libsbmljs — Enabling Web–Based SBML Tools

The SBML standard is used in a number of online repositories for storing systems biology models, yet there is currently no Web–capable JavaScript library that can read and write the SBML format. This is a severe limitation since the Web has become a universal means of software distribution, and the graphical capabilities of modern web browsers offer a powerful means for building rich, interactive applications. Also, there is a growing developer population specialized in web technologies that is poised to take advantage of the universality of the web to build the next generation of tools in systems biology and other fields. However, current solutions require server– side processing in order to support existing standards in modeling. We present libsbmljs, a JavaScript / WebAssembly library for Node.js and the Web with full support for all SBML extensions. Our library is an enabling technology for online SBML editors, model–building tools, and web–based simulators, and runs entirely in the browser without the need for any dedicated server resources. We provide NPM packages, an extensive set of examples, JavaScript API documentation, and an online demo that allows users to read and validate the SBML content of any model in the BioModels and BiGG databases. We also provide instructions and scripts to allow users to build a copy of libsbmljs against any libSBML version. Although our library supports all existing SBML extensions, we cover how to add additional extensions to the wrapper, should any arise in the future. To demonstrate the utility of this implementation, we also provide a demo at https://libsbmljsdemo.github.io/ with a proof–of–concept SBML simulator that supports ODE and stochastic simulations for SBML core models. Our project is hosted at https://libsbmljs.github.io/, which contains links to examples, API documentation, and all source code files and build scripts used to create libsbmljs. Our source code is licensed under the Apache 2.0 open source license.

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Prosedur efektif pengembangan aplikasi basis data

JSAI (Journal Scientific and Applied Informatics) ◽

10.36085/jsai.v2i1.104 ◽

2019 ◽

Vol 2 (1) ◽

Author(s):

Zulkarnaen Hatala

Keyword(s):

Web Application ◽

Specific Requirement ◽

Application System ◽

Web Based ◽

Database Application ◽

Server Side ◽

The Right ◽

Client Side ◽

The Web

Abstract—Efficient and quick procedure to build a web application is presented. The steps are intended to build a database application system with hundreds of tables. The procedure can minimize tasks needed to write code and doing manual programming line by line. The intention also to build rapidly web-based database application. In this method security concerning authentification and authorization already built in ensuring the right and eligible access of the user to the system. The end result is ready to use the web-based 3-tier application. Moreover, the application is still flexible to be customized and to be enhanced to suit more specific requirement in part of each module of the software both the server-side and client-side programming codes. Abstrak—Pada penelitian kali ini diusulkan prosedur cepat dan efisien pengembangan aplikasi basis data menggunakan generator aplikasi. Bertujuan untuk meminimalisir penulisan bahasa pemograman. Keuntungan dari prosedur ini adalah bisa digunakan untuk mengembangkan aplikasi basis data secara cepat terutama dengan sistem basis data yang terdiri dari banyak tabel. Hak akses dan prosedur keamanan standar telah disediakan sehingga setiap user terjamin haknya terhadap entitas tertentu di basis data. Hasil generasi adalah aplikasi basis data berbasis web yang siap pakai. Sistem aplikasi yang terbentuk masih sangat lentur untuk untuk dilakukan penyesuaian setiap komponen aplikasi baik di sisi server maupun di sisi client.

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Software Architectures and Requirements for a Web-Based Survey System

Modelling and Analysis of Enterprise Information Systems ◽

10.4018/978-1-59904-477-4.ch004 ◽

2011 ◽

pp. 87-109

Author(s):

Dirk Baldwin ◽

Suresh Chalasani

Keyword(s):

