Wednesday, May 13, 2020

Tuesday, March 31, 2020

Online Collaboration

BASIL members have been meeting virtually for years – we are primed to continue great work
As a group of scientists and educations located around the country, we have been working together in a virtual environment for years. We find tools such as Google Drive, Slack, and the video conferencing software BlueJeans works well for our needs. Now more than ever these tools allow us to maintain our workflow as well as provide us with a weekly time to check in with each other during this pandemic.

Moving to Online Labs

BASIL is gathering online resources to help the community in the move to online labs
In light of the extenuating circumstances created by Covid-19, many instructors find themselves suddenly teaching lab courses online. We have added a page to the BASIL Biochemistry Curriculum on GitHub to provide extra resources to modify the BASIL curriculum for online access. Check out the Simulated protein purification activity authored by BASIL member Anya Goodman. https://basilbiochem.github.io/basil/online/index.html


BASIL member provides advice in the move to online teaching in ASBMB Today

Rebecca Roberts co-authored an essay in ASBMBToday about how a focus on learning objectives can facilitate the pedagogical switch to online learning. Each BASIL module contains learning objectives that can be used as a guide. The essay can be found at https://www.asbmb.org/asbmb-today/careers/032420/the-surprising-comfort-of-learning-objectives


Thursday, February 20, 2020

Traveling to a conference on a budget

Check out this short article in ASBMB Today about attending a conference when you don't have the budget.  It's a collection of ideas from several BASIL consortium members, and will hopefully help readers stretch those travel dollars!  Can't wait for the 2020 ASBMB Annual Meeting in San Diego--hope to see you there!

https://www.asbmb.org/asbmb-today/careers/013020/attending-a-conference-on-a-budget


Wednesday, January 22, 2020

Using the PDB in the College Classroom


The Protein Data Bank (PDB, https://www.rcsb.org/) was started in 1971 and now contains  almost 148,000 solved structures.  The Protein Structure Initiative (PSI) solved large numbers of protein structures between 2000 and 2015, whether a function was known for the protein or not.  This large pool of structures has deepened our understanding of structure/function relationships.  There are currently approximately 4500 proteins with solved structures but characterized as having “unknown function”.  Identifying functions for these proteins is the focus of the BASIL curriculum—see the BASIL curriculum links at the top of the page for more details.

The PDB can be used in many educational contexts.  In the January 2020 issue of the PDB Education Corner, I had the opportunity to highlight some of my own experiences using the PDB with students(https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2020q1/corner.html#one).  Those uses range from pre-nursing students in a General, Organic and Biochemistry (GOB) course to Biochemistry majors doing independent research projects.  Although I have become comfortable using the PDB with students, it was daunting the first time I had students use PyMOL to look at the details of a PDB file.  My graduate and post-doctoral work did not involve using the PDB, and I had no computational biochemistry experience.  The student worksheet/tutorial provided by Taylor et al. (Taylor, E.V., J.A. Fortune, and C.L. Drennan. “A Research-inspired Laboratory Sequence Investigating Acquired Drug Resistance.” Biochem. Mol. Biol. Educ. 2010. 38, 247-52. DOI:10.1002/bmb.20384) was immensely helpful for understanding how to access the rich detail present in each PDB file, and provided practical ways to engage students with structure/function relationships. 

The PDB itself now has its own excellent visualization tools (my current new favorite is the “Ligand View” in the “3D View” tab).  I find myself using the PDB more and more when teaching Biochemistry, even with non-majors.  I like that the PDB, and especially the Education Corner articles, push me to explore new proteins, new visualization tools, and new ways of interacting with structural information. 

Thursday, January 16, 2020

BASIL 2019 Year in Review

The Biochemistry Authentic Scientific Inquiry Lab (BASIL) team was hard at work in 2019.

  • Eleven BASIL modules with standardized pedagogy were published and are freely available at basilbiochem.github.io/basil/.
  • Twelve institutions across the country and in Ireland carried out BASIL on their campuses.
  • Two papers published.
  • Development of Moltimate – a web application enzyme active site alignment tool.
  • BASIL became part of the CURENet collection (serc.carleton.edu/curenet/collection/220515.html).
  • One member carried out a BASIL-focused sabbatical.
  • A STEM for ALL BASIL video was viewed over 1300 times worldwide (https://stemforall2019.videohall.com/presentations/1420).
  • Workshops at Fayetteville State University and BCCE.
  • 7 presentations at national meetings.
  • BASIL members participated in the ACE-BIO network workshop on assessment.
  • One NSF supplement was funded.
  • One NSF-IUSE proposal was submitted.

2019 STEM for All Video Showcase: Innovations in STEM Education


The BASIL project is a combination of wet bench biochemistry experiments and bioinformatics exercises where students predict the function of a protein and then test their hypotheses. BASIL has been...(43 kB). Just in case the link above does not work, here is the full URL:

https://stemforall2019.videohall.com/presentations/1420