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how_to [2019/10/18 20:57] – [Access a Bioconductor package source code?] adminhow_to [2020/01/02 18:22] – [Write a scientific paper?] admin
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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]]. 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]].
  
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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.
  
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 +
  
 ==== Get older versions using git? ==== ==== Get older versions using git? ====
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 mkdir ~/proj; cd ~/proj mkdir ~/proj; cd ~/proj
 git clone git@git.bioconductor.org:packages/Pigengene git clone git@git.bioconductor.org:packages/Pigengene
 +</code>
 +
 +Now, you can build the package fom the source using:
 +
 +<code>
 +R CMD REMOVE Pigengene; R CMD build Pigengene
 +</code>
 +
 +If the build is successful, a tarbal will be created. You can install the new package using:
 +
 +<code>
 + R CMD INSTALL Pigengene_<Version>.tar.gz
 </code> </code>