Web Application ◽

Application Server ◽

Web Based ◽

Server Side ◽

Business Partners ◽

University Of Wisconsin ◽

Survey System ◽

Survey Responses ◽

The University ◽

The Web

Many businesses obtain feedback by surveying customers and business partners. Increasingly, these surveys are conducted via the Web. This chapter reviews briefly literature regarding Web-based surveys and describes a software architecture for a Web-based survey system. The architecture for the survey system is based on three-tiers comprised of a Web server, Web application server, and database server. The Web application server hosts the application modules that display and process the surveys. The application software consists of packages for establishing connections to the database and for reading static and dynamic data from the database. The processed surveys are written to the database with the survey responses. This system allows for anonymous survey responses and maintains user confidentiality. At the University of Wisconsin-Parkside, we have implemented this Web-based survey system, and used it to conduct three different surveys. This survey system is easily extensible to new surveys, and is used for instructional purposes to teach server-side programming. In this chapter, we discuss the key ideas behind the design and implementation of the extensible survey system, and provide results on its application.

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MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data

PLoS ONE ◽

10.1371/journal.pone.0243609 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243609

Author(s):

Yi-An Chen ◽

Jonguk Park ◽

Yayoi Natsume-Kitatani ◽

Hitoshi Kawashima ◽

Attayeb Mohsen ◽

...

Keyword(s):

Source Code ◽

Phenotype Correlation ◽

Microbial Composition ◽

Phenotypic Data ◽

Web Based ◽

Taxonomic Profiling ◽

Link Type ◽

Analytical Tools ◽

Analysis Platform

With an ever-increasing interest in understanding the relationships between the microbiota and the host, more tools to map, analyze and interpret these relationships have been developed. Most of these tools, however, focus on taxonomic profiling and comparative analysis among groups, with very few analytical tools designed to correlate microbiota and the host phenotypic data. We have developed a software program for creating a web-based integrative database and analysis platform called MANTA (Microbiota And pheNoType correlation Analysis platform). In addition to storing the data, MANTA is equipped with an intuitive user interface that can be used to correlate the microbial composition with phenotypic parameters. Using a case study, we demonstrated that MANTA was able to quickly identify the significant correlations between microbial abundances and phenotypes that are supported by previous studies. Moreover, MANTA enabled the users to quick access locally stored data that can help interpret microbiota-phenotype relations. MANTA is available at https://mizuguchilab.org/manta/ for download and the source code can be found at https://github.com/chenyian-nibio/manta.

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Matchathon: A guide to student-faculty connections in PhD programs

10.1101/2020.11.06.371526 ◽

2020 ◽

Author(s):

Haley Amemiya ◽

Zena Lapp ◽

Cathy Smith ◽

Margaret Durdan ◽

Michelle DiMondo ◽

...

Keyword(s):

Open Source ◽

Source Code ◽

Faculty Members ◽

Retention Rates ◽

Link Type ◽

Shiny App ◽

R Shiny ◽

Web App ◽

Phd Programs ◽

The Web

AbstractRelevant and impactful mentors are essential to a graduate student’s career. Finding mentors can be challenging in umbrella programs with hundreds of faculty members. To foster connections between potential mentors and students with similar research interests, we created a Matchathon event, which has successfully enabled students to find mentors. We developed an easy-to-use R Shiny app (https://github.com/UM-OGPS/matchathon/) to facilitate matching and organizing the event that can be used at any institution. It is our hope that this resource will improve the environment and retention rates for students in the academy.The open source app is publicly available on the web (app: https://UM-OGPS.shinyapps.io/matchathon/; source code: https://github.com/UM-OGPS/matchathon/).

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A Python-WSGI and PHP-Apache Web Server Performance Analysis by Search Page Generator (SPG)

UKH Journal of Science and Engineering ◽

10.25079/ukhjse.v5n1y2021.pp132-138 ◽

2021 ◽

Vol 5 (1) ◽

pp. 132-138

Author(s):

Hataw Jalal Mohammed ◽

Kamaran Hama Ali Faraj

Keyword(s):

