Open-source Web Application Research Articles

Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS.

The rise of intact protein analysis by mass spectrometry (MS) was accompanied by an increasing need for flexible tools allowing data visualization and analysis. These include inspection of the deconvoluted molecular weights of the proteoforms eluted alongside liquid chromatography (LC) through their representation in three-dimensional (3D) liquid chromatography coupled to mass spectrometry (LC-MS) maps (plots of deconvoluted molecular weights, retention times, and intensity of the MS signal). With this aim, we developed a free and open-source web application named VisioProt-MS (https://masstools.ipbs.fr/mstools/visioprot-ms/). VisioProt-MS is highly compatible with many algorithms and software developed by the community to integrate and deconvolute top-down and intact protein MS data. Its dynamic and user-friendly features greatly facilitate analysis through several graphical representations dedicated to MS and tandem mass spectrometry (MS/MS) analysis of proteoforms in complex samples. Here, we will illustrate the importance of LC-MS map visualization to optimize top-down acquisition/search parameters and analyze intact protein MS data. We will go through the main features of VisioProt-MS using the human proteasomal 20S core particle as a user-case.

Proxl (Protein Cross-Linking Database): A Public Server, QC Tools, and Other Major Updates.

Proxl is an open-source web application for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data and results. Proxl's core features include comparing data sets, structural analysis, customizable and interactive data visualizations, access to all underlying mass spectrometry data, and quality-control tools. All features of Proxl are designed to be independent of specific cross-linker chemistry or software analysis pipelines. Proxl's sharing tools allow users to share their data with the public or securely restrict access to trusted collaborators. Since being published in 2016, Proxl has continued to be expanded and improved through active development and collaboration with cross-linking researchers. Some of Proxl's new features include a centralized, public site for sharing data, greatly expanded quality-control tools and visualizations, support for stable isotope-labeled peptides, and general improvements that make Proxl easier to use, data easier to share and import, and data visualizations more customizable. Source code and more information are found at http://proxl-ms.org/ .

Comparative study of the airborne microbial communities and their functional composition in fine particulate matter (PM2.5) under non-extreme and extreme PM2.5 conditions

Asian dust (AD) events increase environmental pollution and have a detrimental effect on human health. Particulate matter with an aerodynamic diameter <2.5 μm (PM2.5) and containing airborne microorganisms increases during AD events due to the transportation of dust by wind from several arid regions in China. This study analyzed the bacterial and fungal communities associated with average daily PM2.5 concentrations less than (on non-event day: ND) and exceeding (on event day: ED) the air quality standard (36 μg PM2.5 m-3) set by the Korean government. The taxon compositions and functional genes of airborne microorganisms were assessed using shotgun metagenomics sequencing and metagenome rapid annotation using subsystem technology (MG-RAST) analysis. MG-RAST is an open source web application, serving as a platform that automatically analyzes uploaded metagenomes. During ND, 51% of total bacteria sequences consisted of those from Proteobacteria, which were closely related to nitrogen-fixing bacterial species. A high percentage of functional genes consisted of those genes related to nitrogen metabolism, suggesting that the airborne microorganisms are associated with environmental nitrogen cycles. During ED, 57% of total bacteria sequences consisted of those from Bacteroidetes, accompanied by high relative abundance of sequences from pathogenic species of Bacillus and Staphylococcus. Fungal sequences were mainly composed of those from the phyla Ascomycota and Basidiomycota, which include spore-forming species transported frequently by wind. The abundance of Ascomycota sequences was higher in ED (81%) than in ND (22%) samples, and mainly included those from the plant pathogens Phaeosphaeria and Pyrenophora. These findings indicated that microbial composition shifted from ND to ED samples, even at the phylum level. This switch was likely due to the sources of dust particles, with those during ED being primarily from arid regions in Mongolia and industrial regions in China. Additional studies are required to further understand the diversification of airborne microbial communities in downwind areas.

MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians.

MotivationThe volume and complexity of biological data increases rapidly. Many clinical professionals and biomedical researchers without a bioinformatics background are generating big ’-omics’ data, but do not always have the tools to manage, process or publicly share these data.ResultsHere we present MOLGENIS Research, an open-source web-application to collect, manage, analyze, visualize and share large and complex biomedical datasets, without the need for advanced bioinformatics skills.Availability and implementationMOLGENIS Research is freely available (open source software). It can be installed from source code (see http://github.com/molgenis), downloaded as a precompiled WAR file (for your own server), setup inside a Docker container (see http://molgenis.github.io), or requested as a Software-as-a-Service subscription. For a public demo instance and complete installation instructions see http://molgenis.org/research.

