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

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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New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform

Briefings in Bioinformatics ◽

10.1093/bib/bbz072 ◽

2019 ◽

Vol 21 (4) ◽

pp. 1397-1410 ◽

Cited By ~ 6

Author(s):

Hebing Chen ◽

Zhuo Zhang ◽

Shuai Jiang ◽

Ruijiang Li ◽

Wanying Li ◽

...

Keyword(s):

Epigenetic Modification ◽

Essential Genes ◽

Integrated Analysis ◽

Loss Of Function ◽

Web Based ◽

Gene Essentiality ◽

Protein Protein Interaction ◽

Interactive Analysis ◽

Analytical Tools ◽

Analysis Platform

Abstract Essential genes are those whose loss of function compromises organism viability or results in profound loss of fitness. Recent gene-editing technologies have provided new opportunities to characterize essential genes. Here, we present an integrated analysis that comprehensively and systematically elucidates the genetic and regulatory characteristics of human essential genes. First, we found that essential genes act as ‘hubs’ in protein–protein interaction networks, chromatin structure and epigenetic modification. Second, essential genes represent conserved biological processes across species, although gene essentiality changes differently among species. Third, essential genes are important for cell development due to their discriminate transcription activity in embryo development and oncogenesis. In addition, we developed an interactive web server, the Human Essential Genes Interactive Analysis Platform (http://sysomics.com/HEGIAP/), which integrates abundant analytical tools to enable global, multidimensional interpretation of gene essentiality. Our study provides new insights that improve the understanding of human essential genes.

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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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GenFam: A web application and database for gene family-based classification and functional enrichment analysis

10.1101/272187 ◽

2018 ◽

Cited By ~ 1

Author(s):

Renesh Bedre ◽

Kranthi Mandadi

Keyword(s):

Gene Family ◽

Web Application ◽

High Throughput Sequencing ◽

Source Code ◽

Enrichment Analysis ◽

Gene Families ◽

Functional Enrichment ◽

Multiple Testing Correction ◽

Web Based ◽

Link Type

ABSTRACTGenome-scale studies using high-throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user-defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new approach, GenFam, which allows classification and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query. GenFam and its integrated database comprises of three-hundred and eighty-four unique gene families and supports gene family classification and enrichment analyses for sixty plant genomes. Four comparative case studies with plant species belonging to different clades and families were performed using GenFam which demonstrated its robustness and comprehensiveness over preexisting functional enrichment tools. To make it readily accessible for plant biologists, GenFam is available as a web-based application where users can input gene IDs and export enrichment results in both tabular and graphical formats. Users can also customize analysis parameters by choosing from the various statistical enrichment tests and multiple testing correction methods. Additionally, the web-based application, source code and database are freely available to use and download. Website: http://mandadilab.webfactional.com/home/. Source code and database: http://mandadilab.webfactional.com/home/dload/.

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UROPA GUI: A web platform for genomic region annotation

10.1101/302091 ◽

2018 ◽

Author(s):

Hendrik Schultheis ◽

Jens Preussner ◽

Annika Fust ◽

Mette Bentsen ◽

Carsten Kuenne ◽

...

Keyword(s):

Graphical User Interface ◽

Bioinformatics Analysis ◽

Source Code ◽

Genomic Region ◽

Command Line ◽

Web Based ◽

Link Type ◽

R Shiny ◽

Considerable Impact ◽

Web Platform

AbstractThe annotation of genomic ranges such as peaks resulting from ChIP-seq/ATAC-seq or other techniques represents a fundamental task of bioinformatics analysis with considerable impact on many downstream analyses. In our previous work, we introduced the Universal Robust Peak Annotator (UROPA), a flexible command line based tool which improves upon the functionality of existing annotation software. In order to reduce the complexity for biologists and clinicians, we have implemented an intuitive web-based graphical user interface (GUI) and fully functional service platform for UROPA. This extension will empower all users to generate annotations for regions of interest interactively.Availability and ImplementationThe open source UROPA GUI server was implemented in R Shiny and Python and is available from http://loosolab.mpi-bn.mpg.de. The source code of our App can be downloaded at https://github.molgen.mpg.de/loosolab/UROPA_GUI under the MIT license.

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CircularLogo: A lightweight web application to visualize intra-motif dependencies

10.1101/098327 ◽

2017 ◽

Author(s):

Zhenqing Ye ◽

Tao Ma ◽

Michael T. Kalmbach ◽

Surendra Dasari ◽

Jean-Pierre A. Kocher ◽

...

Keyword(s):

Binding Sites ◽

Web Application ◽

Source Code ◽

Sequence Logo ◽

Rna Motifs ◽

Biomolecular Structure ◽

Web Based ◽

Link Type ◽

Web Framework ◽

Interactive Application

AbstractBackgroundThe sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available for visualization.ResultWe developed CircularLogo, a web-based interactive application, which is able to not only visualize the position-specific nucleotide consensus and diversity but also display the intra-motif dependencies. Applying CircularLogo to HNF6 binding sites and tRNA sequences demonstrated its ability to show intra-motif dependencies and intuitively reveal biomolecular structure. CircularLogo is implemented in JavaScript and Python based on the Django web framework. The program’s source code and user’s manual are freely available at http://circularlogo.sourceforge.net. CircularLogo web server can be accessed from http://bioinformaticstools.mayo.edu/circularlogo/index.html.ConclusionCircularLogo is an innovative web application that is specifically designed to visualize and interactively explore intra-motif dependencies.

