| Abstract: |
Since the Workshop in Molecular Evolution (MOLE) began being in 1988 at the Marine Biological Laboratory (MBL) in Woods Hole, Massachusetts, MBL records show that, through this workshop, 2021 scientists have been introduced to the state of the art in statistical and computational methods in molecular evolution, comparative genomics, population genetics, and phylogenetics. The scale of modern genomic data sets demands that biologists become comfortable using remote computing resources. Many participants experience their first exposure to bash, ssh, and git, as well as the command-line interfaces to phylogenetic software they need to use for their research, in the MOLE workshop, and our ability to help students over this hurdle was tremendously improved in 2022 through the use of an Xsede allocation, which allowed us to provide virtual machines from Jetstream 2. This provided a consistent and fast computing environment for each participant; light years better than the aging and speed-heterogeneous cluster housed at MBL that was graciously provided for our use in past years by a research lab at MBL (it is not an MBL-wide resource). We are very grateful for continued support through ACCESS for the 2023 and 2024 workshops, and we are proposing to use Jetstream 2 instances once again in the 2025 MOLE workshop. While this application is entirely educational in nature, and no research or publications will result from this project per se, the MOLE workshop serves as a great introduction to the use virtual machines for 45 of the best and brightest senior graduate students and postdoctoral researchers, who will be made aware of the existence and usefulness of computing resources made available through ACCESS in their current and future research. Scientific computing in the future will be increasingly cloud-based, and learning about how to loan a cluster for your computing needs instead of purchasing/maintaining your own cluster is thus an important additional lesson that we can add to this venerable workshop. All lectures and computer lab tutorials presented at this workshop are openly available via the public course web site at https://molevolworkshop.github.io.
We install all software needed and thus just require a base Ubuntu 22.04 install. In the 2024 workshop, we used 69 2-core, 20 GB virtual machines for 11 days, with 6 of these running for a couple of weeks prior to the workshop to allow software installation and testing of tutorials by the course faculty and teaching assistants. This amounts to approximately 42000 ACCESS credits total (which translates to 42000 SUs on IU's Jetstream2). |