Mapping molecular HLA typing data to UNOS antigen equivalents

BackgroundHistocompatibility labs must convert molecular HLA typing data to antigen equivalencies for entry into the United Network for Organ Sharing (UNOS) UNet system. While an Organ Procurement and Transplantation Network (OPTN) policy document provides general guidelines for conversion, the process is complex because no antigen mapping table is available. We present a UNOS antigen equivalency table for all IPD-IMGT/HLA alleles at the A, B, C, DRB1, DRB3/4/5, DQA1, and DQB1 loci. MethodsAn automated script was developed to generate a UNOS antigen equivalency table. Data sources used in the conversion algorithm included the World Marrow Donor Association (WMDA) antigen table, the HLA Dictionary, and UNOS-provided tables. To validate antigen mappings, we converted National Marrow Donor Program (NMDP) high resolution allele frequencies to antigen equivalents and compared with the UNOS Calculated Panel Reactive Antibodies (CPRA) reference panel. ResultsNormalized frequency similarity scores between independent NMDP and UNOS panels for 4 US population categories (Caucasian, Hispanic, African American and Asian/Pacific Islander) ranged from 0.85 to 0.97, indicating correct antigen mapping. An open source web application (ALLele to ANtigen (“ALLAN”)) and web services were also developed to map unambiguous and ambiguous HLA typing data to UNOS antigen equivalents based on NMDP population-specific allele frequencies (http://www.transplanttoolbox.org). ConclusionsComputer-assisted interpretation of molecular HLA data may aid in reducing typing discrepancies in UNet. This work also sets a foundation for molecular typing data to be utilized directly in the UNet match run as well as the virtual crossmatch process at transplant centers.

The HTPmod Shiny application enables modeling and visualization of large-scale biological data

The wave of high-throughput technologies in genomics and phenomics are enabling data to be generated on an unprecedented scale and at a reasonable cost. Exploring the large-scale data sets generated by these technologies to derive biological insights requires efficient bioinformatic tools. Here we introduce an interactive, open-source web application (HTPmod) for high-throughput biological data modeling and visualization. HTPmod is implemented with the Shiny framework by integrating the computational power and professional visualization of R and including various machine-learning approaches. We demonstrate that HTPmod can be used for modeling and visualizing large-scale, high-dimensional data sets (such as multiple omics data) under a broad context. By reinvestigating example data sets from recent studies, we find not only that HTPmod can reproduce results from the original studies in a straightforward fashion and within a reasonable time, but also that novel insights may be gained from fast reinvestigation of existing data by HTPmod.

ODM Data Analysis-A tool for the automatic validation, monitoring and generation of generic descriptive statistics of patient data.

IntroductionA required step for presenting results of clinical studies is the declaration of participants demographic and baseline characteristics as claimed by the FDAAA 801. The common workflow to accomplish this task is to export the clinical data from the used electronic data capture system and import it into statistical software like SAS software or IBM SPSS. This software requires trained users, who have to implement the analysis individually for each item. These expenditures may become an obstacle for small studies. Objective of this work is to design, implement and evaluate an open source application, called ODM Data Analysis, for the semi-automatic analysis of clinical study data.MethodsThe system requires clinical data in the CDISC Operational Data Model format. After uploading the file, its syntax and data type conformity of the collected data is validated. The completeness of the study data is determined and basic statistics, including illustrative charts for each item, are generated. Datasets from four clinical studies have been used to evaluate the application’s performance and functionality.ResultsThe system is implemented as an open source web application (available at https://odmanalysis.uni-muenster.de) and also provided as Docker image which enables an easy distribution and installation on local systems. Study data is only stored in the application as long as the calculations are performed which is compliant with data protection endeavors. Analysis times are below half an hour, even for larger studies with over 6000 subjects.DiscussionMedical experts have ensured the usefulness of this application to grant an overview of their collected study data for monitoring purposes and to generate descriptive statistics without further user interaction. The semi-automatic analysis has its limitations and cannot replace the complex analysis of statisticians, but it can be used as a starting point for their examination and reporting.

