User-friendly data portal provides access to a transient paleoclimate simulation covering the last 21 kyr

Abstract Enhancer RNA (eRNA) is a type of long non-coding RNA transcribed from DNA enhancer regions. Despite critical roles of eRNA in gene regulation, the expression landscape of eRNAs in normal human tissue remains unexplored. Using numerous samples from the Genotype-Tissue Expression project, we characterized 45 411 detectable eRNAs and identified tens of thousands of associations between eRNAs and traits, including gender, race, and age. We constructed a co-expression network to identify millions of putative eRNA regulators and target genes across different tissues. We further constructed a user-friendly data portal, Human enhancer RNA Atlas (HeRA, https://hanlab.uth.edu/HeRA/). In HeRA, users can search, browse, and download the eRNA expression profile, trait-related eRNAs, and eRNA co-expression network by searching the eRNA ID, gene symbol, and genomic region in one or multiple tissues. HeRA is the first data portal to characterize eRNAs from 9577 samples across 54 human tissues and facilitates functional and mechanistic investigations of eRNAs.

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tRic: a user-friendly data portal to explore the expression landscape of tRNAs in human cancers

RNA Biology ◽

10.1080/15476286.2019.1657744 ◽

2019 ◽

Vol 17 (11) ◽

pp. 1674-1679 ◽

Cited By ~ 3

Author(s):

Zhao Zhang ◽

Hang Ruan ◽

Chun-Jie Liu ◽

Youqiong Ye ◽

Jing Gong ◽

...

Keyword(s):

Human Cancers ◽

Data Portal ◽

User Friendly

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Interactive open access to climate observations from Germany

Advances in Science and Research ◽

10.5194/asr-16-75-2019 ◽

2019 ◽

Vol 16 ◽

pp. 75-83 ◽

Cited By ~ 1

Author(s):

Frank Kaspar ◽

Frank Kratzenstein ◽

Andrea K. Kaiser-Weiss

Keyword(s):

Open Access ◽

Meteorological Data ◽

User Requirements ◽

Climate Data ◽

Phenological Data ◽

Web Map ◽

Station Data ◽

Data Portal ◽

User Friendly ◽

Observing Systems

Abstract. During recent years, Germany's national meteorological service (Deutscher Wetterdienst, DWD) has significantly expanded the open access to its climate observations. A first step was a simple FTP-site with the possibility for downloading archives with various categories of data, e.g. national and international station-based meteorological data, derived parameters, gridded products and special categories as e.g. phenological data. The data are based on the observing systems of DWD for Germany as well as international activities of DWD. To improve the interactive and user-friendly access to the data, a new portal has been developed. The portal serves a variety of user requirements that result from the broad range of applications of DWD's climate data. Here we provide an overview of the new climate data portal of DWD. It is based on a systematic implementation of OGC-based technologies. It allows easy graphical access to the station data, but also supports access via technical interfaces, esp. Web-Map- and Web-Feature-Services.

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Biologer: an open platform for collecting biodiversity data

Biodiversity Data Journal ◽

10.3897/bdj.8.e53014 ◽

2020 ◽

Vol 8 ◽

Author(s):

Miloš Popović ◽

Nikola Vasić ◽

Toni Koren ◽

Ivona Burić ◽

Nenad Živanović ◽

...

Keyword(s):

Open Access ◽

Android Application ◽

Detailed Data ◽

Biodiversity Data ◽

Team Members ◽

Open Platform ◽

National Initiatives ◽

Darwin Core ◽

Data Portal ◽

User Friendly

We have developed a new platform named "Biologer" intended for recording species observations in the field (but also from literature resources and collections). The platform is created as user-friendly, open source, multilingual software that is compatible with Darwin Core standard and accompanied by a simple Android application. It is made from the user’s perspective, allowing everyone to choose how they share the data. Project team members are delegated by involved organisations. The team is responsible for development of the platform, while local Biologer communities are engaged in data collection and verification. Biologer has been online and available for use in Serbia since 2018 and was soon adopted in Croatia and Bosnia and Herzegovina. In total, we have assembled 536 users, who have collected 163,843 species observation records data from the field and digitalised 33,458 literature records. The number of active users and their records is growing daily. Out of the total number of gathered data, 89% has been made open access by the users, 10% is accessible on the scale of 10×10 km and only 1% is closed. In the future, we plan to provide a taxonomic data portal that could be used by local and national initiatives in Eastern Europe, aggregate all data into a single web location, create detailed data overview and enable fluent communication between users.

