MolEvolvR BTS:
When and how to build a web-app and software package?
May 15, 2023
13:00 - 17:00
We recently developed a web application, MolEvolvR, to characterize proteins using molecular evolution and phylogeny. This session will serve as a behind-the-scenes (BTS) sneak peek into what MolEvolvR does, how it does it, and its origin story. The hands-on training component will provide the basic principles of why and how to build a dashboard/web-app for your biological problem of interest with R/Shiny, and when and how you would set up your back-end as an R package.
Workshop outline | Rationale with hands-on component
Organizers:
URL: https://github.com/JRaviLab/2023-glbio
Max capacity: 25
Intended audience: Any bioinformatician/computational biologist interested in developing open source software (e.g., R-package) and web applications (e.g., using R/Shiny) for their particular use cases, or for developing more broadly applicable open resources. Familiarity with R/tidyverse would help but is not required.
May 15, 2023
8:00 - 12:00
This workshop aims to equip individuals with an understanding of how to apply reproducibility
skills and version control with GitHub and code review in their daily work. To provide a hands-on
activity to allow attendees to practice these skills and concepts and to provide the attendees
with a useful product, attendees will use our tools, open source tools for training resources
OTTR (https://www.ottrproject.org/), to create or update a free scientific website hosted on
GitHub during the workshop with automated checks and rendering. OTTR uses R packages,
GitHub templates and GitHub actions and is a suite of publishing tools that can automate
portions of the creation process for scientific websites and courses. The workshop is aimed for
individuals who are undergraduates, graduate students, medical students, or postdoctoral
fellows.
The workshop will cover fundamental concepts about reproducibility practices, code review, and
the basics of version control with Git and GitHub. These basics will include pushing and pulling
data and code to GitHub, creating development branches, submission of pull requests, code
review and collaborative coding, hosting free websites with GitHub pages, and automating
processes with GitHub actions. Reproducibility best practices are critical in performing rigorous
and transparent research. This workshop will not only help enable trainees with skills to
incorporate more reproducible practices into their daily work by performing a hands-on activity,
but learners will also leave with a new website with automations to check various aspects of the
website, such as broken urls and misspellings based on a custom dictionary. Now more than
ever, personal scientific websites are extremely helpful for demonstrating an individual's
contributions to the field (for career advancement). In addition, if a learner already has a
personal website, websites to advertise software tools and provide documentation are also vital
for increasing tool usage.
Organizer:
URL: https://www.itcrtraining.org/events#h.q5ddehyh7ec
Scholarship Application to attend: https://forms.gle/
Max capacity: 30
Intended audience: Trainees (undergraduates, graduate students, medical students, or postdoctoral fellows) that work on informatics related code.
May 15, 2023
8:00 - 17:00
A common challenge in the field of bioinformatics is the engineering of an informatics solution from a scientific proof-of-concept. Many people build their own pipelines, which often are consist of a large variety of scripts and software of different origin and quality, including many proof-of-concept scripts developed by researchers with the intention on methodology rather than production code. The complexity of these pipelines, together with a lack of clear standards of software engineering in this research field, make it difficult for institutions and companies to properly deploy, test, update and maintain software solutions – which, nevertheless, are required to be run in production level to serve as the primary competitive advantage in the applications or field of innovation.
In this workshop, we start with an in-depth discussion of “what makes good bioinformatics workflow” and dive into different perspectives of engineering best practices to turn a scientific proof-of-concept into a more repeatable, reproducible, scalable, and interactive/exploratory software solution. We will provide attendees access to Illumina’s cloud software platform tools to facilitate learning processes through hands on exercises, but the concepts are the same regardless of where they get implemented. Attendees may take these concepts and apply in their own infrastructure, on the cloud or on premise to implement better bioinformatics software solutions.
We discuss on requirements, considerations, thoughts, and tools to implement a bioinformatics pipeline to:
We then extend the discussion into how best to organize cohort level population study in genomics, and how to aggregate single sample/subject focused pipelines’ results into a data
warehouse for interactive exploration. Examples we will show include a cohort analysis tool on Illumina’s platform, as well as a crowdsourcing study on temporal transcriptomic coronavirus host infection data - from hypothesis generation to multi-omics validation through an integrative data portal development.
Learning Objectives for the Workshop For the attendees:
Organizers:
URL to see tools that will be taught during the workshop: https://developer.illumina.
Max capacity: 40
Intended audience: Beginner or intermediate level. This tutorial is aimed at bioinformaticians, computational biologists or molecular biologists – anyone who has the need to implement and operationalize a solution based on a scientific prototype in the field of genomics and bioinformatics.