Mock Hosseinzadeh Lab Resources

Initial steps

1. Read the lab agreement and reach out to Parisa with any questions or suggestions. This is a living document.
2. Review the basics of protein biochemistry and protein design in the Protein biochemistry & design section below.
3. Review bash, Python, and Rosetta scripting fundamentals in the Coding section below.
4. Review our biosafety and ethics rules. (coming soon)

Amino acids, proteins and biochemistry

• Lehninger Principles of Biochemistry — chapters on proteins. Available in the lab library (sign up to borrow).
• Video lectures by David Baker:
  • David Baker: Introduction to protein design (YouTube)
  • David Baker: Protein design principles (YouTube)
• Educational videos on techniques used in a protein design lab (Google Doc)

Further reading

• The coming age of de novo protein design (Nature)
• Machine learning for proteins (GitHub resource list)
• Rosetta energy score function review (journal article)
• Overview of Rosetta's collaborative scientific software development (PLOS)
• Macromolecular modeling and design with Rosetta (Nature Methods)

Core scripting

• Bash scripting tutorial for beginners (LinuxConfig) and the ultimate bash crash course (Medium)
• Python course by Google (Google Developers)
• Rosetta tutorials (RosettaCommons)

Rosetta-specific resources

• Rosetta Commons website and Rosetta Commons wiki
• RosettaScripts documentation and tutorial: how to write a RosettaScript
• Full list of Rosetta command-line options
• PyRosetta documentation
• Foldit: learn protein folding through gameplay

Computational platforms

• Jupyter Notebook tutorial (DataQuest)
• Google Colab:
  • Getting started with Google Colab (Towards Data Science)
  • Google Colab features overview (notebook)

Machine Learning

• 3Blue1Brown: visual math and neural network explainers
• Machine learning course by Andrew Ng (Coursera)
• Deep learning tips and tricks cheat sheet (Stanford CS230)
• Convolutional neural networks: Stanford CNN lecture series for image processing (YouTube)
• Graph neural networks and geometric deep learning:
  • Introduction to geometric deep learning (~1 hour, YouTube)
  • Three-part introduction to GNNs and geometric deep learning (Medium)
  • Stanford GNN course series by Jure Leskovec (YouTube playlist)
• Computational biology resources compiled by SO Lab

Grants and fellowships

The fellowship list below applies to postdocs, graduate students, and undergraduates.

• List of potential fellowships (Google Sheet)
• Fellowship application deadlines (Rosetta Commons wiki)
• Grant writing guide (University of Wisconsin–Madison)
• NIH grant application tips (NIGMS)
• NSF GRFP application guide and examples

Well-being

• General well-being resources including apps and books (Google Doc)
• Mental health resources at UO (Student Life) and community resources (Dean of Students)
• On impostor syndrome: Four tips for managing impostor syndrome feelings (Nature) and how to overcome impostor fears in research (Nature). Also recommended: The Secret Thoughts of Successful Women — available in the lab library.
• On perfectionism in research (Nature)

Navigating Academic Life

• Advice on being an effective graduate student advisee (PubMed)
• How to be a great mentee (JPHMP Direct)
• Strategies for managing your relationship with your advisor (Science)
• Time management tactics for academics (Great Research)
• How to keep up with the scientific literature (Science) — including using Feedly to track new papers (Fraser Lab)
• Research career resources compiled by Rocklin Lab
• Hosseinzadeh Lab internal wiki (Confluence, UO)

Explore protein science

• Play Foldit: solve real protein-folding puzzles through gameplay — and watch the community in action with Foldit lab report #1 (YouTube).
• Donate your computer's idle time to scientific research via BOINC — runs in the background while you sleep.
• Located near Eugene? If you're interested in a Rosetta demo at your school, contact us.
• Undergraduate student outside UO looking for summer research? Consider applying to the Rosetta REU program or the Rosetta post-baccalaureate program.

Support organizations

Consider donating to organizations working to build a more inclusive and diverse scientific community.

• Black Girls Code — increasing access and opportunity for women of color in tech. See also this list of action items compiled by Black in Computing.
• M.U.S.E. (Mentorship for Underrepresented STEM Enthusiasts) — supporting mentorship for underrepresented students in STEM.
• Academic Mutual Aid Foundation — financial and social support for students and student employees.
• American Indian Science and Engineering Society (AISES) — advancing representation of Indigenous peoples of North America in STEM.

Science outreach for scientists

If you're a researcher looking to engage with the public and inspire the next generation, here are some opportunities.

• Skype a Scientist — bring a classroom into a virtual conversation about your research.
• Letters to a Pre-Scientist — become a pen pal to a young aspiring scientist.
• Join SACNAS, ABRCMS, or other affinity conference chapters in your area, or attend one of their annual conferences.
• Check your local science museum for volunteer opportunities to engage with the public directly.