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Interactive access to climate data from Germany

10.5194/ems2021-496 ◽

2021 ◽

Author(s):

Frank Kratzenstein ◽

Frank Kaspar

Keyword(s):

Meteorological Data ◽

Free Access ◽

Climate Data ◽

Oracle Database ◽

Phenological Data ◽

Observation Systems ◽

Long Time ◽

Data Portal ◽

Set Up ◽

User Friendly

In recent years, the DWD has significantly expanded free access to its climate observations. A first step was a simple FTP site with the possibility to download archives with different data categories, e.g. national and international station-based meteorological data, derived parameters, gridded products, and special categories like phenological data. The data are based on the DWD's observation systems for Germany as well as on the DWD's international activities.Based on the consistent implementation of OGC standards, an interactive and user-friendly access to the data has been created with the development of the DWD climate portal.In addition to browsing, previewing, running basic analysis and downloading the data, the available OGC services enable users to set up their own services on the DWD data. Along with the free and extended access to the data and services, the users' demands on the availability, quality, and detail of the metadata also increased significantly. Maintaining and linking metadata to the opendata and services remains a challenge. However, INSPIRE and WIGOS are paving the way to a unified solution and overcoming the problems.Another challenging requirement was to provide interactive access to long time series from gridded products to the users. To accomplish this, we have moved away from a previously file-based approach to storing the raster data as a georaster in an Oracle database. This design allows us a combined analysis of raster and station data not only in the climate data portal but also in the central climate database.The presentation will provide a technical and functional overview of the DWD climate data portal.

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Large-scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines

10.1101/2020.07.03.186908 ◽

2020 ◽

Author(s):

Wei Zhao ◽

Jun Li ◽

Mei-Ju Chen ◽

Zhenlin Ju ◽

Nicole K. Nesser ◽

...

Keyword(s):

Cancer Cell ◽

Large Scale ◽

Predictive Power ◽

Drug Sensitivity ◽

Cancer Cell Line ◽

Protein Drug ◽

Systematic Map ◽

Data Portal ◽

Protein Response ◽

User Friendly

SummaryPerturbation biology is a powerful approach to developing quantitative models of cellular behaviors and gaining mechanistic insights into disease development. In recent years, large-scale resources for phenotypic and mRNA responses of cancer cell lines to perturbations have been generated. However, similar large-scale protein response resources are not available, resulting in a critical knowledge gap for elucidating oncogenic mechanisms and developing effective cancer therapies. Here we generated and compiled perturbed expression profiles of ~210 clinically relevant proteins in >12,000 cancer cell-line samples in response to >150 drug compounds using reverse-phase protein arrays. We show that integrating protein response signals substantially increases the predictive power for drug sensitivity and aids in gaining insights into mechanisms of drug resistance. We build a systematic map of protein-drug connectivity and develop an open-access, user-friendly data portal for community use. Our study provides a valuable information resource for a broad range of quantitative modeling and biomedical applications.HighlightsA large collection of cancer cell line protein responses to drug perturbationsPerturbed protein responses greatly increase predictive power for drug sensitivityBuild a systematic map of protein-drug connectivity based on response profilesDevelop a user-friendly, interactive data portal for community use

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GeoNode: an open source framework to build spatial data infrastructures

10.7287/peerj.preprints.27534v1 ◽

2019 ◽

Cited By ~ 1

Author(s):

Paolo Corti ◽

Francesco Bartoli ◽

Alessio Fabiani ◽

Cristiano Giovando ◽

Athanasios Tom Kralidis ◽

...

