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how_to [2019/05/31 16:26]
admin [Install R locally (e.g. on a cluster)?]
how_to [2020/01/13 22:19] (current)
admin [Prepare attractive, scientific presentations ?]
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-Add only [[http://​stackoverflow.com/​questions/​7124726/​git-add-only-modified-changes-and-ignore-untracked-files|modified]] changes and ignore untracked files using git?+===== Add only modified changes and ignore untracked files using git? =====
  
 <​code>​ <​code>​
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 </​code>​ </​code>​
  
-If there is a conflict at push time, first pull. Now, you need to look for ">>>"​ in the code, and manually fix the conflict. Then, push again.+The [[https://​stackoverflow.com/​questions/​7124726/​git-add-only-modified-changes-and-ignore-untracked-files|above]] should work if there is no conflict. ​If there is a conflict at push time, first pull. Now, you need to look for ">>>"​ in the code, and manually fix the conflict. Then, push again.
  
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 +
  
 ==== Use a package that is being developed? ==== ==== Use a package that is being developed? ====
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-**Get familiar with applications of machine learning ​in genetics ​and genomics?** \\ +**Get familiar with machine learning and its applications in computational biology? ** \\ 
-First read [[http://​www.nature.com/​nrg/​journal/​v16/​n6/​abs/​nrg3920.html|this]] 2015 review ​paper and then follow its references.+- Most common ML techniques are very well explained in [[https://​scikit-learn.org/​stable/​user_guide.html|Scikit learn]] with [[https://​scikit-learn.org/​stable/​modules/​decomposition.html|illustrations]] and example Python code. These techniques have been implemented in [[https://​www.kaggle.com/​getting-started/​5243|R]] packages including mlr3 and tidymodels. 
 + 
 +-[[http://​www.nature.com/​nrg/​journal/​v16/​n6/​abs/​nrg3920.html|This]] 2015 paper reviews applications of ML in genetics and genomics. Read it and follow its references.
  
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 <​code>​ <​code>​
-brew install aspell ​--with-lang-en+brew install aspell
 </​code>​ </​code>​
  
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-**Begin learning bioinformatics?​** \\+ 
 +====   Begin learning bioinformatics? ​  ==== 
 Take a course from the [[http://​research.omicsgroup.org/​index.php/​List_of_free_online_bioinformatics_courses|list]] of free online bioinformatics courses e.g., the Computational Molecular Biology [[http://​cmgm.stanford.edu/​biochem218/​index.html|Course]] at Stanford is broad and covers the classic topics but it is not updated, and may become outdated. The same is true for PLOS Translational Bioinformatics [[http://​collections.plos.org/​translational-bioinformatics|Collection]] of articles, which are more advanced. Most central topics are covered in some course from the European Bioinformatics Institute ([[https://​www.ebi.ac.uk/​training/​online/​course-list|EBI]]). Very useful training materials are available from [[https://​www.mygoblet.org/​|GOBLET]]. Videos from the Models, Inference & Algorithms Initiative ([[https://​www.broadinstitute.org/​scientific-community/​science/​mia/​models-inference-algorithms|MIA]]) at Broad are relatively advanced.\\ Take a course from the [[http://​research.omicsgroup.org/​index.php/​List_of_free_online_bioinformatics_courses|list]] of free online bioinformatics courses e.g., the Computational Molecular Biology [[http://​cmgm.stanford.edu/​biochem218/​index.html|Course]] at Stanford is broad and covers the classic topics but it is not updated, and may become outdated. The same is true for PLOS Translational Bioinformatics [[http://​collections.plos.org/​translational-bioinformatics|Collection]] of articles, which are more advanced. Most central topics are covered in some course from the European Bioinformatics Institute ([[https://​www.ebi.ac.uk/​training/​online/​course-list|EBI]]). Very useful training materials are available from [[https://​www.mygoblet.org/​|GOBLET]]. Videos from the Models, Inference & Algorithms Initiative ([[https://​www.broadinstitute.org/​scientific-community/​science/​mia/​models-inference-algorithms|MIA]]) at Broad are relatively advanced.\\
 \\ \\
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-**Install Salmon on OSX?** \\+==== Install Salmon on OSX? ==== 
 + 
 +\\
 If you do not have autoconf, [[http://​mac-dev-env.patrickbougie.com/​autoconf/​|install]] it. Following the installation guidelines, for OSX you need to first [[http://​stackoverflow.com/​questions/​3181468/​how-do-you-install-intel-tbb-on-os-x|install]] Thread Building Blocks (TBB) (brew install tbb) and then check that the installation was successful (brew list). Download the latest [[https://​github.com/​COMBINE-lab/​salmon/​releases|version]] of Salmon source code and uncompress it. Follow Salmon'​s installation [[http://​salmon.readthedocs.org/​en/​latest/​building.html#​installation|guidelines]]. The cmake command in the guidelines will be something like the following for OSX: If you do not have autoconf, [[http://​mac-dev-env.patrickbougie.com/​autoconf/​|install]] it. Following the installation guidelines, for OSX you need to first [[http://​stackoverflow.com/​questions/​3181468/​how-do-you-install-intel-tbb-on-os-x|install]] Thread Building Blocks (TBB) (brew install tbb) and then check that the installation was successful (brew list). Download the latest [[https://​github.com/​COMBINE-lab/​salmon/​releases|version]] of Salmon source code and uncompress it. Follow Salmon'​s installation [[http://​salmon.readthedocs.org/​en/​latest/​building.html#​installation|guidelines]]. The cmake command in the guidelines will be something like the following for OSX:
  
