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Making bioinformatics tools classroom-friendly

Poster on using Cyverse resources to make classroom that make using bioinformatics in the classroom a more manageable experience presented at the 2020 BIOME Institute: Cultivating Scientific Curiosity

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Katie M. Sandlin onto Bioinformatics

Macrosystems EDDIE Links

Overview of Macrosystems EDDIE 

Web pages for Macrosystems EDDIE ecological forecasting teaching modules (which include links to the R Shiny app webpage for each module as well as other teaching materials): 

Module 5: Introduction to Ecological Forecasting 

Module 6: Understanding Uncertainty in Ecological Forecasts 

Module 7: Using Data to Improve Ecological Forecasts 

Module 8: Using Ecological Forecasts to Guide Decision Making 

 

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Katherine Jones onto Sensing the Earth Summit

Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

This laboratory module, published on CourseSource, leads introductory biology students in the exploration of a basic set of bioinformatics concepts and tools.

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Katie M. Sandlin onto Bioinformatics

Running Carpentries Workshops Without Internet Access

Carpentries Offline is a project that aims to bring Carpentries workshops to areas where there is limited or no Internet access. In this video (4:21), we aim to show how we are addressing the challenge.

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Alycia Crall onto Sensing the Earth Summit

From Dirt to <em>Streptomyces</em> DNA

The purpose of this semester-long Lesson is to give students an authentic, course-based undergraduate research experience during which they learn basic and advanced microbiological and molecular biology techniques. This project begins with the isolation of a suspected Streptomyces bacterium from a soil sample and concludes with its identification. Students collect data, regarding colony and cell morphology, biochemical characteristics, the production of secondary metabolites, and employs the PCR using custom-designed primers to the Streptomyces 16s rRNA gene. The project culminates with the identification of their soil isolate using the National Center for Biotechnology Information (NCBI) web site to perform nucleotide blasts. The blastn program provides the final piece of evidence used to confirm, or not, the identification of their isolate as a Streptomyces from 16s rRNA gene sequence data, hence the title “From Dirt to Streptomyces DNA. In addition, the Lesson focuses on the Streptomyces bacteria to address several ASM aligned goals and objectives. These include prokaryotic growth phases and ways in which interactions of microorganisms among themselves and with their environment is determined by their metabolic abilities.  In addition, this Lesson illustrates how microbial metabolism is important to a relevant societal issue, the need for new antibiotic discovery particularly given the rise of antibiotic resistance strains of clinically relevant bacteria. It also illustrates the microbial diversity of soil and the developmental/physiological strategies employed in such a competitive environment. This Lesson hopes to impart both the thrill and challenges associated with scientific discovery.

Primary image: Photomicrograph of Streptomyces colonies growing on ISP 2 agar. The Streptomyces are student isolates showing stages of morphological development. Photomicrograph by Marc A. Brodkin.

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Aga Gałązka onto Microbiology

The Carpentries Toolkit of IDEAS

The Toolkit of IDEAS (Inclusion, Diversity, Equity and Accessibility Strategies) is a practical resource for Carpentries’ Instructors, helpers, and workshop hosts. We know that many people care about inclusion, diversity, equity and accessibility but are not sure how it connects to teaching foundational coding and data science skills. This toolkit aims to bridge this gap. 

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Alycia Crall onto Sensing the Earth Summit

Molecular CaseNet Biweekly meeting related (Nov. 11, 2022)

Case presentations

  • Aeisha Thomas (Streptokinase - Bacteria Sourced Drug For Cardiovascular Disease)
  • Swati Agrawal (A Case study of Drug Resistance in Leishmania)
  • Alexander Escobar (Running Out of Time)

We actually ran out of time. We will hear about more case outlines in the next meeting.

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Shuchismita Dutta onto Meeting Recordings

Life in Urban Environments: The Impact of Urbanization on Life-History Traits in Amphibian Species

This lesson focuses on urbanization and its negative effects on species, specifically amphibians. The lesson will also provide hands-on statistical analyses and critical thinking questions to promote a better understanding of this ecological problem.

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Katie Weglarz onto ForEBio

Coyote Habituation and a Scientist Spotlight on Dr. Christopher Schell

Dr. Christopher Schell is an ecologist who uses a variety of techniques to study mammalian carnivores in urban areas. This scientist spotlight uses graphs from his study on parental habituation to human disturbance in coyotes.

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Katie Weglarz onto ForEBio

Friday Morning Workshop 1 - EDS w/ Python

Here are the files that we'll be using for the Friday morning workshop (EDS w/ Python). 

If you want to follow along and do some coding, please use the live coding notebook (haskell-EDS-demo-live-code.ipynb)

If you want to follow along without doing any coding, please use the solutions notebook (haskell-EDS-demo-soln.ipynb)

There is also a link to the GitHub repository where the notebooks and corresponding data live publicly (https://github.com/CU-ESIIL/Haskell-python-demo.) 

