amica: an interactive and user-friendly web-platform for the analysis of proteomics data

Quantitative proteomics has become an increasingly prominent tool in the study of life sciences. A substantial hurdle for many biologists are, however, the intricacies involved in the associated high troughput data analysis. In order to facilitate this task for users with little background knowledge in proteomics, we have developed amica, a freely available open-source web-based software that accepts proteomic input files from different sources and provides quality control, differential expression, biological network and over-representation analysis on the basis of minimal user input. Scientists can use amica interactively to compare proteins across multiple groups, create customized output graphics, and ultimately export the results in a tab-separated format that can be shared with collaborators. Availability and Implementation: The code for the application, input data and documentation can be accessed online at https://github.com/tbaccata/amica and is also incorporated in the web application. A freely available version of amica is available at https://bioapps.maxperutzlabs.ac.at/app/amica.

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Primer Server - A web application to design primers for the amplification of unique DNA targets in complex genomes

Journal of Student Research ◽

10.47611/jsr.vi.454 ◽

2018 ◽

Author(s):

Takao Shibamoto ◽

Kokulapalan Wimalanathan ◽

Erica Unger-Wallace ◽

Erik Vollbrecht

Keyword(s):

Web Application ◽

Genetic Material ◽

Pcr Primers ◽

Test Tube ◽

Dna Bases ◽

Web Based ◽

User Input ◽

Server Side ◽

Target Binding ◽

User Friendly

Polymerase Chain Reaction (PCR) is one of the most important inventions of the 20th century in molecular biology. PCR is a technique to amplify or make in a test tube many copies of a specific DNA region. Miniscule amounts of the genetic material from any organism can now be amplified to identify individuals, manipulate DNA, detect infectious organisms including the viruses that cause AIDS, hepatitis, and tuberculosis, detect genetic variations including mutations in genes, and numerous other tasks. PCR primers are short, single-stranded DNAs that define the section of DNA to be amplified. Two primers are used in each PCR reaction, designed so that they bind at flanking locations surrounding the target region. Critically, off-target binding may lead to experimental failure or worse, to misleading results. Thus, potential primers of approximately 20 DNA bases in length, must be examined for off-target binding among, for example, the 3.2 billion DNA bases from all human chromosomes, the human genome. The purpose of our study is to make a user-friendly tool (Primer Server) that can design PCR primers efficiently and accurately as well as visualize the designed primers. Our web-based bioinformatics tool selects optimal primer sequences within the starting material by using a C module called primer3 and then prioritizing and/or eliminating potential primers based on comparison of the primer bases against all bases in the genome using an algorithm called BLAST. This tool has an easy-to-use interface which was designed using Angular2, and an efficient server-side code written in Python. While similar tools exist, our tool is more user-friendly, efficient and uses extensive form validation to minimize errors in the user input. Our tool can be used to design primers that will be used in laboratory experiments to amplify DNA from various organisms, including large, complex genomes such as humans, other animals and plants.

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ProVision: a web-based platform for rapid analysis of proteomics data processed by MaxQuant

Bioinformatics ◽

10.1093/bioinformatics/btaa620 ◽

2020 ◽

Vol 36 (19) ◽

pp. 4965-4967

Author(s):

James Luke Gallant ◽

Tiaan Heunis ◽

Samantha Leigh Sampson ◽

Wilbert Bitter

Keyword(s):

Data Analysis ◽

Web Application ◽

Label Free ◽

Proteomics Data ◽

Web Based ◽

Protein Protein Interaction ◽

Tandem Mass Tag ◽

Protein Interaction Prediction ◽

Core Facilities ◽

User Friendly

Abstract Summary Proteomics is a powerful tool for protein expression analysis and is becoming more readily available to researchers through core facilities or specialized collaborations. However, one major bottleneck for routine implementation and accessibility of this technology to the wider scientific community is the complexity of data analysis. To this end, we have created ProVision, a free open-source web-based analytics platform that allows users to analyze data from two common proteomics relative quantification workflows, namely label-free and tandem mass tag-based experiments. Furthermore, ProVision allows the freedom to interface with the data analysis pipeline while maintaining a user-friendly environment and providing default parameters for fast statistical and exploratory data analysis. Finally, multiple customizable quality control, differential expression plots as well as enrichments and protein–protein interaction prediction can be generated online in one platform. Availability and implementation Quick start and step-by-step tutorials as well as tutorial data are fully incorporated in the web application. This application is available online at https://provision.shinyapps.io/provision/ for free use. The source code is available at https://github.com/JamesGallant/ProVision under the GPL version 3.0 license.

