Clustergrammer: web-based heatmap visualization and analysis tool for high-dimensional biological data

BackgroundA major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task.ResultsWe have developed WebGIVI, an interactive web-based visualization tool (http://raven.anr.udel.edu/webgivi/) to explore gene:iTerm pairs. WebGIVI was built via Cytoscape and Data Driven Document JavaScript libraries and can be used to relate genes to iTerms and then visualize gene and iTerm pairs. WebGIVI can accept a gene list that is used to retrieve the gene symbols and corresponding iTerm list. This list can be submitted to visualize the gene iTerm pairs using two distinct methods: a Concept Map or a Cytoscape Network Map. In addition, WebGIVI also supports uploading and visualization of any two-column tab separated data.ConclusionsWebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering, sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI. The WebGIVI tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php.

ATK Mission Research develops analyst tools and automated quality control software in order to assist the Atmospheric Radiation Measurement (ARM) Data Quality Office with their data inspection tasks. We have developed a web-based data analysis and visualization tool, called NCVweb, that allows for easy viewing of ARM NetCDF files. NCVweb, along with our library of sharable Interactive Data Language procedures and functions, allows even novice ARM researchers to be productive with ARM data with only minimal effort. We also contribute to the ARM Data Quality Office by analyzing ARM data streams, developing new quality control metrics, new diagnostic plots, and integrating this information into DQ HandS - the Data Quality Health and Status web-based explorer. We have developed several ways to detect outliers in ARM data streams and have written software to run in an automated fashion to flag these outliers.

ABSTRACTThis article examines the role that business librarians can play in conveying the importance of thorough patent research in the start-up life cycle. It provides a summary of the components of the start-up life cycle and due diligence research as it pertains to entrepreneurs and venture capitalists. An overview of patent research resources and locations is provided, with particular focus on PatentsView, a web-based patent data visualization and analysis tool.

Water Resourcing in China has historically been a complex issue requiring the ability to deal with regular floods, droughts and diverse water needs. Climate change represents another challenge to this sector, albeit one that is not traditionally considered by water managers. In this sector in China water management is predominantly based on historic, seasonal and annual forecast data while multi-annual and (multi-)decadal data are seldom used. In this paper, we present the co-development of a climate service prototype designed to provide water managers with insights into the impacts of climate change on the Upper Yellow River region for the next century. The paper is an outcome from our project that encouraged water resource planners and water resource managers to utilise long-term climate information to understand the uncertainties and the challenges our changing climate is likely to have in the region. Using an interdisciplinary team and adopting a user-centred, co-production approach, a prototype web-based data visualisation tool was developed. The development of the prototype was based on a design specification constructed from the findings of detailed interviews that allowed it to be developed and tested under SARS-CoV-2 pandemic restrictions that prevented the typical development process to be undertaken. The developed prototype presents climate information and communicates uncertainties regarding climate change in the remainder of the century through data sets that are typically used by the water sector in China in a simple, easy to understand style. Models that estimate river levels under different extraction scenarios and results about estimated river level and flow, and flood risk are also presented. The prototype was shown to be successful, as key messages relating to the impact of climate change and the challenges for water resource management could be effectively communicated through the tool interface. Practical implicationsUnderstanding the impacts of climate change on water resourcing is complicated and multifaceted. There is a need for better data about what water there is and how it is moving around between and within catchments. Estimates of past, present and future climate variables along with historical measurements of river flow can be used to help visualise some of the uncertainties and changes that may happen in the next 50 years. In addition, there is a need to understand changing water demands and water resource management practices. Current water resource management practices are based on historical conditions and assumptions that are less likely to hold true in a more variable and warmer climate. Communicating how future changes will impact future water resourcing is critical to water resources in a changing climate (Belcher et al. 2018).This research outlines the construction of a tool to visualise the impacts of climate change on water availability in part of China that is typically water scarce, using models developed using the Soil Water Assessment Toolkit (SWAT). A model of the Upper Yellow River (UYR) was developed to demonstrate the impact of climate change on river levels in the catchment based on climate variables. The rainfall-runoff model was based on climate predictions from the CMIP5 assessment HadGEM3-GC3.05 climate model and incorporated information about water resource allocations for different administrative regions of the catchment The general climate trend for the region is that it is expected to become significantly warmer. The total amount of precipitation is likely to be about the same, and yet it is expected that overall, the catchment will become significantly drier over time as winter shortens and summer lengthens. The outputs from the model reflect the changes in climate variables. The uncertainties were communicated via a Web based tool. Water resource managers in China helped to coproduce the tool by participating in workshops and providing feedback on prototypes. The workshops helped scientists and water resource managers to communicate about climate change impacts on water resources and water resource management.