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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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 **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]].+[[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]]:​ 
 + 
 +<​code>​ 
 +(setq truncate-lines nil) 
 +</​code>​
  
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-**Get older versions using git?** \\+ 
 +==== Get older versions using git? ==== 
 [[https://​githowto.com/​getting_old_versions|Use]] "git log" to see the previous commits and the corresponding hashes, "git checkout <​hash>"​ to get an older version, and "git checkout master"​ to get back. [[https://​githowto.com/​getting_old_versions|Use]] "git log" to see the previous commits and the corresponding hashes, "git checkout <​hash>"​ to get an older version, and "git checkout master"​ to get back.
  
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-**Learn about linear models and ANOVA in R?** \\+ 
 +==== Learn about linear models and ANOVA in R? ==== 
 Review Advanced Statistical Methods II lecture [[https://​www.utdallas.edu/​~ammann/​stat6338/​stat6338.html|notes]] by Dr. Larry Ammann at UT Dallas. Review Advanced Statistical Methods II lecture [[https://​www.utdallas.edu/​~ammann/​stat6338/​stat6338.html|notes]] by Dr. Larry Ammann at UT Dallas.
  
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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?** \\ + 
-It is always better to a install the latest version of a package as directed in the corresponding Bioconductor page (e.g., [[https://​bioconductor.org/​packages/​Pigengene|Pigengene]]). If you need to see more details in the source code, you can clone the source from the Bioconductor ​mirror, e.g.,+==== Access a Bioconductor package source code? ==== 
 + 
 +It is always better to a install the latest version of a package as directed in the corresponding Bioconductor page (e.g., [[https://​bioconductor.org/​packages/​Pigengene|Pigengene]]). If you need to see more details in the source code, or you need the development version, you can clone the source from the Bioconductor ​using the "​Source Repository (Developer Access) " command, which is posted on the corresponding package [[https://​bioconductor.org/​packages/​release/​bioc/​html/​Pigengene.html|page]], e.g.,
  
 <​code>​ <​code>​
 mkdir ~/proj; cd ~/proj mkdir ~/proj; cd ~/proj
-git clone https://github.com/​Bioconductor-mirror/​Pigengene.git+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 createdYou can install the new package using: 
 + 
 +<​code>​ 
 + R CMD INSTALL Pigengene_<​Version>​.tar.gz
 </​code>​ </​code>​
  