Computer Architecture ◽

Source Code ◽

Web Server ◽

The Other ◽

Web Database ◽

Web Servers ◽

Web Technologies ◽

Server Side ◽

The One ◽

The Web

The web servers (WSGI-Python) and (PHP-Apache) are in middleware tier architecture. Middleware architecture is between frontend tier and backend tier, otherwise it’s a connection between frontend tier and backend tier for three tier architecture. The ELearning systems are designed by two different dynamic web technologies. First is by Python-WSGI and the second is by Personal Home Page (PHP-Apache). The two websites were designed with different open source and cross platform web technologies programming language namely; Python and PHP in the same structure and weight will evaluate perform over two different operating systems (OSs): 1) Windows-16 and 2) Linux-Ubuntu 20.4. Both systems run over the same computer architecture (64bit) as a server side with a common backend MySQL web database for both of them. Nevertheless, the middleware for PHP is a cross Apache MySQL PHP Perl (XAMPP), but the middleware for Python is Pycharm and the web server gateway interface (WSGI). WSGI and Apache are both web servers and this paper will show which of them has a better response time (RT). On the one hand, the experimental results demonstrate that the Python-WSGI is even weightier in Mbyte than PHP-Apache, on the other hand Python is still faster and more accurate than PHP. The designed SPG is by handwriting codes: one time designed the SPG by PHP source code and the other time designed by Python source code. Both Python-WSGI and PHP-Apache results are targeted to compare by the least time in milliseconds and take in to account enhanced performance.

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MMseqs2 desktop and local web server app for fast, interactive sequence searches

10.1101/419895 ◽

2018 ◽

Author(s):

Milot Mirdita ◽

Martin Steinegger ◽

Johannes Söding

Keyword(s):

Protein Sequence ◽

Response Times ◽

Source Code ◽

Web Server ◽

Link Type ◽

Server Application ◽

The Web

SummaryThe MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2’s runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST.Availability and implementationThe app is easy to install for non-experts. Source code, prebuilt desktop app packages for Windows, macOS and Linux, Docker images for the web server application, and a demo web server are available at https://[email protected] or [email protected]

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A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience

Neuroinformatics ◽

10.1007/s12021-021-09546-3 ◽

2021 ◽

Author(s):

João P. G. Santos ◽

Kadri Pajo ◽

Daniel Trpevski ◽

Andrey Stepaniuk ◽

Olivia Eriksson ◽

...

Keyword(s):

Parameter Estimation ◽

Systems Biology ◽

Model Building ◽

Web Based ◽

Analysis Process ◽

Single Scale ◽

Custom Made ◽

Phases Of Development ◽

Pathway Models

AbstractNeuroscience incorporates knowledge from a range of scales, from single molecules to brain wide neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a variety of different software tools in the model building and analysis process. Here we focus on the scale of biochemical pathways, which is one of the main objects of study in systems biology. While systems biology is among the more standardized fields, conversion between different model formats and interoperability between various tools is still somewhat problematic. To offer our take on tackling these shortcomings and by keeping in mind the FAIR (findability, accessibility, interoperability, reusability) data principles, we have developed a workflow for building and analyzing biochemical pathway models, using pre-existing tools that could be utilized for the storage and refinement of models in all phases of development. We have chosen the SBtab format which allows the storage of biochemical models and associated data in a single file and provides a human readable set of syntax rules. Next, we implemented custom-made MATLAB® scripts to perform parameter estimation and global sensitivity analysis used in model refinement. Additionally, we have developed a web-based application for biochemical models that allows simulations with either a network free solver or stochastic solvers and incorporating geometry. Finally, we illustrate convertibility and use of a biochemical model in a biophysically detailed single neuron model by running multiscale simulations in NEURON. Using this workflow, we can simulate the same model in three different simulators, with a smooth conversion between the different model formats, enhancing the characterization of different aspects of the model.

