The Protein Benders!
Join us!
Initial Steps
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Read our lab's agreement. Let ParisaH know if you have any questions about any part or have any suggestions and additions. This is a living document.
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Familiarize yourself with basics of protein biochemistry and protein design. Checkout suggested readings in scientific resources.
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Familiarize yourself with basics of bash and python scripting as well as basics of Rosetta scripts. Check videos and chapters in scientific resources.
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Know our biosafety and ethics rules (coming soon).
Protein Biochemistry and Design
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Basics of amino acids, proteins, and Biochemistry
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Educational videos on different techniques used in a protein design lab
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Readings for those interested
Coding
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Basic coding modules
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Useful Rosetta-specific links
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Detailed description of Rosetta scripts and how to create one
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Full list of in-line options
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Beyond Rosetta scripts
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Computational platforms we use
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GitLab
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Jupyter Notebook
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Google CoLab
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Getting started with CoLab
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Machine Learning
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Fun and visually beautiful math refresher, 3Blue1Brown
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Free coursera course by Andrew Ng
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Convolutional neural nets (CNNs)
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Video series on CNNs for image processing
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Graph neural nets (GNNs) and geometric deep learning
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video on geometric deep learning (~1 hour)
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3 part reading on GNNs and geometric deep learning
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Stanford course series on GNNs by Jure Lesovec
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Additional resources collected by a great scientist.
For Trainees
Our lab is dedicated to personal and professional growth of its members. In addition to trainings you get through mentorship and attending meetings, you may find some general resources below:
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Writing a scientific article:
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Writing grants and proposals:
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Handout for writing grants from University of Wisconsin-Madison
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Personal well being:
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A compilation of general resources, including apps and books
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Personal well being and community resources at UO
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Feeling like an imposter? you're not!
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Four tips to ward off impostor feelings
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How to shake off the impostor fears
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Book: "The secret thoughts of successful women" - available in our library
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For postdocs:
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Writing circles through UO
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List of potential fellowships
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Graduate students
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List of potential fellowships
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Guides and examples of NSF GRFP application
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Graduate student resources through UO
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For undergrad researchers:
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UROP
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Guides and examples of NSF GRFP application
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List of potential fellowships
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Other useful links:
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Using Feedly to keep track of literature
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Great suggestions collected by a great scientist