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An Interactive Web Application for the Statistical Analysis of Continuous Glucose Monitoring Data in Epidemiological Studies

Journal of Diabetes Science and Technology ◽

10.1177/1932296820985570 ◽

2021 ◽

pp. 193229682098557

Author(s):

Alysha M. De Livera ◽

Jonathan E. Shaw ◽

Neale Cohen ◽

Anne Reutens ◽

Agus Salim

Keyword(s):

Continuous Glucose Monitoring ◽

Web Application ◽

Diabetes Management ◽

Glucose Monitoring ◽

Epidemiological Studies ◽

Interactive Software ◽

Web Based ◽

Software Applications ◽

Visualization Of Data ◽

User Friendly

Motivation: Continuous glucose monitoring (CGM) systems are an essential part of novel technology in diabetes management and care. CGM studies have become increasingly popular among researchers, healthcare professionals, and people with diabetes due to the large amount of useful information that can be collected using CGM systems. The analysis of the data from these studies for research purposes, however, remains a challenge due to the characteristics and large volume of the data. Results: Currently, there are no publicly available interactive software applications that can perform statistical analyses and visualization of data from CGM studies. With the rapidly increasing popularity of CGM studies, such an application is becoming necessary for anyone who works with these large CGM datasets, in particular for those with little background in programming or statistics. CGMStatsAnalyser is a publicly available, user-friendly, web-based application, which can be used to interactively visualize, summarize, and statistically analyze voluminous and complex CGM datasets together with the subject characteristics with ease.

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G4Killer web application: a tool to design G-quadruplex mutations

Bioinformatics ◽

10.1093/bioinformatics/btaa057 ◽

2020 ◽

Vol 36 (10) ◽

pp. 3246-3247

Author(s):

Vaclav Brazda ◽

Jan Kolomaznik ◽

Jean-Louis Mergny ◽

Jiri Stastny

Keyword(s):

Dna Sequences ◽

Web Application ◽

Rational Design ◽

Therapeutic Potential ◽

Supplementary Information ◽

Web Tool ◽

Web Based ◽

Dna Structures ◽

G Quadruplex ◽

User Friendly

Abstract Motivation G-quadruplexes (G4) are important regulatory non-B DNA structures with therapeutic potential. A tool for rational design of mutations leading to decreased propensity for G4 formation should be useful in studying G4 functions. Although tools exist for G4 prediction, no easily accessible tool for the rational design of G4 mutations has been available. Results We developed a web-based tool termed G4Killer that is based on the G4Hunter algorithm. This new tool is a platform-independent and user-friendly application to design mutations crippling G4 propensity in a parsimonious way (i.e., keeping the primary sequence as close as possible to the original one). The tool is integrated into our DNA analyzer server and allows for generating mutated DNA sequences having the desired lowered G4Hunter score with minimal mutation steps. Availability and implementation The G4Killer web tool can be accessed at: http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.

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Data Browser Matsch | Mazia: Web Application to access microclimatic time series of an ecological research site

Research Ideas and Outcomes ◽

10.3897/rio.7.e63748 ◽

2021 ◽

Vol 7 ◽

Author(s):

Martin Palma ◽

Alessandro Zandonai ◽

Luca Cattani ◽

Johannes Klotz ◽

Giulio Genova ◽

...

Keyword(s):

Time Series ◽

Web Application ◽

Scientific Data ◽

Time Range ◽

Ecological Research ◽

Data Accessibility ◽

Web Based ◽

South Tyrol ◽

Research Site ◽

User Friendly

Easily accessible data is an essential requirement for scientific data analysis. The Data Browser Matsch | Mazia was designed to provide a fast and comprehensible solution to access, visualize and download the microclimatic measurements of the IT 25 LT(S)ER Match | Mazia research site in South Tyrol, Northern Italy, with the overall aim to provide straightforward data accessibility and enhance dissemination. Data Browser Matsch | Mazia is a user-friendly web-based application to visualize and download micrometeorological and biophysical time series of the Long-Term Socio-Ecological Research site Matsch | Mazia in South Tyrol, Italy. It is designed both for the general public and researchers. The Data Browser Matsch | Mazia drop-down menus allow the user to query the InfluxDB database in the backend by selecting the measurements, time range, land use and elevation. Interactive Grafana dashboards show dynamic graphs of the time series.

