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Welcome to the EPP531 wiki!
Links:
To Dos:
- Change class time?
- Review syllabus
- Get everyone on GitHub
- How to use the GitHub wiki
- Assign everyone to a time slot
- How to present - slides
No Class
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Fang Liu
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Article link - Compact graphical representation of phylogenetic data and metadata with GraPhlAn
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Questions for on class discussion
- Is the article looks straightforward to you? If not, why?
- In general sense, do you prefer interactive web-based software or command-driven ones, why?
- Have you ever used other softwares for building taxonomic tree or phylogenetic tree with metadata? How do you think this GraPhlAn compared with what you used?
- What do you think make a software more attractive to researchers? e.g., usefulness, detailed documentations, active support group and so on?
- Based on your understanding of this article, what part do you think does not make sense? What kind of improvements you will do if you were the developer of this software?
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Kyle Bonifer
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Questions:
1)Were you able to get the program to work? Was it user-friendly?
2)Do you believe this program adequately predicts post-translational modification of proteins identified through mass spec? Why, why not?
3)Can you think of any ways in your own research or research generally where this tool could be applicable?
4)What do you feel could have been included in the paper to make their argument more convincing? Do you believe this program is better than its predecessors, or did the fail to convince you?
Optional additional presenter?
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Nourolah Soltani
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Article link: Development of a virus detection and discovery pipeline using next generation sequencing
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Questions:
1- Were you successful in submission a raw sequence data to be analyzed?
2- Did you receive any error after sequence submission? Did you get it solved?
3- Were the obtained results as the same as your expected outcome?
4- How do you see the efficiency of the web-based platform and its simplicity/complexity in data analyses for virus discovery purposes?
5- According to your experience with this tool, what would be your suggestion to add to the four essential keys of a universal bioinformatics tool mentioned in the paper?
- B. McDowell
- Bob Tams
- Helena Pound
- Bridget O'Banion
- Jessica Velez
- Allison Mason
- Ming Chen