C Additional Curricula
Additional resources and curricula that may be of interest to instructors teaching the miniCURE. If you’ve got something to add, let us know! The C-MOOR team has not reviewed all of these materials, but we are happy to share resources that you find helpful.
Also don’t forget to check CourseSource for a large collection of biology curricula covering a wide range of topics, including many CUREs.
Additional C-MOOR Curricula
miniCUREs and CUREs by the C-MOOR team, covering different types of bioinformatic analyses. Contact us if you’d be interested in partnering with us to develop and test these materials.
| Name | Topic(s) | Length | Status |
|---|---|---|---|
| 16S Microbiome miniCURE | Microbiome | 3 labs + Project Work | Under development |
| Microbial Mysteries | Metagenomics | 1 semester | beta-testing |
| scRNA-seq CURE | Single-cell RNA-seq | 1 semester | piloted |
Expanding on the RNA-seq Process
Additional CUREs for instructors who wish to explore different research questions or go into more depth on various parts of the RNA-seq process.
| Name/Research Topic | Length | Wet Lab | Computing |
|---|---|---|---|
| Maize response to abiotic stress | 3 weeks | Yes | Yes (R) |
| Effect of sequencing quality on inference of sex differences in gene expression in human placenta | 7.5 weeks CURE, required 7.5 week pre-req computing course | No | Yes (R) |
| Plant response to light | 1 semester | Yes | Yes (Cyverse,R) |
| Yeast environmental stress response | 2 semesters | Yes | ? |
Other Genomics miniCUREs
miniCUREs focusing on different types of genomic analyses.
| Name/Research Topic | Length | Wet Lab | Computing |
|---|---|---|---|
| Genomics Education Partnership (Drosophila genomics) | flexible | No | Yes (many options) |
| Nanopore Sequencing to Assemble and Compare Chloroplast Genomes | 2-3 weeks | Yes | Yes (Notebook-based pipeline) |
| Allen Brain Map | 4 weeks | No | Yes (GUI) |
| San Diego Biodiversity Project (DNA barcoding of invertebrates) | 1 month | Yes | Yes (varied across institutions) |
| Bean Beetle Microbiome Project | 6 weeks or 12 weeks | Yes | Yes (6-week:BLAST, 12-week:DNA Subway, R) |
Diving Deeper into R
We recommend thinking carefully about your goals for students with regards to coding and RNA-seq analysis, and where the miniCURE fits in their journey. We know this miniCURE only brushes the surface, and it is very tempting to add more. For our first-year students, we found that backing off on the coding helped give them bandwidth to concentrate on the biology and scientific thinking, with the goal of attracting them to semester-long classes that have space to go deeper. If you would like to dive a bit deeper into R, here are some useful resources:
| Name | Description |
|---|---|
| Additional learnR tutorials (available on SciServer and GitHub, along with the miniCURE materials) | Variety of topics, including basics of vectors, dataframes, and functions as well as introducing R Notebooks. |
| Introduction to data analysis with R and Bioconductor | Two day hands-on workshop |
| swirl | Interactive tutorials for use in any R Console covering base R |
| R for Data Science | Foundational book covering tidyverse |
Additional Resources
| Name | Description |
|---|---|
| Understanding Science 101 | Website explaining “how science works” |
| Next Generation Sequencing Quality Analysis with Emoji | CourseSource lesson |
| RNA-seq Data Analysis Tutorial Using Galaxy | CourseSource lesson |
| Analyzing RNA-seq data with DESeq2 | DESeq2 vignette |
| Biomedical Knowledge Mining using GOSemSim and clusterProfiler | clusterProfiler book |
| RNA-seq analysis with Bioconductor | Two day hands-on workshop |
| R for Data Science | Foundational book covering tidyverse |