Development of Human Face Literature Database Using Text Mining Approach: Phase I.

The face is an important part of the human body by which an individual communicates in the society. Its importance can be highlighted by the fact that a person deprived of face cannot sustain in the living world. The amount of experiments being performed and the number of research papers being published under the domain of human face have surged in the past few decades. Several scientific disciplines, which are conducting research on human face include: Medical Science, Anthropology, Information Technology (Biometrics, Robotics, and Artificial Intelligence, etc.), Psychology, Forensic Science, Neuroscience, etc. This alarms the need of collecting and managing the data concerning human face so that the public and free access of it can be provided to the scientific community. This can be attained by developing databases and tools on human face using bioinformatics approach. The current research emphasizes on creating a database concerning literature data of human face. The database can be accessed on the basis of specific keywords, journal name, date of publication, author's name, etc. The collected research papers will be stored in the form of a database. Hence, the database will be beneficial to the research community as the comprehensive information dedicated to the human face could be found at one place. The information related to facial morphologic features, facial disorders, facial asymmetry, facial abnormalities, and many other parameters can be extracted from this database. The front end has been developed using Hyper Text Mark-up Language and Cascading Style Sheets. The back end has been developed using hypertext preprocessor (PHP). The JAVA Script has used as scripting language. MySQL (Structured Query Language) is used for database development as it is most widely used Relational Database Management System. XAMPP (X (cross platform), Apache, MySQL, PHP, Perl) open source web application software has been used as the server.The database is still under the developmental phase and discusses the initial steps of its creation. The current paper throws light on the work done till date.

ResearchMaps.org for integrating and planning research.

To plan experiments, a biologist needs to evaluate a growing set of empirical findings and hypothetical assertions from diverse fields that use increasingly complex techniques. To address this problem, we operationalized principles (e.g., convergence and consistency) that biologists use to test causal relations and evaluate experimental evidence. With the framework we derived, we then created a free, open-source web application that allows biologists to create research maps, graph-based representations of empirical evidence and hypothetical assertions found in research articles, reviews, and other sources. With our ResearchMaps web application, biologists can systematically reason through the research that is most important to them, as well as evaluate and plan experiments with a breadth and precision that are unlikely without such a tool.

RANCANG BANGUN SISTEM ADMINISTRASI KERJA PRAKTEK DAN TUGAS AKHIR BERBASIS WEB MENGGUNAKAN FRAMEWORK CODEIGNITER

Information system is a set of components that interconnect, collect, process, store, and distribute information to support decision making and supervision within an organization. Today the information system can not be separated with computer technology that feels growing rapidly along with our increasingly complex needs. These developments can be seen from the many organizations or institutions in various fields that use computerized systems to perform various jobs quickly and with great accuracy. The use of computerized systems is expected to minimize errors made by humans thereby reducing large losses. And can mengefisienkan time in completing the work quickly and accurately. One concept of building a computerized information system is dengfan MVC model. Model-View-Controller (MVC) is a concept introduced by the inventor of Smalltalk (Trygve Reenskaug) to encapsulate data along with processing (model), isolate from the process of manipulation (controller) and view to be represented on a user interface . The MVC architecture has the benefit of separating between model and view allowing multiple views using the same model. As a result, an application model component is easier to implement, test, and maintain, because all access to the model runs through this component. One of the frameworks that works based on the MVC concept is Codeigniter. Codeigniter is an open source web application framework that is used to build dynamic php applications. The main purpose of Codeigniter development is to help developers to work on applications faster than writing all the code from scratch. Because of the superiority of codeigniter that the system of practical work administration and the final task is built using the framework..

Webpic: A flexible web application for collecting distance and count measurements from images.

Despite increasing ability to store and analyze large amounts of data for organismal and ecological studies, the process of collecting distance and count measurements from images has largely remained time consuming and error-prone, particularly for tasks for which automation is difficult or impossible. Improving the efficiency of these tasks, which allows for more high quality data to be collected in a shorter amount of time, is therefore a high priority. The open-source web application, webpic, implements common web languages and widely available libraries and productivity apps to streamline the process of collecting distance and count measurements from images. In this paper, I introduce the framework of webpic and demonstrate one readily available feature of this application, linear measurements, using fossil leaf specimens. This application fills the gap between workflows accomplishable by individuals through existing software and those accomplishable by large, unmoderated crowds. It demonstrates that flexible web languages can be used to streamline time-intensive research tasks without the use of specialized equipment or proprietary software and highlights the potential for web resources to facilitate data collection in research tasks and outreach activities with improved efficiency.

