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-=====   Prepare or review computational biology papers for Nature methods?   ===== +===== Prepare or review computational biology papers for Nature methods? =====
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-=====   =====+
  
 Read their "Reviewing computational methods" ([[http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3686.html|2015]]) and "Guidelines for algorithms and software in Nature Methods" ([[http://blogs.nature.com/methagora/2014/02/guidelines-for-algorithms-and-software-in-nature-methods.html|2014]]) articles. Provide source code, pseudocode, compiled executables, and the mathematical description. Softwares must be accompanied with documentation, sample data and the expected output, and a license (e.g., GPL≥2). Have a look at [[:the_list_of_computational_biology_papers_in_nature_methods|The list of computational biology papers in Nature Methods]] published in 2015, and the [[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&cad=rja&uact=8&ved=0ahUKEwic2Oum3dvJAhUGeSYKHWurD-EQFghQMAg&url=http%3A%2F%2Ford.ntu.edu.tw%2Ftc%2Fincludes%2FGetFile.ashx%3FmID%3D253%26id%3D1744%26chk%3De15262f3-87bf-4a7e-be6a-4103cbc61968&usg=AFQjCNHfNXyryLDQMWBRrInOpJVKIL0LCA&sig2=8C9UE1arY4vi2q_CUdsdiQ|hints]] by an editor of Nature Communications. Read their "Reviewing computational methods" ([[http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3686.html|2015]]) and "Guidelines for algorithms and software in Nature Methods" ([[http://blogs.nature.com/methagora/2014/02/guidelines-for-algorithms-and-software-in-nature-methods.html|2014]]) articles. Provide source code, pseudocode, compiled executables, and the mathematical description. Softwares must be accompanied with documentation, sample data and the expected output, and a license (e.g., GPL≥2). Have a look at [[:the_list_of_computational_biology_papers_in_nature_methods|The list of computational biology papers in Nature Methods]] published in 2015, and the [[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&cad=rja&uact=8&ved=0ahUKEwic2Oum3dvJAhUGeSYKHWurD-EQFghQMAg&url=http%3A%2F%2Ford.ntu.edu.tw%2Ftc%2Fincludes%2FGetFile.ashx%3FmID%3D253%26id%3D1744%26chk%3De15262f3-87bf-4a7e-be6a-4103cbc61968&usg=AFQjCNHfNXyryLDQMWBRrInOpJVKIL0LCA&sig2=8C9UE1arY4vi2q_CUdsdiQ|hints]] by an editor of Nature Communications.
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-**Set the default width of fill mode (line length) in emacs?** \\+===== Set the default width of fill mode (line length) in emacs? ===== 
 [[http://stackoverflow.com/questions/3566727/how-to-set-the-default-width-of-fill-mode-to-80-with-emacs|Use]] 'M-x customize-variable' to set 'fill-column' (100 in Oncinfo). Use DejaVu Sans Mono (~[[http://www.leancrew.com/all-this/2009/10/the-compleat-menlovera-sans-comparison/|Menlo]] on MacOS) size 18-20 is an [[http://ergoemacs.org/emacs/emacs_unicode_fonts.html|appropriate]] font for programming in Emacs. To do so, you may need to manually edit your .emacs in [[https://stackoverflow.com/questions/4821984/emacs-osx-default-font-setting-does-not-persist|macOS]], and add the following [[https://stackoverflow.com/questions/4879785/can-i-break-the-long-line-in-emacs-non-windows-to-the-next-line|line]]: [[http://stackoverflow.com/questions/3566727/how-to-set-the-default-width-of-fill-mode-to-80-with-emacs|Use]] 'M-x customize-variable' to set 'fill-column' (100 in Oncinfo). Use DejaVu Sans Mono (~[[http://www.leancrew.com/all-this/2009/10/the-compleat-menlovera-sans-comparison/|Menlo]] on MacOS) size 18-20 is an [[http://ergoemacs.org/emacs/emacs_unicode_fonts.html|appropriate]] font for programming in Emacs. To do so, you may need to manually edit your .emacs in [[https://stackoverflow.com/questions/4821984/emacs-osx-default-font-setting-does-not-persist|macOS]], and add the following [[https://stackoverflow.com/questions/4879785/can-i-break-the-long-line-in-emacs-non-windows-to-the-next-line|line]]:
  
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-**Convert gene or protein IDs?** \\+===== Convert gene or protein IDs? ===== 
 [[https://www.biostars.org/p/22/|Use]] [[https://biodbnet-abcc.ncifcrf.gov/db/db2db.php|bioDBnet]], BioMart - Ensembl, or [[https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html|AnnotationDbi]] package in R to convert between Entrez Gene, RefSeq, Ensemble, and many more. [[https://www.biostars.org/p/22/|Use]] [[https://biodbnet-abcc.ncifcrf.gov/db/db2db.php|bioDBnet]], BioMart - Ensembl, or [[https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html|AnnotationDbi]] package in R to convert between Entrez Gene, RefSeq, Ensemble, and many more.
  
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-**Prepare attractive,** **scientific presentations****?** \\+ 
 +===== Prepare attractive, scientific presentations ? ===== 
 Use a "home slide". Also, learn about other tips from Susan [[https://www.youtube.com/watch?v=Hp7Id3Yb9XQ|McConnell]]. Use a "home slide". Also, learn about other tips from Susan [[https://www.youtube.com/watch?v=Hp7Id3Yb9XQ|McConnell]].
  
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 ==== Access a Bioconductor package source code? ==== ==== Access a Bioconductor package source code? ====
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 Logitech Control Center may help on the [[https://support.logi.com/hc/en-gb/articles/360025297833-Logitech-Control-Center-for-Macintosh-OS-X|Logitech]] MX mice older than 2019. Logitech Control Center may help on the [[https://support.logi.com/hc/en-gb/articles/360025297833-Logitech-Control-Center-for-Macintosh-OS-X|Logitech]] MX mice older than 2019.
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 +===== Choose a solid state (SSD) external drive? =====
 +
 +The non-volatile memory express (NVMe) devices are [[https://ssd.borecraft.com/SSD_Buying_Guide_List.pdf|better]] than SATA solid state drives. Good brands include [[https://smile.amazon.com/gp/product/B07X6CKHH1/ref=ox_sc_act_title_1?smid=A29Y8OP2GPR7PE&psc=1|Sabrent]] (Nano is smaller than Pro but gets hot when extensivly used), Seagete, Addlink, and Team. As of 2020, a speed of 1000 Mb/s is possible using USB 3.2.
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