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Automated Gene Data Integration with Databio

10.1101/768077 ◽

2019 ◽

Author(s):

Robert W Reid ◽

Jacob W Ferrier ◽

Jeremy J Jay

Keyword(s):

Data Structures ◽

Computational Analysis ◽

Source Code ◽

Data Provenance ◽

Data Sets ◽

Time Data ◽

Specialized Knowledge ◽

Link Type ◽

Gene Data ◽

The Web

AbstractSummaryDatabio is capable of providing fast and accurate annotation of gene-oriented data sets, coupled with an integrated identifier conversion service to empower downstream data mining and computational analysis. Databio is enabled by fast real-time data structures applied to over 137 million unique identifiers, and uses automated heuristics to permit accurate data provenance without highly specialized knowledge and bioinformatics training.Availability and ImplementationFreely available on the web at https://datab.io/. Source code and binaries are freely available for download at https://github.com/joiningdata/databio/, implemented in Go and supported on Linux, Windows, and macOS.

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VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments

BMC Bioinformatics ◽

10.1186/s12859-021-04275-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yingbo Cui ◽

Zihang Wang ◽

Johannes Köster ◽

Xiangke Liao ◽

Shaoliang Peng ◽

...

Keyword(s):

Source Code ◽

Read Count ◽

Analysis Framework ◽

Web Based ◽

General Application ◽

Screening Analysis ◽

Guide Rna ◽

Link Type ◽

Screening Experiments ◽

Interactive Environment

Abstract Background VISPR is an interactive visualization and analysis framework for CRISPR screening experiments. However, it only supports the output of MAGeCK, and requires installation and manual configuration. Furthermore, VISPR is designed to run on a single computer, and data sharing between collaborators is challenging. Results To make the tool easily accessible to the community, we present VISPR-online, a web-based general application allowing users to visualize, explore, and share CRISPR screening data online with a few simple steps. VISPR-online provides an exploration of screening results and visualization of read count changes. Apart from MAGeCK, VISPR-online supports two more popular CRISPR screening analysis tools: BAGEL and JACKS. It provides an interactive environment for exploring gene essentiality, viewing guide RNA (gRNA) locations, and allowing users to resume and share screening results. Conclusions VISPR-online allows users to visualize, explore and share CRISPR screening data online. It is freely available at http://vispr-online.weililab.org, while the source code is available at https://github.com/lemoncyb/VISPR-online.

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Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology

10.1101/054601 ◽

2016 ◽

Cited By ~ 8

Author(s):

Kiri Choi ◽

J. Kyle Medley ◽

Caroline Cannistra ◽

Matthias König ◽

Lucian Smith ◽

...

Keyword(s):

Systems Biology ◽

Synthetic Biology ◽

Computational Models ◽

Model Building ◽

Stochastic Simulations ◽

Superior Performance ◽

Markup Language ◽

Development Environment ◽

Dimensional Parameter ◽

Simulation Engine

AbstractIn this article, we present Tellurium, a powerful Python-based integrated environment designed for model building, analysis, simulation and reproducibility in systems and synthetic biology. Tellurium is a modular, cross-platform, and open-source integrated development environment (IDE) composed of multiple libraries, plugins, and specialized modules and methods. Tellurium ensures exchangeability and reproducibility of computational models by supporting SBML (Systems Biology Markup Language), SED-ML (Simulation Experiment Description Markup Language), the COMBINE archive, and SBOL (Synthetic Biology Open Language). Tellurium is a self-contained modeling platform which comes with a fully configured Python distribution independent of other local Python installations on the target machine. The main interface is based on the Spyder IDE which has a highly accessible user interface akin to MATLAB (https://www.mathworks.com/). Tellurium uses libRoadRunner as the default SBML simulation engine due to its superior performance, scalability and ease of integration. libRoadRunner supports deterministic simulations, stochastic simulations and steady state analyses. Tellurium also includes Antimony, a human-readable model definition language which can be converted to and from SBML. Other standard Python scientific libraries such as NumPy, SciPy, and matplotlib are included by default. Additionally, we include several user-friendly plugins and advanced modules for a wide-variety of applications, ranging from visualization tools to complex algorithms for bifurcation analysis and multi-dimensional parameter scanning. By combining multiple libraries, plugins, and modules into a single package, Tellurium provides a unified but extensible solution for biological modeling and simulation.

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