Since many of the groups in CTBP rely heavily the development and application of novel computing tools, we have established a Computing Working Group. This group involves CTBP graduate students, postdocs and faculty, as well as collaborators. The idea is that pooling our collective knowledge can lower technical barriers, which will facilitate more exciting scientific progress. Since many groups are working with openMM, we are beginning with discussions that focus on this particular tool. However, we plan to expand the scope of this working group, as needed.
If you are interested in participating in this working group, please sign up for one of our listserves. Due to potential firewall issues, we have lists hosted by Rice University and Northeastern University. Announcements go to both lists.
Tech Talks - 2024 and 2025
We are pleased to announce the 2024/2025 Tech Talk series. We have scheduled 6 talks during Fall 2024 and plan to have an additional 5-6 talks during the Spring 2025 semester. If you are interested in participating in tech talks, please sign up here. Talks will be held at 12pm Eastern Time (11am Central Time).
Fall 2024 Talks
- October 16 Avoiding embarrassment when reporting timescales in coarse-grained and simplified molecular models, Prof. Paul Whitford (Northeastern Univ)
- October 23 Managing the benefits and perils of open-source software, Dr. Vinicius Contessoto (Rice Univ.)
- October 30 Ensuring your science is reproducible with version-controlled software (i.e. GIT), Dr. Antonio Oliveira (Rice Univ)
- November 6 Navigating and developing complex code (using VS code), Dr. Vinîcius Contessoto (Rice Univ)
- November 13 Making professional molecular images, Dr. Esteban Dodero-Rojas (St. Judes Hospital)
- November 20 Making publication-worthy figures with Inkscape, Prof. Paul Whitford (Northeastern U)
Spring 2025 Topics
- Using and creating containers with Docker and SIngularity
- Dimensional reduction methods
- High performance computing best practices
- AI/ML applied to biomolecular dynamics
- How to effectively use a compute cluster scheduler (SLURM)
Tech Talks - 2023
Each talk has files made available for participants. See our Github repo for all supporting documents.
- October 4 Advanced visualization with VMD, Esteban Dodero-Rojas (Rice Univ)
- October 11 Introduction to using and creating containers for Docker and Singularity, Prof. Paul Whitford (Northeastern U)
- October 18 Becoming a pro beginner with Git, Dr. Antonio Oliveira (Rice U)
- October 25 Becoming competent with Git, Dr. Antonio Oliveira (Rice U)
- November 1 HPC and cluster computing best practices, Dr. Vinicius Contessoto (Rice U)
- November 8 Thread-based parallelism with OpenMP, Prof. Paul Whitford (Northeastern U)
- November 15 MPI-based parallelism, Prof. Paul Whitford (Northeastern U)
- November 29 Parallel computing with Python, Dr. Vinicius Contessoto (Rice U)
- December 6 Introduction to Structure-based models, SMOG 2 and OpenSMOG, Prof. Ronaldo Oliveira (Rice U)
- December 13 Advanced techniques with SMOG models, Esteban Dodero-Rojas (Rice U)
Tech Talks - 2021
April 21, 2021 - Wei Lu - Building a coarse-grained force field with openMM
May 5, 2021 - Carlos Bueno
May 19, 2021 - Vinicius Contessoto and Antonio Junior
June 2, 2021 - Iryna Zaporozhets - Parameterization of coarse-grained protein models based on experimental data
June 16, 2021 - Paul Whitford - Basic HPC Considerations
September 22, 2021 - Paul Whitford - Visualization Tips