Spring 2024 Workshops
Workshop 4: Biomolecular Modelling & Molecular Dynamics February 15th, 2024 (2:00 - 5:00 PM)
Instructor: Drs. Pratul Agarwal & Benny Borin
Style: Virtual
Location: Zoom
Prerequisite: None
Duration: 3 hours
Cost: Free. Open to all OSU students, faculty and researchers.
Registration: Closed
Style: Virtual
Location: Zoom
Prerequisite: None
Duration: 3 hours
Cost: Free. Open to all OSU students, faculty and researchers.
Registration: Closed
Molecular modeling is a popular technique used commonly for research in the fields
of biology, chemistry, polymer sciences, and more. In particular, physical and chemical
aspects of biomolecules are regularly investigated using molecular dynamics simulations.
Molecular docking is used for investigating protein-protein, protein-DNA, protein-RNA,
and other biomolecular docking. Further, molecular docking is routinely used in drug
discovery.
This workshop will provide hands on introduction to molecular modeling. The topics
covered will include using biomolecular visualization software such as PyMOL and Chimera,
using molecular dynamics and molecular docking software. Quantum chemistry (electronic
structure calculations) will also be covered briefly. Different software used for
these calculations will also be discussed.
No prior experience is required, and especially recommended for researchers who would
like to use molecular dynamics simulations and docking in their research.
Workshop 5: Advanced Bioinformatics: RNA-seq March 14th, 2024 (2:00 - 5:00 PM)
Instructor: Dr. Fares Z. Najar
Style: Hybrid
Style: Hybrid
Location: Edmon Low Library 206
Prerequisite: Familiarity with basic Linux commands and R
Duration: 3 hours
Cost: Free. Open to all OSU students, faculty and researchers.
Registration: Closed
Prerequisite: Familiarity with basic Linux commands and R
Duration: 3 hours
Cost: Free. Open to all OSU students, faculty and researchers.
Registration: Closed
The advancement of sequencing technology and its affordability have enabled the exploration
of gene expression in different organisms and under different conditions. Delving
into the transcriptomics via RNA-seq technique allowed us to explore genes regulation
and relations with higher resolution than ever before.
This advanced hands-on workshop aims to cover the Bioinformatics aspects of transcriptomics
research using the Linux platform.
It is expected that you have familiarity in Linux basic commands and in “R”.
It is expected that you have familiarity in Linux basic commands and in “R”.
Workshop 6: Introduction to Machine Learning for Research April 18th, 2024 (2:00 - 5:00 PM)
Instructor: Dr. Chelsea L Murphy
Style: Hybrid
Style: Hybrid
Location: Edmon Low Library Digital Scholarship Center
Prerequisite: For the hands on section, familiarity with the command line and Python.
Duration: 3 hours
Cost: Free. Open to all OSU students, faculty and researchers.
Registration: Closed
Prerequisite: For the hands on section, familiarity with the command line and Python.
Duration: 3 hours
Cost: Free. Open to all OSU students, faculty and researchers.
Registration: Closed
This workshop will introduce the terminology and concepts of machine learning, including
random forests, gradient boosting classifiers, and neural networks, and how they can
be applied to research. In addition to theory, participants will be able to work with
a sample dataset to have a more practical understanding of how to implement simple
machine learning strategies and apply them to their own datasets. This workshop will
focus on implementation in Python using sci-kit.
For questions, please email director-hpcc@okstate.edu.