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Enabling Data Analysis on High-Throughput Data in Large Data Depository Using Web-Based Analysis Platform - A Case Study on Integrating QUEST with GenePattern in Epigenetics Research

2009 IEEE International Conference on Bioinformatics and Biomedicine ◽

10.1109/bibm.2009.84 ◽

2009 ◽

Author(s):

Terry Camerlengo ◽

Hatice Gulcin Ozer ◽

Pearlly Yan ◽

Jeffrey Parvin ◽

Tim Huang ◽

...

Keyword(s):

Data Analysis ◽

High Throughput ◽

Large Data ◽

Web Based ◽

High Throughput Data ◽

Analysis Platform

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ComPath: An ecosystem for exploring, analyzing, and curating mappings across pathway databases

10.1101/353235 ◽

2018 ◽

Author(s):

Daniel Domingo-Fernández ◽

Charles Tapley Hoyt ◽

Carlos Bobis-Álvarez ◽

Josep Marín-Llaó ◽

Martin Hofmann-Apitius

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Web Application ◽

Biological Systems ◽

Source Code ◽

Major Pathway ◽

Link Type ◽

Pathway Databases ◽

The Web

AbstractAlthough pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an ecosystem that supports curation of pathway mappings between databases and fosters the exploration of pathway knowledge through several novel visualizations. We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson’s disease that illustrates how ComPath can generate new biological insights by identifying pathway modules, clusters, and cross-talks with these mappings. The ComPath source code and resources are available at https://github.com/ComPath and the web application can be accessed at http://compath.scai.fraunhofer.de/.

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libsbmljs — Enabling Web–Based SBML Tools

10.1101/594804 ◽

2019 ◽

Author(s):

J Kyle Medley ◽

Joseph Hellerstein ◽

Herbert M Sauro

Keyword(s):

Systems Biology ◽

Model Building ◽

Source Code ◽

Stochastic Simulations ◽

Web Based ◽

Server Side ◽

Link Type ◽

Software Distribution ◽

Api Documentation ◽

The Web

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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SISTEM INFORMASI MANAJEMEN PENGARSIPAN BERBASIS FRAMEWORK CODE IGNITER UNTUK MENTERTIBKAN PELAYANAN SURAT MENYURAT

INTERNAL (Information System Journal) ◽

10.32627/internal.v2i1.70 ◽

2019 ◽

Vol 2 (1) ◽

pp. 1-16

Author(s):

Nana Suarna

Keyword(s):

Source Code ◽

Web Based

Seiring waktu, jumlah surat dalam sebuah perusahaan semakin hari makin banyak, sehingga muncul permasalahan dalam mengelolanya administrasi suarat, baik ketika dalam pencatatan surat maupun proses disposisi, serta pada saat pencarian arsip surat. Hampir sebagai besar surat yang ada di kantor-kantor masih disimpan dalam bentuk file-file yang masih bersifat manual, sehingga memungkinkan surat tersebut menunpuk, dan memerlukan waktu yang lama dalam pencarian dan pemrosesannya. Dengan dibangunnya sistem manajemen pengarsipan bertujuan untuk mengatasi permasalahan-permasalahan tersebut di atas. Pemrograman saat ini, baik desktop maupun web based, semakin marak pengerjaannya menggunakan framework code igniter berbasis PHP. Framework CI memang dikembangkan untuk memudahkan dalam developing aplikasi dengan struktur file source code-nya menggunakan pendekatan Models-Views-Controller (MVC) dan pemrograman berorientasi objek, oleh sebab itu penulis menggunakan CI dalam developing aplikasi ini. Aplikasi sistem manajemen surat dan pengarsipan ini dapat diakses dalam internal perusahaan web, yang bertujuan untuk memudahkan karyawan dalam pengelolaan dan mengaksesnya surat menyurat, selain itu aplikasi ini juga memberikan kemudahan dalam proses pencatatan surat, disposisi, dan proses pencarian sehingga aplikasisi ini memiliki performa yang handal, mudah untuk di-maintenance dan dikembangkan lebih lanjut seiring perkembangan kebutuhan penggunanya.

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A Case Study on Web-based Learning Environment Evaluation in Higher Education: Learner Perspectives in a Private University in Malaysia.

International Journal of Creative Multimedia ◽

10.33093/ijcm.2020.1.2.2 ◽

2020 ◽

Vol 1 (2) ◽

pp. 18-33

Author(s):

Zarina Che Imbi ◽

Tse-Kian Neo ◽

Mai Neo

Keyword(s):

Higher Education ◽

Learning Environment ◽

Private University ◽

Systematic Evaluation ◽

Digital Learning ◽

Mixed Method Research ◽

Web Based ◽

Web Based Learning ◽

Kirkpatrick’S Model

In the era of digital learning, multimedia-based classroom has been commonly used in higher education including Malaysian higher education institutions. A case study has been performed to evaluate web-based learning using Level 1 to 3 of Kirkpatrick's model in a multi-disciplinary course at Multimedia University, Malaysia. In this study, mixed method research was employed in which triangulation was performed from multiple sources of data collection to give deeper understanding. Students perceived that learning with multimedia was enjoyable. They were also motivated in learning and engaged through the use of web module as multimedia was perceived to motivate them and make learning fun. Students showed significant improvements in their knowledge based on the pre-test and post-test results on learning evaluation. Students were perceived to transfer the learning from web-based learning into the learning outcome. The systematic evaluation can provide the feedback that educators and institution as a whole need to improve the learning environment and programme quality. This study contributes to the research field by adding another perspective in evaluations of web-based learning. It also provides empirical evidence on student perspectives, learning and behaviour in a private university. It demonstrated that the Kirkpatrick's model is useful as an evaluation tool to be used in higher education.

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