With the advancement of Information technologies and applications, a copious amount of data is generated, which attracts both the research community to utilize this information for extracting knowledge and the industry for developing the knowledge-based system. Visualization of data, pattern mining from datasets and analyzing data drift for the different features are three highly used applications of machine learning and data science fields. A generic web-based tool integrated with such features will provide prodigious support for preprocessing the dataset and thus extracting accurate information. In this work, we propose such a data visualization tool, named VIM, which is a web-based comprehensive tool for generic data visualization, data preprocessing and mining suitable knowledge with drift analysis of data. Given a dataset, it can envisage the distribution of data with convenient statistical diagrams for different selected features. Moreover, users can employ VIM to generate association rules by selecting multiple features. We have developed VIM using Python Django framework and GraphLab library. We have deployed this tool to make this publicly usable, which can be accessed at http://210.4.73.237:9999/

<p>ESA's Swarm mission continues to deliver excellent data providing insight into a wide range of geophysical phenomena. The mission is an important asset whose data are used within a number of critical resources, from geomagnetic field models to space weather services. As the product portfolio grows to better deliver on the mission's scientific goals, we face increasing complexity in accessing, processing, and visualising the data and models. ESA provides “VirES for Swarm” [1] (developed by EOX IT Services) to help solve this problem. VirES is a web-based data retrieval and visualisation tool where the majority of Swarm products are available. VirES has a graphical interface but also a machine-to-machine interface (API) for programmable use (a Python client is provided). The VirES API also provides access to geomagnetic ground observatory data, as well as forwards evaluation of geomagnetic field models to give data-model residuals. The "Virtual Research Environment" (VRE) adds utility to VirES with a free cloud-based JupyterLab interface allowing scientists to immediately program their own analysis of Swarm products using the Python ecosystem. We are augmenting this with a suite of Jupyter notebooks and dashboards, each targeting a specific use case, and seek community involvement to grow this resource.</p><p>[1] https://vires.services</p>

BackgroundMicroarray and other high-throughput technologies are producing large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information in the gene sets.ResultsWe have created a web-based tool for data analysis and data visualization for sets of genes called GOTree Machine (GOTM). This tool was originally intended to analyze sets of co-regulated genes identified from microarray analysis but is adaptable for use with other gene sets from other high-throughput analyses. GOTree Machine generates a GOTree, a tree-like structure to navigate the Gene Ontology Directed Acyclic Graph for input gene sets. This system provides user friendly data navigation and visualization. Statistical analysis helps users to identify the most important Gene Ontology categories for the input gene sets and suggests biological areas that warrant further study. GOTree Machine is available online at .ConclusionGOTree Machine has a broad application in functional genomic, proteomic and other high-throughput methods that generate large sets of interesting genes; its primary purpose is to help users sort for interesting patterns in gene sets.

BackgroundHigh-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is supported in data warehouses such as tranSMART, when querying relational databases for hundreds of different patient gene expression records queries are slow due to poor performance. Non-relational data models, such as the key-value model implemented in NoSQL databases, hold promise to be more performant solutions. Our motivation is to improve the performance of the tranSMART data warehouse with a view to supporting Next Generation Sequencing data.ResultsIn this paper we introduce a new data model better suited for high-dimensional data storage and querying, optimized for database scalability and performance. We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google's BigTable storage system. An experimental performance comparison was carried out against the traditional relational data model implemented in both MySQL Cluster and MongoDB, using a large publicly available transcriptomic data set taken from NCBI GEO concerning Multiple Myeloma. Our new key-value data model implemented on HBase exhibits an average 5.24-fold increase in high-dimensional biological data query performance compared to the relational model implemented on MySQL Cluster, and an average 6.47-fold increase on query performance on MongoDB.ConclusionsThe performance evaluation found that the new key-value data model, in particular its implementation in HBase, outperforms the relational model currently implemented in tranSMART. We propose that NoSQL technology holds great promise for large-scale data management, in particular for high-dimensional biological data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new data model as a basis for migrating tranSMART's implementation to a more scalable solution for Big Data.

