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--- bioinformatics_essay2 [2022/02/07 16:32] – 134.190.232.106
+++ bioinformatics_essay2 [2022/02/16 12:47] (current) – 134.190.232.106
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-Don’t waste it: Tidying up your bioinformatics work into appropriate publications
+**Don’t waste it: tidy up your bioinformatics work into appropriate publications**
+{{:tidy_up.jpg?600|}}
 I was writing late another day at my apartment due to the common fear outside – new variant virus. Bang! Bang! (Running sound from up-floor) Wow! Wow! (Yelling sound from downstairs). Obviously, I was not the only person working from home. The “gym” and “night bar” were also moved in the building offering the “service”. Proficiently, I took out an A4 paper from a drawer and followed each step sorted in a pipeline. In a few minutes, the mid-night noises were quieted down and the A4 paper titled with “Protocol for non-nature noise control in nocturnal animal” was safely put back.
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 The similar things happened in other projects as well. Functional annotations of protein-coding genes can be annoying when obtaining the best BLAST hits from some non-redundant protein sequence database such as NCBI NR databases, SwissProt [#] and TrEMBL[#], because of the hypothetical and uncharacterized proteins might pop up at the top list. Therefore, I wrapped up a hands-on protocol paper called NoBadWordsCombiner v1.0 [#] to demonstrate how to automatically merge the BLAST results from the eukaryotic databases. More importantly, it can strengthen the gene definition by minimizing those protein function descriptions containing ‘bad words’, such as hypothetical and uncharacterized proteins. In a multiple species’ phylogeny project, I wrapped up my mid-step bioinformatics work into a hands-on protocol TreeTuner [#], which is very helpful for those researchers who are willing to explore the tree diversity and then more rigorous downstream re-analysis on specific OTUs.
-Nowadays, many bioinformatics related questions could be found via Biostars, GitHub, and Stack Overflow websites etc. This is same to seek the noise complain questions from Google, Reddit or other discussion platforms. However, will the Google scholar be ready for more mid-step bioinformatics papers? Will it be the trend to see more downstream polished bioinformatics papers, such as InterProScan_parser, KEGG_decipher or NCBI_explorer. I don’t know the answers, but surely the authors of this paper are looking for ways to publish the “noise control A4 paper”.
+Nowadays, many bioinformatics related questions could be found via Biostars, GitHub, and Stack Overflow websites etc. This is same to seek the noise complain questions from Google, Reddit or other discussion platforms. However, will the Google scholar be ready for more mid-step bioinformatics papers? Will it be the trend to see more downstream polished bioinformatics papers, such as InterProScan_parser, KEGG_decipher or NCBI_explorer. I don’t know the answers, but surely the author of this paper are looking for ways to publish the “noise control A4 paper”.
+<Xi Zhang, PhD
+Postdoctoral Fellow,
+Archibald Lab, Dalhousie University>
+<Last updated by Xi Zhang on Jan 9th,2022>