Keyword(s):

Open Source ◽

Spatial Data ◽

Open Data ◽

Content Management ◽

Data Infrastructure ◽

Open Source Framework ◽

Data Infrastructures ◽

Data Portal ◽

Spatial Data Infrastructures ◽

User Friendly

GeoNode is an open source framework designed to build geospatial content management systems (GeoCMS) and spatial data infrastructure (SDI) nodes. Its development was initiated by the Global Facility for Disaster Reduction and Recovery (GFDRR) in 2009 and adopted by a large number of organizations in the following years. Using an open source stack based on mature and robust frameworks and software like Django, OpenLayers, PostGIS, GeoServer and pycsw, an organization can build on top of GeoNode its SDI or geospatial open data portal. GeoNode provides a large number of user friendly capabilities, broad interoperability using Open Geospatial Consortium (OGC) standards, and a powerful authentication/authorization mechanism. Supported by a vast, diverse and global open source community, GeoNode is an official project of the Open Source Geospatial Foundation (OSGeo).

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GeoNode: an open source framework to build spatial data infrastructures

10.7287/peerj.preprints.27534 ◽

2019 ◽

Author(s):

Paolo Corti ◽

Francesco Bartoli ◽

Alessio Fabiani ◽

Cristiano Giovando ◽

Athanasios Tom Kralidis ◽

...

Keyword(s):

Open Source ◽

Spatial Data ◽

Open Data ◽

Content Management ◽

Data Infrastructure ◽

Open Source Framework ◽

Data Infrastructures ◽

Data Portal ◽

Spatial Data Infrastructures ◽

User Friendly

GeoNode is an open source framework designed to build geospatial content management systems (GeoCMS) and spatial data infrastructure (SDI) nodes. Its development was initiated by the Global Facility for Disaster Reduction and Recovery (GFDRR) in 2009 and adopted by a large number of organizations in the following years. Using an open source stack based on mature and robust frameworks and software like Django, OpenLayers, PostGIS, GeoServer and pycsw, an organization can build on top of GeoNode its SDI or geospatial open data portal. GeoNode provides a large number of user friendly capabilities, broad interoperability using Open Geospatial Consortium (OGC) standards, and a powerful authentication/authorization mechanism. Supported by a vast, diverse and global open source community, GeoNode is an official project of the Open Source Geospatial Foundation (OSGeo).

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The Added Value of Graphical Input and Display for Electron Lens Design

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100179701 ◽

1990 ◽

Vol 48 (1) ◽

pp. 190-191

Author(s):

B. Lencova ◽

G. Wisselink

Keyword(s):

Flux Density ◽

Numerical Data ◽

Added Value ◽

Lens Design ◽

Step Size ◽

Magnetic Lens ◽

Flux Lines ◽

Fine Mesh ◽

Electron Lens ◽

User Friendly

Recent progress in computer technology enables the calculation of lens fields and focal properties on commonly available computers such as IBM ATs. If we add to this the use of graphics, we greatly increase the applicability of design programs for electron lenses. Most programs for field computation are based on the finite element method (FEM). They are written in Fortran 77, so that they are easily transferred from PCs to larger machines.The design process has recently been made significantly more user friendly by adding input programs written in Turbo Pascal, which allows a flexible implementation of computer graphics. The input programs have not only menu driven input and modification of numerical data, but also graphics editing of the data. The input programs create files which are subsequently read by the Fortran programs. From the main menu of our magnetic lens design program, further options are chosen by using function keys or numbers. Some options (lens initialization and setting, fine mesh, current densities, etc.) open other menus where computation parameters can be set or numerical data can be entered with the help of a simple line editor. The "draw lens" option enables graphical editing of the mesh - see fig. I. The geometry of the electron lens is specified in terms of coordinates and indices of a coarse quadrilateral mesh. In this mesh, the fine mesh with smoothly changing step size is calculated by an automeshing procedure. The options shown in fig. 1 allow modification of the number of coarse mesh lines, change of coordinates of mesh points or lines, and specification of lens parts. Interactive and graphical modification of the fine mesh can be called from the fine mesh menu. Finally, the lens computation can be called. Our FEM program allows up to 8000 mesh points on an AT computer. Another menu allows the display of computed results stored in output files and graphical display of axial flux density, flux density in magnetic parts, and the flux lines in magnetic lenses - see fig. 2. A series of several lens excitations with user specified or default magnetization curves can be calculated and displayed in one session.

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