bioinformatics_essay28
Differences
This shows you the differences between two versions of the page.
| Next revision | Previous revision | ||
| bioinformatics_essay28 [2022/12/25 12:25] – created 134.190.232.124 | bioinformatics_essay28 [2023/01/01 10:20] (current) – 134.190.232.124 | ||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ProtocolMaker: | + | **ProtocolMaker: |
| + | ** | ||
| //The difference between a good student and a great one is that a good student is concerned more about the outcome while a great one is fascinated by the process of learning. - Prof. Feynman// | //The difference between a good student and a great one is that a good student is concerned more about the outcome while a great one is fascinated by the process of learning. - Prof. Feynman// | ||
| - | {{:pipeline.png?400|}} | + | {{:pipeline2.png?600|}} |
| Dealing with bioinformatics projects can produce many challenges. Overcoming these challenges means progress. And surely, there is bonus pay throughout this process. However, the real exploration is not limited to the data analysis itself. There are better ways to spread the mid-step work, such as which method you choose, how you proceed the analysis, and what if the outcome is unexpected. These mid-step efforts can also become bioinformatic publications. Here, as an early career researcher working on different bioinformatics projects, I will share my experience with real protocol cases, such as using a pipeline for minimizing redundancy and complexity in large phylogenetic datasets, executing a tool to merge and minimize “bad words” from BLAST hits against multiple eukaryotic gene annotation databases, and running a web server for identifying, | Dealing with bioinformatics projects can produce many challenges. Overcoming these challenges means progress. And surely, there is bonus pay throughout this process. However, the real exploration is not limited to the data analysis itself. There are better ways to spread the mid-step work, such as which method you choose, how you proceed the analysis, and what if the outcome is unexpected. These mid-step efforts can also become bioinformatic publications. Here, as an early career researcher working on different bioinformatics projects, I will share my experience with real protocol cases, such as using a pipeline for minimizing redundancy and complexity in large phylogenetic datasets, executing a tool to merge and minimize “bad words” from BLAST hits against multiple eukaryotic gene annotation databases, and running a web server for identifying, | ||
| Line 12: | Line 14: | ||
| - Clarity – Are the steps clear and easy to understand? | - Clarity – Are the steps clear and easy to understand? | ||
| - | |||
| - Timing – Do the authors include information about the time that each step or section of the protocol takes? | - Timing – Do the authors include information about the time that each step or section of the protocol takes? | ||
| - | |||
| - Critical Steps – Do the authors note the critical steps that must be followed exactly? | - Critical Steps – Do the authors note the critical steps that must be followed exactly? | ||
| - | |||
| - Troubleshooting – The authors should include some tips for users on what went wrong in their lab. What steps did they find tricky, and what were the solutions? Do the authors refer to the corresponding protocol step in the Troubleshooting section? | - Troubleshooting – The authors should include some tips for users on what went wrong in their lab. What steps did they find tricky, and what were the solutions? Do the authors refer to the corresponding protocol step in the Troubleshooting section? | ||
| - | |||
| - Alternates – Are there any reagents or pieces of equipment that cannot be substituted, | - Alternates – Are there any reagents or pieces of equipment that cannot be substituted, | ||
| + | |||
| + | **References: | ||
| + | - Xi Zhang*, Yining Hu, David Roy Smith*. (2021). Protocol for HSDFinder to help identify, categorize and annotate duplicate genes in eukaryotic nuclear genomes. STAR Protocols. DOI: 10.1016/ | ||
| + | - Xi Zhang*, Yining Hu, David Roy Smith*. (2021). Protocol for using NoBadWordsCombiner to merge and minimize ‘bad words’ from BLAST hits against multiple eukaryotic gene annotation databases. DOI: 10.1016/ | ||
| + | - Xi Zhang*, Yining Hu, Laura Eme, Shinichiro Maruyama, Robert JM Eveleigh, Bruce A. Curtis, Shannon J. Sibbald, Julia F. Hopkins, Gina V. Filloramo, Klaas J. van Wijk, John M. Archibald*. (2022) TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets.DOI: | ||
| + | - Xi Zhang*, Yining Hu, Zhenyu Cheng, John M. Archibald*. (2022). HSDecipher: pipeline for comparative genomics analysis of highly similar duplicates data in eukaryotic genomes. Star Protocols. | ||
| + | |||
| + | |||
| <Last updated by Xi Zhang on Dec 25th, | <Last updated by Xi Zhang on Dec 25th, | ||
bioinformatics_essay28.1671985509.txt.gz · Last modified: by 134.190.232.124