基于CartoDB的神农架国家级自然保护区金丝猴生活习性分析研究

CartoDB是一款基于开源网络应用程序和交互式地图制作工具，能够在web上快速存储和虚拟化地理数据。为了更有效、针对性的对金丝猴进行保护，文章利用神农架国家级自然保护区金丝猴位置监测数据和无线传感网环境监测数据，结合生境数据及坡度信息，对哺乳期金丝猴与非哺乳期金丝猴位置及生活习性进行研究。综合分析得出哺乳期金丝猴更适宜在低纬度、低温、土壤湿度高、区域平缓范围内活动，受人为影响大，非哺乳期金丝猴活动范围纬度跨度较大，温度和土壤湿度影响小，但均在偏高温度和土壤湿度区域活动，在区域平缓和陡坡均较活跃，受人为影响偏小，经常越过道路活动。实验也证明了基于CartoDB无需安装GIS软件即可在有网络的环境下可视化现有数据，具有一定的推广价值。 CartoDB is an open source web application and interactive mapping tool, which can quickly store and virtualize geographic data. To protect golden monkey more effective and targeted, the paper researched the position and behavior habits of golden monkey in lactation and non-lactation period by using the location monitoring data, wireless sensor network environmental monitoring data in Shennongjia Nature Reserve. In the experiment, it is also combined with the habitat data and slope information. Comprehensive analysis concluded that the golden monkey in lactation is more suitable for activities in low latitude, low temperature, high soil moisture and gentle regional range, and is greatly affected by human activities, the activities range of golden monkey in the non-lactation period is larger in latitude span and is less affected by temperature and soil moisture, but they all active in the region of high temperature and soil moisture, and are also more active in the area of gentle and steep slope and are less affected by human being; they frequently cross the road for activities. The experiment proved that the users do not need to install GIS software only by using the browser and visualize the existing data anytime based on CartoDB, which deserved to be generalized.

SATORI: a system for ontology-guided visual exploration of biomedical data repositories

MotivationThe ever-increasing number of biomedical datasets provides tremendous opportunities for re-use but current data repositories provide limited means of exploration apart from text-based search. Ontological metadata annotations provide context by semantically relating datasets. Visualizing this rich network of relationships can improve the explorability of large data repositories and help researchers find datasets of interest.ResultsWe developed SATORI—an integrative search and visual exploration interface for the exploration of biomedical data repositories. The design is informed by a requirements analysis through a series of semi-structured interviews. We evaluated the implementation of SATORI in a field study on a real-world data collection. SATORI enables researchers to seamlessly search, browse and semantically query data repositories via two visualizations that are highly interconnected with a powerful search interface.Availability and implementationSATORI is an open-source web application, which is freely available at http://satori.refinery-platform.org and integrated into the Refinery Platform.Supplementary information Supplementary data are available at Bioinformatics online.

Open-Source Neural Machine Translation API Server

Abstract We introduce an open-source implementation of a machine translation API server. The aim of this software package is to enable anyone to run their own multi-engine translation server with neural machine translation engines, supporting an open API for client applications. Besides the hub with the implementation of the client API and the translation service providers running in the background we also describe an open-source demo web application that uses our software package and implements an online translation tool that supports collecting translation quality comparisons from users.

Designing and Developing Cell Phone Applications for Qualitative Research

Recent technological developments have made it feasible for qualitative researchers to develop their own digital tools. As an example, the goal of this article is to explore the design process involved in developing cell phone applications for qualitative research. Cell phones, ubiquitous in our daily lives, can serve researchers in many ways. Cell phones can be used for recording conversations during interviews and taking pictures during observations. We will introduce two cell phone applications—Interview and Observation Tools—developed by the first author in response to data collection and analysis tasks carried out in discussion with the second author, his dissertation advisor. We will also introduce App Inventor, which is an open-source web application for the android operating system that the first author used to program and develop both applications. We will discuss why and how we included specific features based on the first author’s reflections. This work will provide qualitative researchers with practical tips for developing their own digital tools and generate ideas for future research by introducing the methodological problems the first author encountered and how he addressed them in the design and development processes of his cell phone applications.