ArrayCyGHt is a web-based application tool for analysis and visualization of microarray-comparative genomic hybridization (array-CGH) data. Full process of array-CGH data analysis, from normalization of raw data to the final visualization of copy number gain or loss, can be straightforwardly achieved on this arrayCyGHt system without the use of any further software. ArrayCyGHt, therefore, provides an easy and fast tool for the analysis of copy number aberrations in any kinds of data format. ArrayCyGHt can be accessed at http://genomics.catholic.ac.kr/arrayCGH/

Data clustering is an important technique for data visualization and statistical data analysis. Using data clustering technique for geo-located data analysis and visualization has been shown to be useful in many practical domains. Although there are numerous studies for data clustering algorithms, the implementations and applications based on these algorithms are rare and inadequate, especially for web-based data visualization services. In this research, a new web-based interactive data clustering prototype is proposed for geo-located data visualization. The necessary web-based infrastructure for geo-located data analysis and visualization is designed and implemented at first. And then the new interactive data clustering prototype using multi-dimensional K-Means algorithm is implemented on the existing infrastructure. In order to assess whether the new prototype can contribute meaningfully to architectural design and urban studies, qualified users with urban study or architectural backgrounds are invited to use the prototype and then make their comments and evaluations. To make it clear how this new prototype might apply in real world settings, an application scenario in which the user might interact with the prototype is provided and analyzed.

The post-transcriptional sequence modification of transcripts through RNA editing is an important mechanism for regulating protein function and is associated with human disease phenotypes. The identification of RNA editing or RNA-DNA difference (RDD) sites is a fundamental step in the study of RNA editing. However, a substantial number of false-positive RDD sites have been identified recently. A major challenge in identifying RDD sites is to distinguish between the true RNA editing sites and the false positives. Furthermore, determining the location of condition-specific RDD sites and elucidating their functional roles will help toward understanding various biological phenomena that are mediated by RNA editing. The present study developed RNA-sequence comparison and annotation for RNA editing (RCARE) for searching, annotating, and visualizing RDD sites using thousands of previously known editing sites, which can be used for comparative analyses between multiple samples. RCARE also provides evidence for improving the reliability of identified RDD sites. RCARE is a web-based comparison, annotation, and visualization tool, which provides rich biological annotations and useful summary plots. The developers of previous tools that identify or annotate RNA-editing sites seldom mention the reliability of their respective tools. In order to address the issue, RCARE utilizes a number of scientific publications and databases to find specific documentations respective to a particular RNA-editing site, which generates evidence levels to convey the reliability of RCARE. Sequence-based alignment files can be converted into VCF files using a Python script and uploaded to the RCARE server for further analysis. RCARE is available for free at http://www.snubi.org/software/rcare/.

Smartphones are now an integral part of our everyday life - people carry them around almost everywhere every time and use them in diverse contexts. Therefore, a smartphone can be used as a life- logging device that constantly and naturally records people's life for future reference. We developed a smartphone-based life-logging platform with which users can record diverse contextual information such as smartphone activities, timestamps, locations, and accompanying people, along with other sensor data. Using this platform, we collected smartphone-based life-logs from a group of university students. To enable users to visually explore one's life-logs based on the multidimensional data gathered from their mobile devices, we designed and implemented a web-based interactive visualization tool. We reported preliminary findings we made through our visualization tool.

High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community.Database URL: http://www.maayanlab.net/ESCAPE

A Web-based visualization tool has been developed and used for teaching undergraduate students about flow and thermodynamic property variations in isentropic (shock-free) and non-isentropic (normal shock embedded) one-dimensional compressible flows in nozzles. The Web-based module simulates these flow regimes by numerically solving conservation laws for mass, momentum and energy, and enables real time visualization of results using an animation program. The module through its interactivity feature permits students to change operating pressure conditions to visualize flow property variations inside a supersonic nozzle by clicking and dragging action of a computer mouse. The module through a variety of visual images of physical phenomenon also provides student the engineering context of underlying engineering principles and governing equations

BackgroundVisualizing the complex probability landscape of stochastic gene regulatory networks can further biologists’ understanding of phenotypic behavior associated with specific genes.ResultsWe present PRODIGEN (PRObability DIstribution of GEne Networks), a web-based visual analysis tool for the systematic exploration of probability distributions over simulation time and state space in such networks. PRODIGEN was designed in collaboration with bioinformaticians who research stochastic gene networks. The analysis tool combines in a novel way existing, expanded, and new visual encodings to capture the time-varying characteristics of probability distributions: spaghetti plots over one dimensional projection, heatmaps of distributions over 2D projections, enhanced with overlaid time curves to display temporal changes, and novel individual glyphs of state information corresponding to particular peaks.ConclusionsWe demonstrate the effectiveness of the tool through two case studies on the computed probabilistic landscape of a gene regulatory network and of a toggle-switch network. Domain expert feedback indicates that our visual approach can help biologists: 1) visualize probabilities of stable states, 2) explore the temporal probability distributions, and 3) discover small peaks in the probability landscape that have potential relation to specific diseases.