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piNET: a versatile web platform for downstream analysis and visualization of proteomics data

Nucleic Acids Research ◽

10.1093/nar/gkaa436 ◽

2020 ◽

Vol 48 (W1) ◽

pp. W85-W93 ◽

Cited By ~ 3

Author(s):

Behrouz Shamsaei ◽

Szymon Chojnacki ◽

Marcin Pilarczyk ◽

Mehdi Najafabadi ◽

Wen Niu ◽

...

Keyword(s):

Quantitative Proteomics ◽

Large Scale ◽

Model Organism ◽

Proteomics Data ◽

Primary Input ◽

Network Analyses ◽

Enzyme Substrate ◽

Chemical Inhibitors ◽

Downstream Analysis ◽

Web Platform

Abstract Rapid progress in proteomics and large-scale profiling of biological systems at the protein level necessitates the continued development of efficient computational tools for the analysis and interpretation of proteomics data. Here, we present the piNET server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with the LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. The primary input for the server consists of a set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. Several interconnected workflows can be used to generate: (i) interactive graphs and tables providing comprehensive annotation and mapping between peptides and proteins with PTM sites; (ii) high resolution and interactive visualization for enzyme-substrate networks, including kinases and their phospho-peptide targets; (iii) mapping and visualization of LINCS signature connectivity for chemical inhibitors or genetic knockdown of enzymes upstream of their target PTM sites. piNET has been built using a modular Spring-Boot JAVA platform as a fast, versatile and easy to use tool. The Apache Lucene indexing is used for fast mapping of peptides into UniProt entries for the human, mouse and other commonly used model organism proteomes. PTM-centric network analyses combine PhosphoSitePlus, iPTMnet and SIGNOR databases of validated enzyme-substrate relationships, for kinase networks augmented by DeepPhos predictions and sequence-based mapping of PhosphoSitePlus consensus motifs. Concordant LINCS signatures are mapped using iLINCS. For each workflow, a RESTful API counterpart can be used to generate the results programmatically in the json format. The server is available at http://pinet-server.org, and it is free and open to all users without login requirement.

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RaDMaX online: a web-based program for the determination of strain and damage profiles in irradiated crystals using X-ray diffraction

Journal of Applied Crystallography ◽

10.1107/s1600576720002514 ◽

2020 ◽

Vol 53 (2) ◽

pp. 587-593

Author(s):

A. Boulle ◽

V. Mergnac

Keyword(s):

Web Application ◽

The Internet ◽

Programming Environment ◽

X Ray Diffraction ◽

Web Browser ◽

Web Based ◽

X Ray ◽

Depth Profiles ◽

User Friendly

RaDMaX online is a major update to the previously published RaDMaX (radiation damage in materials analysed with X-ray diffraction) software [Souilah, Boulle & Debelle (2016). J. Appl. Cryst. 49, 311–316]. This program features a user-friendly interface that allows retrieval of strain and disorder depth profiles in irradiated crystals from the simulation of X-ray diffraction data recorded in symmetrical θ/2θ mode. As compared with its predecessor, RaDMaX online has been entirely rewritten in order to be able to run within a simple web browser, therefore avoiding the necessity to install any programming environment on the users' computers. The RaDMaX online web application is written in Python and developed within a Jupyter notebook implementing graphical widgets and interactive plots. RaDMaX online is free and open source and can be accessed on the internet at https://aboulle.github.io/RaDMaX-online/.

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The Framework for Web-Based Automated Online Question Paper Generator through JEE

International Journal of Engineering & Technology ◽

10.14419/ijet.v7i3.13573 ◽

2018 ◽

Vol 7 (3) ◽

pp. 1415

Author(s):

Vinayak Hegde ◽

Lavanya V Rao ◽

Shivali B S

Keyword(s):

