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

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/).

scholarly journals DrawAlignR: An interactive tool for across run chromatogram alignment visualization

2020 ◽  
Author(s):  
Shubham Gupta ◽  
Justin Sing ◽  
Arshia Mahmoodi ◽  
Hannes Röst
Keyword(s):  
Open Source ◽  
Web Application ◽  
Source Code ◽  
Link Type ◽  
Interactive Tool ◽  
Cumulative Score ◽  
Alignment Algorithms ◽  
R Shiny ◽  
Software Platforms

AbstractMulti-run alignment is widely used in proteomics to establish analyte correspondence across runs. Generally alignment algorithms return a cumulative score, which may not be easily interpretable for each peptide. Here we present a novel tool, DrawAlignR, to visualize each chromatographic alignment for DIA/SWATH data. Furthermore, we have developed a novel C++ based implementation of raw chromatogram alignment which is 35 times faster than the previously published algorithm. This not only enables users to plot alignment interactively by DrawAlignR, but also allows other software platforms to use the algorithm. DrawAlignR is an open-source web application using R Shiny that can be hosted using the source-code available at https://github.com/Roestlab/DrawAlignR.

scholarly journals metaCOVID: An R-Shiny application for living meta-analyses of COVID-19 trials

2021 ◽  
Author(s):  
Theodoros Evrenoglou ◽  
Isabelle Boutron ◽  
Anna Chaimani
Keyword(s):  
Evidence Synthesis ◽  
Source Code ◽  
Decision Makers ◽  
Sensitivity Analyses ◽  
Preventive Interventions ◽  
Primary Interest ◽  
Link Type ◽  
R Shiny ◽  
Meta Analyses ◽  
Shiny Application

Abstract“Living” evidence synthesis is of primary interest for decision-makers to overcome the COVID-19 pandemic. The COVID-NMA provides open-access living meta-analyses assessing different therapeutic and preventive interventions. Data are posted on a platform (https://covid-nma.com/) and analyses are updated every week. However, guideline developers and other stakeholders also need to investigate the data and perform their own analyses. This requires resources, time, statistical expertise, and software knowledge. To assist them, we created the “metaCOVID” application which, based on automation processes, facilitates the fast exploration of the data and the conduct of analyses tailored to end-users needs. metaCOVID has been created in R and is freely available as an R-Shiny application. The application conducts living meta-analyses for every outcome. Several options are available for subgroup and sensitivity analyses. The results are presented in downloadable forest plots. metaCOVID is freely available from https://covid-nma.com/metacovid/ and the source code from https://github.com/TEvrenoglou/metaCovid.

scholarly journals Covidex: an ultrafast and accurate tool for virus subtyping

2020 ◽  
Author(s):  
Marco Cacciabue ◽  
Pablo Aguilera ◽  
María Inés Gismondi ◽  
Oscar Taboga
Keyword(s):  
Open Source ◽  
Web Application ◽  
Classification Models ◽  
Genome Sequences ◽  
Link Type ◽  
Shiny App ◽  
Cross Platform ◽  
Model Generator ◽  
Free Machine ◽  
Subtyping Tool

SummaryCovidex is an open-source, alignment-free machine learning subtyping tool for viral species. It is a shiny app that allows a fast and accurate classification in pre-defined clusters for SARS-CoV-2 and FMDV genome sequences. The user can also build its own classification models with the Covidex model generator.AvailabilityCovidex is open-source, cross-platform compatible, and is available under the terms of the GNU General Public License v3 (http://www.gnu.org/licenses/gpl.txt). Covidex is available via SourceForge https://sourceforge.net/projects/covidex or the web application https://cacciabue.shinyapps.io/shiny2/[email protected]; [email protected]

scholarly journals Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

2021 ◽  
Author(s):  
Soohyun Lee ◽  
Carl Vitzthum ◽  
Burak H. Alver ◽  
Peter J. Park
Keyword(s):  
Quality Control ◽  
Open Source ◽  
Source Code ◽  
Three Dimensional ◽  
File Format ◽  
Interaction Data ◽  
Text File ◽  
Storage And Retrieval ◽  
Link Type ◽  
Efficient Storage

AbstractSummaryAs the amount of three-dimensional chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files.AvailabilityThe format specification and source code are available at https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/[email protected] or [email protected]

Utilizing Interactive Technologies to Engage, Integrate, Involve, and Increase Community amongst College Students

2012 ◽  
pp. 13-27
Author(s):  
Pamela M. Golubski
Keyword(s):  
Higher Education ◽  
College Students ◽  
Web 2.0 ◽  
Faculty Members ◽  
Retention Rates ◽  
Campus Community ◽  
Interactive Technologies ◽  
Face To Face ◽  
Technological Tools ◽  
The Web

Retention in higher education is a forefront goal for most administration, staff, and faculty members. For this goal to be achieved, college professionals must go above and beyond to ensure students are engaged socially, successfully integrated into the campus community, and actively involved during college. When these interactions occur, students are more likely to experience a sense of belonging, as, evident from developmental research theories, an institution could experience an increase in overall retention rates. However, to achieve engagement, integration, involvement, and feelings of belonging, it requires staff and faculty members to offer and encourage continuous interactions with students, both inside and outside the classroom. While these interactions in the past usually happened through face-to-face methods, today, the Web 2.0 and virtual technological tools have extended opportunities for college professionals to interact more often with students. Two such virtual technologies are Google Wave and Wimba Collaboration Suite (Voice, Pronto, and Classroom).

scholarly journals UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties

2017 ◽  
Author(s):  
Jake R Conway ◽  
Alexander Lex ◽  
Nils Gehlenborg
Keyword(s):  
Open Source ◽  
R Package ◽  
Link Type ◽  
Euler Diagrams ◽  
Shiny App ◽  
Quantitative Visualization

AbstractVenn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. UpSetR is available at https://cran.r-project.org/package=UpSetR and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/.

scholarly journals BioJS: an open source standard for biological visualisation – its status in 2014

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 55 ◽  
Author(s):  
Manuel Corpas ◽  
Rafael Jimenez ◽  
Seth J Carbon ◽  
Alex García ◽  
Leyla Garcia ◽  
...  
Keyword(s):  
Open Access ◽  
Open Source ◽  
Source Code ◽  
Biological Information ◽  
Modular Architecture ◽  
Community Based ◽  
Know How ◽  
Set Up ◽  
Functional Components ◽  
The Web

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.

scholarly journals A RESTful API to serve BAM file with OAuth2 compatible authorization

2017 ◽  
Author(s):  
Julien Delafontaine ◽  
Sylvain Pradervand
Keyword(s):  
Open Source ◽  
Source Code ◽  
Variant Calling ◽  
Use Case ◽  
Web Interface ◽  
Sensitive Data ◽  
Link Type ◽  
Restful Service

AbstractSummaryBam-server is an open-source RESTful service to query slices of BAM files securely and manage their user accesses. A typical use case is the visualization of local read alignments in a web interface for variant calling diagnostic, without exposing sensitive data to unauthorized users through the network, and without moving the original - heavy - file. Bam-server follows the standard implementation of a protected resource server in the context of a typical token-based authorization protocol, supporting HMAC- and RSA-hashed signatures from an authorization server of choice.AvailabilityThe source code is available at https://github.com/chuv-ssrc/bam-server-scala, and a complete documentation can be found at http://bam-server-scala.readthedocs.io/en/latest/[email protected]

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

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]

Sign in / Sign up

Export Citation Format

Share Document