Picasso: A Modular Framework for Visualizing the Learning Process of Neural Network Image Classifiers

Picasso is a free open-source (Eclipse Public License) web application written in Python for rendering standard visualizations useful for analyzing convolutional neural networks. Picasso ships with occlusion maps and saliency maps, two visualizations which help reveal issues that evaluation metrics like loss and accuracy might hide: for example, learning a proxy classification task. Picasso works with the Tensorflow deep learning framework, and Keras (when the model can be loaded into the Tensorflow backend). Picasso can be used with minimal configuration by deep learning researchers and engineers alike across various neural network architectures. Adding new visualizations is simple: the user can specify their visualization code and HTML template separately from the application code.

Jaqpot Quattro: A Novel Computational Web Platform for Modeling and Analysis in Nanoinformatics.

Engineered nanomaterials (ENMs) are increasingly infiltrating our lives as a result of their applications across multiple fields. However, ENM formulations may result in the modulation of pathways and mechanisms of toxic action that endanger human health and the environment. Alternative testing methods such as in silico approaches are becoming increasingly popular for assessing the safety of ENMs, as they are cost- and time-effective. Additionally, computational approaches support the industrial safer-by-design challenge and the REACH legislation objective of reducing animal testing. Because of the novelty of the field, there is also an evident need for harmonization in terms of databases, ontology, and modeling infrastructures. To this end, we present Jaqpot Quattro, a comprehensive open-source web application for ENM modeling with emphasis on predicting adverse effects of ENMs. We describe the system architecture and outline the functionalities, which include nanoQSAR modeling, validation services, read-across predictions, optimal experimental design, and interlaboratory testing.

TouchTerrain: A simple web-tool for creating 3D-printable topographic models

An open-source web-application, TouchTerrain, was developed to simplify the production of 3D-printable terrain models. Direct Digital Manufacturing (DDM) using 3D Printers can change how geoscientists, students, and stakeholders interact with 3D data, with the potential to improve geoscience communication and environmental literacy.No other manufacturing technology can convert digital data into tangible objects quickly at relatively low cost; however, the expertise necessary to produce a 3D-printed terrain model can be a substantial burden: knowledge of geographical information systems, computer aided design (CAD) software, and 3D printers may all be required. Furthermore, printing models larger than the build volume of a 3D printer can pose further technical hurdles.The TouchTerrain web-application simplifies DDM for elevation data by generating digital 3D models customized for a specific 3D printer's capabilities. The only required user input is the selection of a region-of-interest using the provided web-application with a Google Maps-style interface. Publically available digital elevation data is processed via the Google Earth Engine API. To allow the manufacture of 3D terrain models larger than a 3D printer's build volume the selected area can be split into multiple tiles without third-party software. This application significantly reduces the time and effort required for a non-expert like an educator to obtain 3D terrain models for use in class. The web application is deployed at http://touchterrain.geol.iastate.edu, while source code and installation instructions for a server and a stand-alone version are available at Github: https://github.com/ChHarding/TouchTerrain_for_CAGEO.

The Best Tool for the Job: Revisiting an Open Source Library Project

Sometimes the best tool for the job isn't the newest. It can be an existing tool that only requires a bit of polishing. This case study describes how a new digital services librarian, using a systematic approach, worked with colleagues to inaugurate a technology program within an academic library. In the process a previously-established open source web application was revived, extending its utility to contemporary development platforms. At the Queens College Libraries, an open source room reservation and scheduling system provided an answer to two important questions, and a means for building a new program.

Debugging experiment machinery through time‐course event sequence analysis

This application note describes an open-source web application software package for viewing and analysing time-course event sequences in the form of log files containing timestamps. Web pages allow the visualisation of time-course event sequences as time curves and the comparison of sequences against each other to visualise deviations between the timings of the sequences. A feature allows the analysis of the sequences by parsing selected sections with a support vector machine model that heuristically calculates a value for the likelihood of an error occurring based on the textual output in the log files. This allows quick analysis for errors in files with large numbers of log events. The software is written in ASP.NET with Visual Basic code-behind to allow it to be hosted on servers and integrated into web application frameworks.