Web Application ◽

Large Scale ◽

Educational Institution ◽

Faculty Members ◽

Educational Institutions ◽

Small Scale ◽

Web Based ◽

Educational Institute ◽

User Friendly ◽

Word Format

Examinations are an indispensable part of a student’s life. In the conventional mechanism, the question paper generation is time-consuming work for the faculty members of the educational institution. Every educational institute mandatorily expects exam setters to follow its own typesetting format. We have designed the automated question paper setting software to be user-friendly so that, paper setters can overcome from the typographic problem. Presently in most of the educational institutions question papers are set manually. It is time-consuming work and there may be chances of repetition of the same questions. So, in order to make the question paper generation more convenient to use, the web application is developed using Java Enterprise Edition (JEE) that can be accessed from LAN/Intranet.The application comes with the Admin Module and Teachers Module. The Admin grants access to the users by registering them. The faculty can access the system once they are registered. The faculty can enter questions in the database daily as per their free time. In this way, the question pool can be generated. The questions are approved by the chairperson and substandard questions are discarded. The question paper is then generated by selected course experts. The Fisher-Yates Shuffling algorithm used to choose questions randomly from the pool of questions from the database. Text Mining Algorithm aids in duplicity removal from the paper. The generated question paper will be in Word Format. In our application, we assure better security, removal of duplicity, cost-effectiveness, and human intervention avoidance. It can be used by small-scale and large-scale institutions.

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G4Hunter web application: a web server for G-quadruplex prediction

Bioinformatics ◽

10.1093/bioinformatics/btz087 ◽

2019 ◽

Vol 35 (18) ◽

pp. 3493-3495 ◽

Cited By ~ 22

Author(s):

Václav Brázda ◽

Jan Kolomazník ◽

Jiří Lýsek ◽

Martin Bartas ◽

Miroslav Fojta ◽

...

Keyword(s):

Data Storage ◽

Web Application ◽

Data Representation ◽

Complete Characterization ◽

Supplementary Information ◽

Web Based ◽

Rna Molecules ◽

Dna And Rna ◽

Sorting Data ◽

User Friendly

Abstract Motivation Expanding research highlights the importance of guanine quadruplex structures. Therefore, easy-accessible tools for quadruplex analyses in DNA and RNA molecules are important for the scientific community. Results We developed a web version of the G4Hunter application. This new web-based server is a platform-independent and user-friendly application for quadruplex analyses. It allows retrieval of gene/nucleotide sequence entries from NCBI databases and provides complete characterization of localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application includes an interactive graphical data representation with many useful options including visualization, sorting, data storage and export. Availability and implementation G4Hunter web application can be accessed at: http://bioinformatics.ibp.cz. Supplementary information Supplementary data are available at Bioinformatics online.

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MALBoost: a web-based application for gene regulatory network analysis in Plasmodium falciparum

Malaria Journal ◽

10.1186/s12936-021-03848-2 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Roelof van Wyk ◽

Riëtte van Biljon ◽

Lyn-Marie Birkholtz

Keyword(s):

Gene Regulatory Network ◽

Regulatory Network ◽

Web Application ◽

Regulatory Networks ◽

Web Based ◽

Time Estimates ◽

Gene Regulatory ◽

Validation Set ◽

User Friendly ◽

Case Validation

Abstract Background Gene Regulatory Networks (GRN) produce powerful insights into transcriptional regulation in cells. The power of GRNs has been underutilized in malaria research. The Arboreto library was incorporated into a user-friendly web-based application for malaria researchers (http://malboost.bi.up.ac.za). This application will assist researchers with gaining an in depth understanding of transcriptomic datasets. Methods The web application for MALBoost was built in Python-Flask with Redis and Celery workers for queue submission handling, which execute the Arboreto suite algorithms. A submission of 5–50 regulators and total expression set of 5200 genes is permitted. The program runs in a point-and-click web user interface built using Bootstrap4 templates. Post-analysis submission, users are redirected to a status page with run time estimates and ultimately a download button upon completion. Result updates or failure updates will be emailed to the users. Results A web-based application with an easy-to-use interface is presented with a use case validation of AP2-G and AP2-I. The validation set incorporates cross-referencing with ChIP-seq and transcriptome datasets. For AP2-G, 5 ChIP-seq targets were significantly enriched with seven more targets presenting with strong evidence of validated targets. Conclusion The MALBoost application provides the first tool for easy interfacing and efficiently allows gene regulatory network construction for Plasmodium. Additionally, access is provided to a pre-compiled network for use as reference framework. Validation for sexually committed ring-stage parasite targets of AP2-G, suggests the algorithm was effective in resolving “traditionally” low-level signatures even in bulk RNA datasets.

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