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how_to [2024/08/20 14:27] – [Review a paper?] habilhow_to [2025/01/28 14:27] (current) – [Write a scientific paper?] habil
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 ==== Download files to where you cannot login or click using a GUI? ==== ==== Download files to where you cannot login or click using a GUI? ====
  
-Login using GUI on another computer. Click to start downloading. While it is downloading, right-click on the page and then click on "Inspect". Then, click on "Network" on the top of the panel and find the file. Get the cURL [[https://www.youtube.com/watch?v=udfCVWuobhc|command]] and run it in terminal to download the file in the other computer.+Login using GUI on another computer. Click to start downloading. While it is downloading, right-click on the page and then click on "Inspect". Then, click on "{{:screenshot2024-12-04at1.18.56pm.png?linkonly|Network}} " on the top of the panel and find the file. Get the cURL [[https://www.youtube.com/watch?v=udfCVWuobhc|command]] and run it in terminal to download the file in the other computer.
  
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 ==== Supercharge your YouTube experience and minimize ads? ==== ==== Supercharge your YouTube experience and minimize ads? ====
  
-"[[https://chrome.google.com/webstore/detail/youtube-enhancer/ejcniippeghnejiodjkkmndlelbagmah|Enhancer]] for YouTube" is a popular browser extension that enhances the YouTube viewing experience by providing additional features and customization options, but it may contains malware! While it doesn't explicitly focus on blocking ads, it offers some options to minimize or hide them. Use [[https://chrome.google.com/webstore/detail/autoskip-for-youtube-ads/hmbnhhcgiecenbbkgdoaoafjpeaboine|Autoskip]] to automatically skip ads that pass the Enhancer filter.+"[[https://chrome.google.com/webstore/detail/youtube-enhancer/ejcniippeghnejiodjkkmndlelbagmah|Enhancer]] for YouTube" is a popular browser extension that enhances the YouTube viewing experience by providing additional features and customization options, but it may contains malware! While it doesn't explicitly focus on blocking ads, it offers some options to minimize or hide them. Use [[https://chrome.google.com/webstore/detail/autoskip-for-youtube-ads/hmbnhhcgiecenbbkgdoaoafjpeaboine|Autoskip]] to automatically skip ads that pass the Enhancer filter. \\ 
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 +The above solutions reduces the income of the person or the team who created and posted the YouTube video. Better than the above solutions is to use a YouTube **premium** account. In this way, you a) save your time and focus by avoiding ads and b) support the person who created the video. Youtube [[https://support.google.com/youtube/answer/7060016?hl=en#:~:text=How YouTube Premium supports creators,monthly membership fee with creators.|pays]] creators a little money for every minute we watch their video with a premium account.
  
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 ===== Write a scientific paper? ===== ===== Write a scientific paper? =====
  
-Put the figures together and then [[http://www.scidev.net/global/publishing/practical-guide/how-do-i-write-a-scientific-paper-.html|draft]] different [[https://www.nature.com/articles/nmeth.4532?WT.ec_id=NMETH-201712&spMailingID=55474826&spUserID=MTIyMzczNjc4MDI2S0&spJobID=1285409878&spReportId=MTI4NTQwOTg3OAS2|sections]]. Focus the [[http://www.grantcentral.com/strategies-for-avoiding-common-problems-with-research-manuscripts/|Discussion]]. Be careful about [[http://colah.github.io/posts/2019-05-Collaboration/index.html|authorship]]. It might be easier to write the [[https://plos.org/resource/how-to-write-a-great-abstract/?utm_medium=email&utm_source=internal&utm_campaign=modnewsletters&utm_content=modnewsletter|abstract]]//after//  other sections are drafted. You can use your [[https://www.nature.com/articles/d41586-018-02404-4|own]] voice.+Put the figures together and then [[http://www.scidev.net/global/publishing/practical-guide/how-do-i-write-a-scientific-paper-.html|draft]] different [[https://www.nature.com/articles/nmeth.4532?WT.ec_id=NMETH-201712&spMailingID=55474826&spUserID=MTIyMzczNjc4MDI2S0&spJobID=1285409878&spReportId=MTI4NTQwOTg3OAS2|sections]]. Focus the [[http://www.grantcentral.com/strategies-for-avoiding-common-problems-with-research-manuscripts/|Discussion]]. Be careful about [[http://colah.github.io/posts/2019-05-Collaboration/index.html|authorship]]. It might be easier to write the [[https://plos.org/resource/how-to-write-a-great-abstract/?utm_medium=email&utm_source=internal&utm_campaign=modnewsletters&utm_content=modnewsletter|abstract]] //after// other sections are drafted. You can use your [[https://www.nature.com/articles/d41586-018-02404-4|own]] voice. Explain in the [[https://www.springernature.com/gp/researchers/the-source/blog/blogposts-getting-published/boosting-your-acceptance-chances-as-an-author/24029788?sap-outbound-id=DC97DCEC6E137F198032918A1405F895E5D09A72&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030721_CONR_JRNLS_REP1_GL_PHSS_034NE_NATWINBRC5&utm_content=EN_56630_20250128&mkt-key=42010A0550671EEA9BA13B2C4609D4AD|cover]] letter how your work would be interesting to the journal audiance.
  
 Many journals require vectorized figures and different tweaks to the fonts and colors. So, make sure your figures are easily reproducible. At the submission stage, you can change to a [[https://docs.google.com/document/d/1L49DoVzBfhJaavIvW5CvrxmwV-RHNDJcuFIZy39dS2g/edit|vectorized]] format like eps or pdf using different tools including [[http://blog.linuxgrrl.com/2013/08/12/how-to-produce-vector-eps-with-cmyk-color-using-free-software/|Inkscape]]. Many journals require vectorized figures and different tweaks to the fonts and colors. So, make sure your figures are easily reproducible. At the submission stage, you can change to a [[https://docs.google.com/document/d/1L49DoVzBfhJaavIvW5CvrxmwV-RHNDJcuFIZy39dS2g/edit|vectorized]] format like eps or pdf using different tools including [[http://blog.linuxgrrl.com/2013/08/12/how-to-produce-vector-eps-with-cmyk-color-using-free-software/|Inkscape]].
  
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 ===== Prepare or review computational biology papers for Nature methods? ===== ===== Prepare or review computational biology papers for Nature methods? =====
  
-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. Several [[https://en.wikipedia.org/wiki/Computational_biology#Research|journals]] publish papers in this field.
  
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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? =====