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Teaching Population Dynamics with Data and HHMI BioInteractive

Presented at NABT 2019, we demonstrate how the Population Dynamics Click & Learn resource can be customized for any organism - using the Lionfish invasion as an example

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Katie Weglarz onto ForEBio

IndigiData: Indigenous Data Science Education

Website for a project led by the Native BioData Consortium to train and engage tribal undergraduate and graduate students in informatics.

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Alycia Crall onto Sensing the Earth Summit

Sensing the Earth Tribal College Faculty Data Science Experience Flyer

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Alycia Crall onto Sensing the Earth Summit

Materials for Teaching the SIR Epidemic Model

This web page contains materials created by faculty of the University of Nebraska-Lincoln Department of Mathematics to teach basic fundamentals of mathematical epidemiology.

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Katie Weglarz onto ForEBio

A CURE for <i>Salmonella</i>: A Laboratory Course in Pathogen Microbiology and Genomics

Rapid advances in genomics and bioinformatics, the vast amount of data generated by next-generation sequencing, and the penetration of the ‘-omics’ into many areas of biology have created a need for students with hands-on experience with computational and ‘big data’ methods. Additionally, laboratory experience in the isolation, identification, and characterization of unknown bacteria is a vital part of a microbiology student’s training. This lesson is a course-based undergraduate research experience (CURE) focusing on Salmonella enterica, a common and relatively low-virulence foodborne pathogen. In Module 1, students isolate and identify S. enterica strains from stream sediment, poultry litter, or other sources. They conduct phenotypic evaluation of antimicrobial resistance (AMR) and can search for plasmids. Isolates’ whole genomes may be sequenced by the United States FDA or public health laboratories, typically at no charge. In Module 2, students learn basic methods of genome assembly, analysis, annotation, and comparative genomics. They use easily accessible, primarily web-based tools to assemble their genomes and investigate areas of interest including serotype, AMR genes, and in silico evidence of mobile genetic elements. Either module can be used as a standalone learning experience. After course completion, students will be able to isolate and identify Salmonella from natural sources, and use computational analysis of microbial genomic data, particularly of the Enterobacteriaceae. This lesson offers undergraduate microbiologists a genuine research experience and a real-world microbiology application in genomic epidemiology, as well as a valuable mix of field, laboratory, and computational skills and experiences.

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Valeri Sawiccy onto CURE

Caleb Trujillo shared this assignment

Use as is or adapt.

Reach out to Caleb for further discussions - calebtru@uw.edu

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Shuchismita Dutta onto Scientist Spotlight related

resources to develop lessons around

have students review these resources and reflect. Change in attitudes?

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Shuchismita Dutta onto Scientist Spotlight related

Molecular CaseNet Biweekly meeting related (Oct 28, 2022)

Alex P. shared her case outline and how she is working with a student to develop the case. She will be piloting parts of the case this semester (in a Biology/pharmacology course) and other parts next semester (in a Biochem course). Candace shared possible storylines based on plant biology - why do roots grow downwards while shoots grow up? Disease resistance in plants.

Shuchi reviewed a figure that describes instructions for writing case studies. The working document link is shared here. Feel free to review and provide feedback.

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Shuchismita Dutta onto Meeting Recordings

A New Curriculum Development Model for Improving Undergraduate Students’ Data Literacy and Self-Efficacy in Online Astronomy Classrooms

We created a curricular model used to inform the development of a data-driven, citizen science-based activity to teach undergraduate, introductory astronomy students about the transit method of exoplanet detection. The activity was pilot tested with 1099 students during the 2020-2021 academic year. An analysis of student survey results indicated that after engaging with our activity, students’ self-efficacy improved on survey items that assessed their beliefs regarding their ability to make meaningful contributions to scientific research, and their confidence using data representations to answer an array of scientific questions.

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Molecular CaseNet Biweekly meeting related (Oct 14, 2022)

Elizabeth and Keith shared their experiences writing molecular case studies. (Keith's slides attached)

Keith also shared the poster that his students prepared to share their MCS idea. A template pptx for you to create a similar poster to share is included too.

Shuchi introduced the idea of storytelling and its role in writing case studies

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Shuchismita Dutta onto Meeting Recordings

Awareness and prep for DEI work

Passion, Awareness, Skills, and Knowledge Inventory (PASK). This set of tools is very useful for teacher self reflection.

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Pat Marsteller onto Inclusive Teaching Inventories

Paper on first day information sheets

This paper has interesting suggestions for learning about your students.

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Pat Marsteller onto Inclusive Teaching Inventories

Students writing case studies

The MCS Standards is adapted from the spring discussions with MolCaseNet.

The writing assignment that I have used for the course (2 spring semesters) is shared.  

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Keith A. Johnson onto Communities of Practice

Student infographic assignment

I have used two infographics assignments in my course.  One early on focuses on polypeptide structures and chemical bonds (serves as a tool to remind students what we are looking at).  The second one is done for their group case study.  

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Keith A. Johnson onto Communities of Practice

Molecular CaseNet Biweekly meeting related (Sep 30, 2022)

Recordings and files from meeting

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Shuchismita Dutta onto Meeting Recordings