Two articles introducing the Human Genome Project-Write and asking questions about the ethics of the project.

This is an ethical reflection for students on an issue in genome engineering and the resurrection and synthesis of historically important, but potentially lethal viruses.  The case study asks students to reflect on material in this article. Also included is the grading rubric.

This is an ethical reflection for students on an issue in metabolic engineering and the potential for "home-brew" morphine.  The case study asks students to reflect on material in this article. Also included is the grading rubric.

This is an ethical reflection for students on an issue in gene editing.  The case study asks students to reflect on material in these two articles. Also included is the grading rubric.

This is a syllabus for a full semester Synthetic Biology course. It includes a lab that meets once a week for 4 hours. In one version of the course we performed synthesis of RFP and yeast Scramble and in another we performed RFP synthesis and phage synthesis. 

Some Useful links for Open Education curated by Karen Cangialosi

Spreadsheet of resources for open education curated by Karen Cangialosi Susan Whittemore

Nationally validated set of core competency learning outcomes. We are in the process of designing a user-friendly "brochure" and writing up the development process for publication. Links to both will be uploaded when available. While the Guide is still pre-publication, please include the following link when sharing: https://qubeshub.org/qubesresources/publications/1305/1.

Summary: Increasing user diversity is a key component of maintaining and expanding digital collections. Diverse users are more engaged, and engage in ways that are both novel and serendipitous - often creating uses for our data that the curators couldn't imagine. However, increasing our user base can also serve another goal - providing an entrance ramp for people who maintain views, locations, and life histories that are underrepresented in our ranks. Here my colleagues and I demonstrate how digital collections can help lower barriers to participation across multiple axes, including cost, location and disability status. Our goal in highlighting this is to show the broader impacts of our work, and how through helping people understand biological diversity we can help improve the diversity within our own community.

Presenter: Dr. Joshua Adam Drew from the Department of Ecology, Evolution and Environmental Biology, at Columbia University.

Summary: Increasing user diversity is a key component of maintaining and expanding digital collections. Diverse users are more engaged, and engage in ways that are both novel and serendipitous - often creating uses for our data that the curators couldn't imagine. However, increasing our user base can also serve another goal - providing an entrance ramp for people who maintain views, locations, and life histories that are underrepresented in our ranks. Here my colleagues and I demonstrate how digital collections can help lower barriers to participation across multiple axes, including cost, location and disability status. Our goal in highlighting this is to show the broader impacts of our work, and how through helping people understand biological diversity we can help improve the diversity within our own community.

Presenter: Dr. Joshua Adam Drew from the Department of Ecology, Evolution and Environmental Biology, at Columbia University.

Abstract:

Although bioinformatics is becoming increasingly central to research in the life sciences, bioinformatics skills and knowledge are not well integrated into undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed. To that end, we here report the results of a survey of biology faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists as well as considerable agreement about which skills are necessary. Perceptions of the importance of some skills varied with the respondent’s degree of training, time since degree earned, and/or the Carnegie Classification of the respondent’s institution. To assess which skills are currently being taught, we analyzed syllabi of courses with bioinformatics content submitted by survey respondents. Finally, we used the survey results, the analysis of the syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate biology students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.

Course resources from the Genomics Education Partnership

Drew and Tripplett 

J Microbiol Biol Educ. 2008; 9(1): 3–11. 

Published online 2008 Dec 17. 

PMCID: PMC3577148

PMID: 23653818

This blog post by Parul Pandey has a nice description of the resources available around the Google "What-if Tool". 

What-If Tool is an interactive visual tool that is designed to investigate the Machine Learning models. Abbreviated as WIT, it enables the understanding of a Classification or Regression model by enabling people to examine, evaluate, and compare machine learning models. Due to its user-friendly interface and less dependency on complex coding, everyone from a developer, a product manager, a researcher or a student can use it for their purpose.

Be sure to see the essay titled, "Playing with AI Fairness" by David Weinberger which talks about using the What-if tool environment to "try on five different types of fairness". I found it to be an accessible introduction to the different approaches to making real world decisions with ML tools.