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-**Use git via proxy or vpn?** \\+ 
 +==== Use git via proxy or vpn? ==== 
 Use [[https://​github.com/​apenwarr/​sshuttle|sshuttle]],​ e.g., sshuttle -r h_[[mailto:​z14@nyx.cs.txstate.edu|mailto:​z14@nyx.cs.txstate.edu]] 0.0.0.0/0 -vv\\ Use [[https://​github.com/​apenwarr/​sshuttle|sshuttle]],​ e.g., sshuttle -r h_[[mailto:​z14@nyx.cs.txstate.edu|mailto:​z14@nyx.cs.txstate.edu]] 0.0.0.0/0 -vv\\
 The list of servers at Texas Sate University are listed [[https://​cs.txstate.edu/​resources/​labs/​accounts/​linux/​|here]]. The list of servers at Texas Sate University are listed [[https://​cs.txstate.edu/​resources/​labs/​accounts/​linux/​|here]].
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 **Silence a gene?** \\ **Silence a gene?** \\
-Small interfering (si) RNAs and miRNAs [[https://​www.youtube.com/​watch?​v=cK-OGB1_ELE|bindd ]] to mRAN and prevent it from being translated.+Small interfering (si) RNAs and miRNAs [[https://​www.youtube.com/​watch?​v=cK-OGB1_ELE|bind ]]to mRAN and prevent it from being translated.
  
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 **Avoid misinterpretation of biological experiments?​** \\ **Avoid misinterpretation of biological experiments?​** \\
-[[https://​www.nature.com/​nrc/​journal/​v17/​n7/​full/​nrc.2017.32.html|Reasoning]] must be logical. Report enough details of the methods to reproduce the results. Assess the robustness of the findings with respect to minor perturbations to the experimental settings. To prove that drug A targets protein X, it is not sufficient to confirm that treatment with A leads to killing cells that have X. Maybe the cells are killed because of some other mechanism. Use "​rescue experiments"​ as in the A=imatinib X=BCR–ABL case.+[[https://​www.nature.com/​nrc/​journal/​v17/​n7/​full/​nrc.2017.32.html|Reasoning]] must be logical. Report enough details of the methods to reproduce the results. Assess the robustness of the findings with respect to minor perturbations to the experimental settings. To prove that drug A targets protein X, it is not sufficient to confirm that treatment with A leads to killing cells that have X. Maybe the cells are killed because of some other mechanism. Use "​rescue experiments"​ as in the A=imatinib X=BCR–ABL case. Always, avoid [[https://​elifesciences.org/​articles/​48175|these]] ten common statistical mistakes.
  
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 ==== Aks people'​s opinion? ==== ==== Aks people'​s opinion? ====
  
-Create a [[https://​doodle.com/​|Doodle]] to find a common time for scheduling events. For longer surveys, use [[https://​www.surveymonkey.com/​|SurveyMonkey]] for offline, and [[https://​www.pollev.com/​|Poll]] Everywhere for online interaction with audiance.+Create a [[https://​doodle.com/​|Doodle]] to find a common time for scheduling events. For longer surveys, use [[https://​www.surveymonkey.com/​|SurveyMonkey]] for offline, and [[https://​www.pollev.com/​|Poll]] Everywhere for online interaction with audience. 
 + 
 +---- 
 + 
 +==== Disable scroll acceleration in macOS? ==== 
 + 
 +Install and [[https://​www.reddit.com/​r/​osx/​comments/​6kx6zb/​how_to_disable_mouse_scrolling_acceleration/​|use]] USB [[http://​www.usboverdrive.com/​USBOverdrive/​Information.html|Overdrive]] to set Wheel up and down "​Speed"​ to say, 6 lines. The following [[https://​apple.stackexchange.com/​questions/​253111/​how-to-disable-scroll-acceleration-in-macos-sierra|command]] does NOT work: 
 + 
 +<​code>​ 
 +defaults write .GlobalPreferences com.apple.scrollwheel.scaling -1 
 +</​code>​ 
 + 
 +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.