For our second meeting of the fall semester, we:
- Shared resources for conducting remote and/or virtual research with students
- Discussed how to use these resources effectively
A summary of our discussion follows.
- Schedule adequate time to explore the resources before beginning any projects with students. This will probably be a lot more time than you would normally need for project planning, as the topics and procedures are likely to be different from the research you normally conduct.
- As you review available data sources, jot down as many possible research questions as you can. Then curate the research questions, ensuring that related hypotheses can be tested with available data. This will provide students with a variety of viable options to choose from, according to their interests.
- Use YouTube videos (or videos you create yourself) to help students learn how research is done. For example, there are many short, high-quality how-to videos available on topics such as selecting a research topic, doing a literature review, reading and understanding primary literature, properly formatting references, properly formatting in-text citations, etc.
- Science Forward: This website from CUNY’s Macaulay Honors College includes a links to collection of resources for helping STEM students do remote/virtual research. I found many of the data sources listed below on this site.
- Here is their page with links to open data sets: https://eportfolios.macaulay.cuny.edu/science-forward/open-data-sets/
- And here is their page with links to free data analysis and visualization tools: https://eportfolios.macaulay.cuny.edu/science-forward/data-analysis-tools/
- Global Biodiversity Information Facility: This website contains links to MANY high-quality open biodiversity data sets from all over the world. https://www.gbif.org/what-is-gbif
- Click “Get data” at the top left to start exploring
- Use it to find a specific data set (see examples below), to locate occurrence data for specific organisms, or to examine trends in biodiversity.
- Examples of available datasets:
- eBird from Cornell’s Lab or Ornithology, with species occurrence data
- Paleobiology Database, with info on the location and age of countless fossil species
- iNaturalist species occurrence data (research grade)
- Many taxonomic databases (plants, animals, marine species, etc)
- DNA barcode database (International Barcode of Life)
- World Health Organization: Here you can access the World Health Data Platform, with MANY open data sets https://www.who.int/data/collections
- You can explore the data and trends by country and year for topics such as immunization data, maternal health, antimicrobial resistance, invasive disease vectors (such as Anopheles mosquitoes), etc.
- USDA: I was surprised to see how much is available on this site. https://www.ers.usda.gov/data-products/
- It is geared toward economic data, but other data are available as well, such as information on the adoption of genetically engineered crops in the US.
- US Geological Survey: Includes open data on topics such as volcano and earthquake hazards, phenology, and water resources in the US https://data.usgs.gov/datacatalog/#fq=dataType%3A(collection%20OR%20non-collection)&q=*%3A*
- US Department of the Interior: Includes open survey data for topics such as disturbance due to fires, seafloor topography, etc https://data.doi.gov/dataset
- gov https://www.data.gov/ is a clearinghouse for all open US government data, and includes data related to climate, human health, energy, agriculture, maritime, etc.
- Cancer BioPortal: open data related to cancer genomics https://www.cbioportal.org/
- Here you can perform sophisticated queries and harness the power of data submitted from numerous studies on cancer genomics. The site provides tutorials (it’s a steep learning curve) and free, professional data visualization tools
- BudBurst (open phenology data) https://accounts.budburst.org/data
- The National Phenology Network https://www.usanpn.org/usa-national-phenology-network You may contribute data or analyze existing phenology data, exploring questions related to climate change, invasive species, etc.
- NCBI (National Center for Biotechnology Information) hosts open databases and many data analysis tool on its website https://www.ncbi.nlm.nih.gov/ Data and software starting page: https://www.ncbi.nlm.nih.gov/guide/data-software/
Online data analysis tool and resources:
- The website https://www.socscistatistics.com/ offers free tools for statistical analysis, as well as a tool to help you select the appropriate statistical tests for your data.
- NCBI and PubMed have collaborated to offer the Protein database of sequence data from a variety of sources (GenBank, RefSeq, TPA, etc). https://www.ncbi.nlm.nih.gov/protein Links to tools such as BLAST and LinkOut are posted on this page as well.
- There are several online tools available for predicting protein structure from sequence data:
- PyMOL https://pymol.org/2/
- Phyre2 (protein homology/analogy recognition engine) http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
- PEP-FOLD 3 https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3/
- PredictProtein https://predictprotein.org/
- Protopedia: Like Wikipedia for protein structures. Includes 3D animations that you can download for free. https://proteopedia.org/wiki/index.php/Main_Page
- Clustal Omega: online tool for multiple sequence alignment https://www.ebi.ac.uk/Tools/msa/clustalo/
- Mega X: this site provides free tools for auto or manual sequence alignment, inferring phylogenetic trees, and various types of statistical analysis for phylogenetics, as well as visualization tools https://www.megasoftware.net/
- Pivot Tables on Microsoft Excel—creates various data visualizations of your data to help summarize large data sets. Many video tutorials are availble, e.g, https://www.youtube.com/watch?v=qu-AK0Hv0b4
Citizen science websites:
- Zooniverse Numerous projects in which the public can participate (many are gamified) https://www.zooniverse.org/projects?page=1&status=live
- iNaturalist (data can also be used to test hypotheses; see above in Resources) https://www.inaturalist.org/
- FoldIt: protein folding citizen science projects https://fold.it/
- NASA https://www.nasa.gov/stem This is a page of resources for educators to increase STEM engagement. The citizen science page (https://www.nasa.gov/education/materials/) had links to various projects the public can get involved in, although I’m not sure whether the data are publicly available.