Embed Size (px)
Citation preview
Accelerating bioinformatic learning
The University of Toronto worked with Coursera to
deliver two massive, open, online courses (https://
www.coursera.org/learn/bioinformatics-methods-1
and https://www.coursera.org/learn/bioinformatics-
methods-2) to teach students bioinformatic
methods, in order to better understand biology. One
area in this field that is important is
understanding when and where genes
are active, based on "RNA-seq" data.
Students explore this aspect in the 5th week
of the second course.
Challenge
Analyzing RNA-seq data can be done with
Bioconductor, and in the first iteration of the course,
the instructor, Nicholas Provart, had the students
install R and Bioconductor on their own computers.
This proved to be a stumbling point because of the
many different operating systems and dependencies
between different packages on different platforms.
Solution
RStudio Server Pro offered a great solution. By being
able to set up a web-accessible instance of
Bioconductor running on RStudio on Amazon Web
Services, students could proceed to learn the
methods for analyzing RNA-seq data instead of
spending time futzing with installation issues. “We
used an AWS c4.large VM as in the schematic below
to run up to 16 RStudio Server Pro instances,
depending on the load.
A php-based LDAP server was used to handle the
authentication for student logins.”
Why RStudio Server Pro?
RStudio Server Pro offered the ability to have
multiple users connect to the Bioconductor
environment, each with his/her own workspace
where work can be maintained from session to
session, and pre-existing data folders can be shared
with users.
Open source & enterprise-ready professional software for R
The Payoff
Far fewer complaints on the Discussion Forums
associated with the RNA-Seq lab and happier
students! Professor Provart is also using the online
course material to teach his University of Toronto
class, on which these courses were based. By
moving the Bioconductor component to the "cloud"
a n d u s i n g R S t u d i o S e r v e r P r o , s y s t e m s
administration headaches with University of Toronto
computer labs were also alleviated. The Univeristy of
Toronto is excited to be teaching so many students
and educating future bioinformatic professionals on
state-of-the-art analytics: 34,000 students have
enrolled in the 2nd course so far!
About RStudio
RStudio provides open source and enterprise-ready
professional software for the R community. We are
inspired by the people who use our products to
understand and improve the world through data
analysis.
RStudio® and Shiny™ are trademarks of RStudio, Inc. All rights reserved rstudio.com 844-448-1212 [email protected]
“RStudio Server Pro gave us the ability to have multiple users at once logged into Bioconductor, each with his/her own workspace. Much easier to manage the complete system and user experience.”
Nicholas Provart - Professor, Plant Cyberinfrastructure & Systems Biology
