The KAUST Information Technology Department blog
05 July, 2020
Building and publishing a web site hosting your research can be daunting. Add on top of that the necessity to have something that can easily be moved to a public cloud provider in the future, you could stop in your tracks.
We met recently with Dr. Amhed Missael Vargas Velazquez, a postdoctoral fellow in Prof. Christian Frokjaer-Jensen’s Laboratory of Synthetic Genome Biology in the BESE division here at KAUST. Dr. Amhed reached out to IT Research Computing for guidance on creating a web site that could be published in KAUST but also moved to a public cloud provider in the future.
Our lab is interested in understanding the general design principles of how gene expression is regulated at the genomic level in multicellular organisms; and as such, we focus on the development of bioinformatics tools and experimental techniques
that allow us to interrogate these questions in the model organism C. elegans.
One feature of C. elegans is the existence of non-coding DNA structures that are associated with genes expressed in its germline. One of these structures is known as Periodic A/T Clusters, or PATCs, which were first identified by
the Nobel laureate Andrew Fire in 2006. These structures are difficult to see by the human eye; fortunately, Andrew developed a computational algorithm that could detect and assign a value to any DNA sequence. The problem for our field has been
that this algorithm runs fast but it has been written in a now neglected programming language called Pascal; not everyone is familiar with it nor know how to use it. We wanted to enable researchers with fewer bioinformatics skills in our scientific
community to be able to analyze sequences for PATCs on an online web interface.
Our laboratory’s limited experience with developing online apps. We had a general idea of what tools we wanted to use: R language (R is a programming language and free software environment for statistical computing and graphics) and
Amazon Web Services cloud provider; but had no experience setting this up. IT Research Computing was very helpful in this regard. They scheduled an in-person meeting and discussed the options with me
and my post-doctoral advisor. We settled on a strategy that would enable us to deploy a web app written in R language and created thanks to the Shiny library (Shiny is an R package that makes it easy to build interactive web apps straight
from R). IT Research Computing not only helped us publish online, https://wormbuilder.kaust.edu.sa/, but
also suggested improvements to the code and performed security checks so we could be sure to limit any potential external exploit.
Currently, we are developing other web tools that surely will help the research of mechanisms controlling germline gene expression in C. elegans. We will reach out again to IT Research Computing so they will help us
publish all these new web sites.
IT Research Computing helped Dr. Amhed by applying its GitOps knowledge and expertise to build a GitLab pipeline that checked the code was syntactically correct, that it would build a Docker image so he can easily
deploy elsewhere in the future, run tests to make sure a regression bug was not introduced, and finally deploy it to his customers. This pipeline not only makes Dr. Amhed confident his changes will not break things, but it
also makes him independent. He can push fixes and new features to his customers all on his own without any further help from IT Research Computing.
Creating a Shiny web site is just a matter of clicks away using a GitLab template created by IT Research Computing for its customers.
Dr. Amhed Vargas (on the left in photo) has joined KAUST from Mexico. During the COVID-19 pandemic, Dr. Amhed has used his time to study machine learning methods and to learn how to play the electric bass.
Prof. Christian Frokjaer-Jensen (on the right in photo) is the first Danish to join KAUST as a Professor.
Article written by: Antonio Arena
