This repository contains information about Bioinformatics lab 3 deliverables. This assignment invites students to find and demonstrate online tools for Bioinformatics research.
- To gain skill and experience in looking for tools for particular types of research tasks.
- To gain writing and speaking skills for demonstrating the tool to the other members of the class.
You can work alone or in a group. If you are working in a group (up to two people), please find a partner before you click on the below repository link. A group leader will click on the link and then establish the group's name. After that step, the other group member(s) may join the group by clicking on the list of names (after clicking on the link). Caution: your click cannot be corrected if you click on the wrong group name.
Repository link (The group leader clicks the link first to establish the group name!): https://classroom.github.com/a/VpI9VO2f
- In class, you were given a link to GitHub Classroom. Clicking on this link implied that you accepted the assignment and you were then given a newly created personal repository for your project work.
- In your work-repository, you can locate a link that you can use to clone the work on your local machine. There, you can begin to work locally using your own editor, Python interpreter, and /or other resources.
- Please be sure to commit and push your work periodically using the commands shown below.
git add -A
git commit -m ``Your notes about the commit here''
git push
After you have pushed your work to your repository, please visit the repository at the GitHub website (you may have to log-in using your browser) to verify that your files were correctly sent.
Much research in Bioinformatics can be performed by free and open source tools. In addition, much of the data that would be applied to these tools is also free, open source and therefore conveniently accessible to the public.
In this lab, you are given an opportunity to locate and explore a bioinformatics tool that is valuable in DNA, RNA, and protein research. Once you have explored the tool, you are to give a brief presentation and demonstration of the tool to the member of the class during the next lab.
Research an Important Tool: Working alone or with a partner, you are to spend ample time to find an important tool for research that you are interested in learning more about. The tool that you choose to study must be;
- Free and available to all for no charge.
- Built for data which is also freely accessible.
- Well documented in terms applications in research, and also for how to use it with data.
- Have a citation in the form of an article or reference to a programming library.
Although not necessary for this project work, you might consider finding tools with graphical interfaces and outputs that serve to facilitate in the use and digestion of results.
In your investigation of online tools, please keep your concentration of the below types of themes.
- Task or research questions: What application does the tool have in research?
- Data: What kinds of data does the tool use?
- Algorithms: What does the tool do with the data (computationally) to reach conclusions.
- Outputs: What are the outputs and how do they help to answer a task or research question?
- Greater implications: How is research simplified by the involvement of this tool?
- Ethical implications: How could this tool be used in anyway which could lead to suffering on the part of those from whom the data was extracted?
In the writing/reflections.md, you will be addressing the questions already in the file. Each working repository is to submit a single document in which each partner has contributed equally.
Present the Tool Next Lab Session:Working alone or with a partner, you are to introduce the class to the tool using slides or other visual materials to cover some of the above-mentioned themes.
In addition, you are to use a computer to run and showcase the functionality of the tool. Please spend time to discuss the necessary data (type, origins and etc.) during your talk. Once the tool has run, you are to spend time to help the members of the class understand the results.
Your presentation will be about five-seven minutes. It is not necessary to submit your slides with your deliverable for this lab.
You can check the baseline writing and commit requirements for this lab assignment by running department's assignment checking gatorgrade tool. To use gatorgrade, you first need to make sure you have Python3 installed (type python --version to check). If you do not have Python installed, please see:
- Setting Up Python on Windows
- Python 3 Installation and Setup Guide
- How to Install Python 3 and Set Up a Local Programming Environment on Windows 10
Then, if you have not done so already, you need to install gatorgrade:
- First, install
pipx - Then, install
gatorgradewithpipx install gatorgrade
Finally, you can run gatorgrade:
gatorgrade --config config/gatorgrade.yml
- Write a reflection of about 200 words to describe the tool. The above-mentioned themes of Part 1 to consider are also to be addressed in your
writing/reflections.mddocument.
The grade that a student receives on this assignment will have the following components.
-
Mastery of Technical Writing [up to 70%]:: Students will also receive a checkmark grade when the responses to the writing questions presented in the
reflections.mdreveal a proficiency of both writing skills and technical knowledge. To receive a checkmark grade, the submitted writing should have correct spelling, grammar, and punctuation in addition to following the rules of Markdown and providing conceptually and technically accurate answers. -
Presentation [up to 30%]: Students will receive a checkmark grade for presentations. Student must be present to receive credit for group's presentation.