Overview of Chamaecrista Genomics Research
Genomics research requires:
- A biological question
- Sequences
- Computational methods to analyze the sequence data
- A critical researcher to evaluate the results and connect the results to larger picture
The
Chamaecrista Explorer is designed to help you develop genomics research questions and get you started analyzing genomics data by guiding you through different strategies. The web interface guides you through strategies for exploring genomics data and using it to understand biological questions about
Chamaecrista fasciculata.
The Chamaecrista Explorer has been developed and evaluated with support from the National Science Foundation (DUE-0837375 and DEB-0746571.)
Using the Chamaecrista Genomics Explorer
Making sense of genomics data can be a bit daunting. The Explorer is designed to get you started analyzing genomics data by guiding you through five different strategies. You can start with any one of the strategies to ask and answer thoughtful questions. As you get more comfortable with the data, you'll find yourself combining several strategies to ask and answer more sophisticated questions. Approach the Explorer like you would a pick your own adventure type of book.
The strategies:
- Chamaecrista biology
- Candidate genes
- Gene expression
- Variation among genotypes
- Functional genomics
One of the challenges in analyzing genomes is the vast number of tools available. The interface will guide you to data and bioinformatics tools that will help you answer questions and form new questions about shoot development in Chamaecrista plants. The interface is designed to keep you focused on the biology and give you a framework to move through the complex array of tools and data available to you. Keep coming back to the Chamaecrista Genomics Explorer as you work on your project. The site is organized around different strategies for exploring genomes. You can pick any of the six strategies available as a starting point. As you ask and answer questions, you will likely use several of the strategies iteratively. Each research team has an electronic journal to record your data, ponderings, hypotheses, and conclusions as you work through the site.
When you encounter a UAG - Stop and Reflect button, take the time to consider the question and record your answer. As you visit other sites and collect data, you can paste your data into your electronic lab notebook. Your notebook is also the place to record what you are doing. As you explore the Chamaecrista genome, you will venture down many paths and without your journal it will be difficult to reconstruct what you have done.
As you explore web resources that take you away from this interface, be sure to come back and record your progress in your notebook. Depending on your browser preferences, links may open in a new tab or separate window format. Decide which format works best for you. You can right click on your mouse when you click on a new link and choose whether you want to open a new tab or new window.
Discuss with your team members how you can effectively use your group notebook. You may not always be working on the site together. Do you want to leave questions for each other in journal? Would initialing your entries help with group conversations? Frame and record a question you would like to ask using whole transcriptome data from Chamaecrista
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