Wednesday, July 10, 2019

BASIL Update from Ursinus

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Ursinus students in Rebecca Roberts's lab perform interdisciplinary research outlined in the BASIL curriculum, which is being adopted in science classrooms around the world.

Here is a link to a great article on the Ursinus College web site. I have pasted in the image and content as best I could.

Ursinus-led BASIL Curriculum Takes Root in Science Classrooms
July 10, 2019

Ursinus College is one of eight institutions that have collaborated on an inventive new biochemistry curriculum designed for lab courses at the high school, undergraduate and graduate levels.

After a number of years of development, the BASIL (Biochemistry Authentic Scientific Inquiry Lab) curriculum, developed in part by Rebecca Roberts, an associate professor of biology at Ursinus, has been published and is publicly accessible online for any institution to incorporate into their science lab classrooms.

It is an effort funded by a grant from the National Science Foundation and developed in tandem with California Polytechnic State University, San Luis Obispo; Hope College; Oral Roberts University; Purdue University; Rochester Institute of Technology; St. Mary’s University; and SUNY Oswego.

“The idea is that anyone can utilize it,” says Roberts, who is lead author on a forthcoming article about the curriculum in Biochemistry and Molecular Biology Education, a leading international journal.

In BASIL, students predict the function of a protein and then study that protein in the lab. The curriculum is flexible and can be adapted to match the available facilities, the strengths of the instructor and the learning goals of an institution, Roberts says.

At Ursinus, it’s part of two Ursinus courses: Structural Biology and Biochemistry II. The structural biology students use computational tools to investigate protein structure and deduce a possible function. Then, biochemistry students express and purify the protein and, informed by the insights of their structural biology peers, assay the protein for the proposed function.

The curriculum aims to get students to work across disciplines and transition from thinking like students to thinking like scientists, Roberts says.

In addition to the development group of institutions, the curriculum has already been adopted by one high school in Massachusetts and a college in Great Britain.

“Graduate students have also picked up on it and so have independent researchers,” Roberts says. “We’re starting to think about how to expand BASIL even more beyond the initial development team and that’s exciting.”

The BASIL initiative, she says, provides broader course-based research experiences for students.

“It’s allowing these students to have a scientific inquiry-based experience,” Roberts says. “They’re learning cutting-edge bioinformatics skills and it gets them to think cooperatively and as part of an interdisciplinary team. That’s how science works now.”

Wednesday, May 15, 2019

BASIL Starter Pack

If you are interested in trying the BASIL curriculum on your campus, you can now order a "BASIL Starter Pack" for just $25 from DNASu, thanks to our own Mike Pikaart. The kit was designed to include ten plasmids that have performed well in our undergraduate teaching labs.

Saturday, May 11, 2019

BASIL Manual

The complete BASIL student manual is now online at the following URL:, thanks to contributions from many of our members, especially to everyone who spend two very fruitful and productive writing days in Rochester in March. A special thanks to Ashley Ringer MacDonald, who build the Github site that supports the manual. Additional information is available to registered university faculty. To register, contact us from your university email address and include your name university affiliation, and the courses where you are considering using the BASIL curriculum. Please use the subject line BASIL Registration in your email.

Tuesday, April 30, 2019

News from San Antonio April 2019

BASIL was a topic of discussion at two venues in San Antonio in the same week. On Saturday April 27, Colette Daubner presented the BASIL curriculum, with rationale and results, at a symposium  titled "Enzymes, from Isotope Effects to Allostery", held in the UT Health Science San Antonio Greehey Children's Cancer Research Center. This photo shows Dr. Daubner giving her opening slide.

Then on Tuesday April 30, the end-of-year poster session was held for all students enrolled in "CURE" courses  in the Biology Department at St. Mary's University. Several teams of Biochemistry students presented their findings about unknown proteins at the session. Here are photos showing the proud teams of students:

Friday, April 26, 2019

Teach the Teachers: Python training for faculty from the Molecular Sciences Software Institute

The Molecular Sciences Software Institute (MolSSI) is offering instructor training on August 8-9, 2019 to train new instructors to teach their Python scripting and data analysis workshop.  The workshop is free and no prior Python programming experience is required!  BASIL faculty member Ashley Ringer McDonald will be one of the instructors for the workshop.  You can find out more and register here.  Registration closes July 7, 2019. 

Thursday, April 25, 2019

Active Site Alignment on the Moltimate web page

A team of four software engineering students at RIT (George Herde, Shannon McIntosh, Joshua Miller and Steven Teplica) are completing their senior capstone project with Herbert Berntstein and Paul Craig.  They have created Moltimate, a web application that performs active site alignments for query structures by comparison to a library of 942 active site templates derived from the Mechanism and Catalytic Site Atlas.

Here is a video of their final project presentation.

Sunday, April 14, 2019

BASIL at Fayetteville State University

Andrea Carter and Paul Craig presented a protein bioinformatics workshop to the RISE students at Fayetteville State University. We worked with protein structures and sequences from the Protein Data Bank, explored the use of enzyme commission classes and active site templates at the Mechanism and Catalytic Site Atlas, and also used BLAST, Pfam and Clustal Omega for sequence analysis. We also spent some time exploring enzyme active site alignments on a new web interface that we hope to use in place of ProMOL and PyMOL in the near future. Once a beta version of that site is up we'll post it to the blog.

In the picture below (left to right), Paul Craig and his wife Elsa, joined James Raynor and Sambit Bhattacharya at Antonella's restaurant in Fayetteville for dinner on Friday evening.