synthetic lethal if mutations in both genes result in impaired cell viability, while mutation of either gene does not affect the cell survival. The potential usage of synthetic lethality (SL) in anticancer therapeutics has attracted many researchers to identify synthetic lethal gene pairs. To include newly identified SLs and more related knowledge, we present a new version of the SynLethDB database to facilitate the discovery of clinically relevant SLs. We extended the first version of SynLethDB database significantly by including new SLs identified through CRISPR screening, a knowledge graph about human SLs, and new web interface, etc. Over 16,000 new SLs and 26 types of other relationships have been added, encompassing relationships among 14,100 genes, 53 cancers, and 1,898 drugs, etc. Moreover, a brand-new web interface has been developed to include modules such as SL query by disease or compound, SL partner gene set enrichment analysis and knowledge graph browsing through a dynamic graph viewer. The data can be downloaded directly from the website or through the RESTful APIs. The database is accessible online at http://synlethdb.sist.shanghaitech.edu.cn/v2.

Cartografía de la revista Profesional de la información: mapa visual de 30 años de historia

The process of creating a cartography, an interactive visualization, from the bibliographic data of the contents of the scientific journal Profesional de la información during its almost 30 years of life is presented. The cartography is available on the EPI journal website: https://profesionaldelainformacion.com/cartografia/EPI_GLOBAL/index.html. Its objective is to serve as a navigable index for the quick localization of information of interest to readers as well as a visual map that highlights the characteristics of the knowledge network that these data form through the interconnection of relationships between its nodes. This device has been created by extracting data from the journal’s website using web scraping tools and the free software Gephi for network visualization. A graph viewer allows access and manipulation through the web. Navigation through the bibliographic data network is facilitated by different strategies: (1) the use of different colors for each category of node (author, keyword, number, and article); (2) the viewer’s search tools, including a node label finder, a zoom bar, a magnifying glass, and a button to hide the network of relationships; and (3) the possibility of displaying different linked graphs. Selecting a node opens a side-space where all the attributes providing information about that node are displayed and that enables a new window to be opened, displaying all the information linked to an external page. The information on the authors is obtained from the Directory of Experts in the Management of Information (EXIT). This tool thus undeniable provides a useful source of secondary information on the journal, as were printed indexes in their day, with the advantage that it can be updated almost simultaneously with the publication of new issues. The data obtained will be used to carry out other analyses of the evolution of the journal, the topics of interest to the profession, and its stakeholders. Resumen Se presenta el proceso de realización de una cartografía, una visualización interactiva, a partir de los datos bibliográficos de los contenidos de la revista científica Profesional de la Información en sus casi 30 años de vida. La cartografía se puede consultar en el sitio web de la revista EPI: https://profesionaldelainformacion.com/cartografia/EPI_GLOBAL/index.html. Su objetivo es servir como índice navegable para la localización rápida de información de interés para los lectores, así como un mapa visual que resalta las características de la red de conocimiento que esos datos forman a través de la interconexión de relaciones entre sus nodos. Este dispositivo ha sido realizado a partir de la extracción de datos de la web de la propia revista mediante programas de web scraping, y el software libre Gephi para la visualización de las redes. Un visor de gráficos permite el acceso y su manipulación a través de la web. La navegación por la red de datos bibliográficos se facilita mediante distintas estrategias: (1) la diferenciación por colores de cada categoría de nodo (autor, palabra clave, número y artículo); (2) las herramientas de búsqueda del visor: un buscador de etiquetas de nodo, una barra para acercar y alejar la red, una lupa y un botón para ocultar la red de relaciones; y (3) la posibilidad de mostrar distintas gráficas enlazadas. La selección de un nodo abre un espacio lateral donde se muestran todos los atributos que dan información sobre ese nodo y permite abrir en una ventana nueva toda la que está enlazada con una página exterior. La información sobre los autores se obtiene del Directorio de Expertos en el Tratamiento de la Información (EXIT). Se constituye así en una fuente de información secundaria sobre la revista de innegable utilidad, como lo fueron en su día los índices impresos, con la ventaja de que su actualización puede realizarse de forma casi simultánea a la publicación de nuevos números. Los datos obtenidos servirán para la realización de otros análisis de la evolución de la revista, de las temáticas de interés de la profesión y sus actores.

G-Graph: An interactive genomic graph viewer

MotivationEffective and efficient exploration of numeric data and annotations as a function of genomic position requires specialized software.ResultsWe present G-Graph, an interactive genomic scatter plot viewer. G-Graph stacks or tiles multiple data series in one graph using different colors and markers. It displays gene annotation and other metadata, allows easy changes to the appearance of data series, implements stack-based undo functionality, and saves user-selected application views as image and pdf files. G-Graph delivers smooth and rapid scrolling and zooming even for datasets with millions of points and line segments. The primary target user is a researcher examining many copy number profiles to identify potentially deleterious variants. G-Graph runs under Linux, Mac OSX and Windows.Availabilityhttps://github.com/docpaa/mumdex/ or https://mumdex.com/ggraph/[email protected] (or [email protected])

Simulasi Alat Photoplethysmograph (PPG)

Heart is a vital organ in the human body. The heart functions circulated the blood throughout the body. The volume of blood in a body organ will vary due to blood pumping by the heart. Photoplethysmograph (PPG) is a device that can detect changes in blood volume using optical sensors. The purpose of this research is to make Photoplethysmograph monitoring system online. That is a device to monitor blood volume changes and display the change graph. Fluctuations in blood volume changes are influenced by the rhythm of blood pumping by the heart. Each peak on the PPG signal is correlated with one heartbeat. Photoplethysmograph charts can be used to determine the condition and abnormalities of a person's heart. Photoplethysmograph system online is realized in the form of sensors, amplifiers, LPF, ADC, and microcontroller as a serial interface, wiz610wi module, and web applications as online PPG graph viewer. Sensors composed of red LED and photoresistor (LDR) are placed on the fingers. The rays emitted by the LEDs are received by the LDR. The signals received by the LDR vary according to the volume of blood changes. The sensor output signal is then amplified and filtered. Incoming filter output signal ADC, serial interface by AT89C2051 then by wiz610wi module transmitted for display and monitored. Obtained Devices and apps created have worked well. The signal shown is pretty good, clean of noise. Transmission distance measured up to 70 m with delay less than 200 ms. The average heart rate calculation was in error 3%

Hyperbolic Wheel: A Novel Hyperbolic Space Graph Viewer for Hierarchical Information Content

Tree and graph structures have been widely used to present hierarchical and linked data. Hyperbolic trees are special types of graphs composed of nodes (points or vertices) and edges (connecting lines), which are visualized on a non-Euclidean space. In traditional Euclidean space graph visualization, distances between nodes are measured by straight lines. Displays of large graphs in Euclidean spaces may not utilize efficiently the available space and may impose limitations on the number of graph nodes. The special hyperbolic space rendering of tree-graphs enables adaptive and efficient use of the available space and facilitates the display of large hierarchical structures. In this paper we report on a newly developed advanced hyperbolic graph viewer, Hyperbolic Wheel, which enables the navigation, traversal, discovery and interactive manipulation of information stored in large hierarchical structures. Examples of such structures include personnel records, disc directory structures, ontological constructs, web-pages and other nested partitions. The Hyperbolic Wheel framework provides an intuitive and dynamic graphical interface to explore and retrieve information about individual nodes (data objects) and their relationships (data associations). The Hyperbolic Wheel is freely available online for educational and research purposes.