Syllabus development

Course: Data science research in biology

Course learning outcomes:

  1. Experience the process of scientific discovery, including the iterative nature of biological research. This includes:
    • discover and formulate their own scientific questions with clear, testable hypotheses.
    • draw conclusions from analysis of novel data
    • apply background knowledge to develop and interpret their research
  2. Engage in highly collaborative research teams to carry out a scientific research project
  3. Learn common scientific practices employed by biologists, including common tools, instruments, and software
  4. Communicate their research and discoveries at both technical and non-technical levels

These are the CLOs for BIO 197: Culminating Experience CLO 1. Scholarship — the ability to effectively marshal the literature to frame a merited original research proposal. PLOs 2, 4 CLO 2. Research Project Proposal — PLO 2,4,6 CLO 3. Research Project — PLO 3,4,6 CLO 4. Presentation — PLO 6

Program Learning outcomes:

  • PLO 2. An ability to develop and critique hypotheses and to design experiments, models, and/or calculations to address these hypotheses.
  • PLO 3. The ability to use appropriate instrumentation and computational tools to collect, analyze and interpret data.
  • PLO 4. The ability to read, evaluate, interpret, and apply numerical and general scientific information.
  • PLO 6. An ability to communicate biological science topics in written, oral and visual formats

Integrate PLOs as goals on course description

Course Description: 75 word max

The main goal of the course is for students to learn state-of-the-art computational tools to design experiments and models that will allow them to propose and critique biological hypotheses in ecology and evolution (PLO 2). Students will collect, analyze, interpret and generate open and FAIR data to test relevant hypotheses (PLO 3). Additionally, students will learn computational tools fore reproducibility, to communicate biological science topics in written, oral and visual formats (PLO 6).

Describe the content of the course-work to be completed outside of class meetings:

Outside of the class meetings, students will work in groups to develop a research project proposal. Students will search the general literature and identify a topic and a research question they are interested to work on; 2) search specialized literature on the topic to establish appropriate and testable hypotheses; 3) use the knowledge acquired in class to design the appropriate computational methodology to test the proposed hypotheses. Project proposals will be discussed in class and refined accordingly to suggestions from other students. Students will be able to change groups according to their interests. Once project proposals have been fine tuned, students will then work outside of class on their project proposal in groups.

Explain how student learning in this course will be assessed

Summary: We will use a mixture of formative and summative exercises throughout the course to assess student’s learning of CLOs.

Formative assessments will be informative (not graded), and key to gauge students’ learning progress to tailor classes and activities. For CLO1 (PLOs 3, 4), students’ learning of theoretical concepts and research skills will be assessed weekly with silent polls about subject matter at the beginning/end of class, as well as homework assignments related to in-class research lab activities. For CLOs 2-5 (PLOs 2-4, 6), students’ progress will be assessed with weekly check-ins, in which students will have to think and write about what worked and what did not work for them to make progress on their project proposals.

Summative assessments will be graded and applied monthly. They will also be chosen by the students from a set of options provided by the instructor. For CLO1 (PLOs 3, 4), students’ theoretical knowledge will be assessed with a live coding session, a hackathon, or an asynchronous coding session to solve a relevant problem. For CLO2-4 (PLOS 2-4), students will work on a reproducible lab notebook to document project proposal progress. The notebook and the project proposal will be reviewed by other groups, and an in-class discussion for students to provide feedback for other teams on positive aspects and points of improvement on proposals will be moderated by the instructor. Students will have the option to be assessed by their participation during discussion, by the writing of a synopsis of the discussion, by their project notebooks For CLO5 (PLO 6), students will present a poster, tutorial or blog post on the results of their research project. A discussion on final results will be moderated by students. Students will have the option to be assessed by their participation as moderators, by the writing of a synopsis of the discussion, or by their final presentations.

List: CLO 1 (PLOs 3, 4). Theoretical knowledge. Formative assessments –– Weekly. Silent polls about subject matter at the beginning/end of class Homework assignments Summative assessment –– Monthly. Chosen by students. Options are: Live coding session. Hackathon. Asynchronous coding session.

CLO 2 and 3 (PLO 2, 4). Develop a research project proposal collaboratively. Formative assessment –– Weekly. Create a project notebook. Weekly check-in: what worked? What didn’t? Summative assessment –– Once. Review of peers project proposals. In-class group discussion: positive aspects and points of improvement for proposals.

CLO 4 (PLO 3). Work on a research project collaboratively. Formative assessment –– Weekly. Weekly check ins: what worked? What didn’t? Summative assessment –– Final project notebook.

CLO 5 (PLO 6). Final presentation of project results. Formative assessment –– Weekly. Weekly check ins: what worked? What didn’t?

Summative assessment –– Chosen by students. Some options are: Debate and write a synopsis of results. Presentation itself.

Describe how CLOs fit the GE badges - Requirements | General Education

In this course, students will design, develop, implement and interpret research results during a semester-long collaborative project, by utilizing newly acquired knowledge of state-of-the-art computational tools and statistical skills to answer relevant questions in ecology and evolution. This will earn students four different GE Intellectual Experience badges, as well as the Culminating Experience Upper Division requirement. Quantitative and Numerical Analysis badge: (CLO1, PLO3; CLO2, PLO2) The students will learn and apply statistical techniques to analyse “big” data in biology, with an emphasis on methods in ecological and evolutionary research. This will gain them experience in data evaluation, and will allow them to develop and consolidate quantitative reasoning skills. Scientific Method badge: (CLO2, PLO2) The students will practice how to choose and process data appropriately to test hypotheses and answer research questions in ecology and evolution. This will allow them to apply the scientific method in full, as well as experience how it leads to new knowledge in the field. They will immerse themselves in the exercise of processing and analysing empirical evidence, and applying the appropriate cognitive tools to compare and integrate their results to established knowledge in the field. Literary and Textual Analysis badge: (CLO4, PLO3) Students will learn the notions of scientific reproducibility, open science and Findable, Accessible, Interoperable, and Reusable (FAIR) data. They will understand how previous understanding of these notions have created ambiguity that has led to poor scientific practices in the past. They will explore recent and current research that has created a meaningful and practical conceptualization of these notions. They will implement best practices for reproducibility, open science and FAIR data by developing a reproducible document of their research project. Media and Visual Analysis badge: (CLO5, PLO6) Students will design and develop a visual summary of the results of their research project, in the form of a poster, a tutorial or a blog post. With this, they will explore and experience how media and images create, shape, and express meaning in biological science. Culminating Experience requirement: This course content will provide students with tools and experience that will gain them intellectual independence to conduct scientific research in ecology and evolution, contributing to student readiness for a career in academia or the private sector.

Luna L. Sánchez Reyes
Postdoctoral Research Scholar
University of California, Merced