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how_to [2019/05/17 02:55]
admin [Install R locally (e.g. on a cluster)?]
how_to [2020/05/28 07:33] (current)
shiva [Get familiar with machine learning and its applications in computational biology?]
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 ---- ----
 +
 +==== Work with screen sessions? ====
 +
 +There are five main [[http://​www.pixelbeat.org/​lkdb/​screen.html|commands]] while working with screen session:
 +
 +  - Start and name a screen: ''​screen -S <NAME of the screen>''​
 +  - Detach from a screen: ''​Ctrl+a d''​
 +  - See the list of active screens: ''​screen -ls''​
 +  - Reattach to a screen: ''​screen -r <NAME of the screen>''​
 +  - Quit and kill your screen: ''​Ctrl+a '' ​ then ''​Ctrl+\''​
 +
 +----
 +
 +
 +==== Read and write excel files in R ====
 +
 +Use [[https://​cran.r-project.org/​web/​packages/​openxlsx/​index.html|openxlsx]] package to read, write and edit xlsx files in R. Package'​s integration with C++ makes it faster and easier to use. Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of '​Rcpp',​ read/write times are comparable to the '​xlsx'​ and '​XLConnect'​ packages with the added benefit of removing the dependency on Java.
 +
 +<​code>​
 +E.g. Writing four dataframes in four sheets of excel workbook can be done as follows:
 +library(openxlsx)
 +listDataFrames <- list("​GO-BP"​=data.frame(egoBP),​ "​GO-MF"​=data.frame(egoMF),​
 +                       "​KEGG"​ = data.frame(eKEGG),​ "​NCG"​ = data.frame(ncg))
 +xlsFile <- file.path(resultPath,​ paste0(l1, "​_ORA_results.xlsx"​))
 +write.xlsx(x=listDataFrames,​ file=xlsFile)
 +</​code>​
 +
 +----
 +
  
 ==== Set local mirror for Rscript ==== ==== Set local mirror for Rscript ====
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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.
  
 ---- ----
 +
  
 ==== Use a package that is being developed? ==== ==== Use a package that is being developed? ====
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 ==== Install R locally (e.g. on a cluster)? ==== ==== Install R locally (e.g. on a cluster)? ====
 +
 +If you want to install the latest __development__ version of R on your macOS, first install [[https://​github.com/​fxcoudert/​gfortran-for-macOS/​releases|Fortran]] if you do not have it. You may also need to update [[https://​superuser.com/​a/​664326|PCRE]].
  
 If you do not have sudo permissions,​ like when you are working on a cluster, you should either use the software module, or install it locally in your home directory. E.g., you can install R on Stampede or Maverick as follows: If you do not have sudo permissions,​ like when you are working on a cluster, you should either use the software module, or install it locally in your home directory. E.g., you can install R on Stampede or Maverick as follows:
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 ---- ----
  
-**Write in xls files from R?** \\ 
-Use [[http://​www.inside-r.org/​packages/​cran/​XLConnect/​docs/​writeWorksheetToFile|writeWorksheetToFile]]() function from [[http://​cran.r-project.org/​web/​packages/​XLConnect/​index.html|XLConnect]] package like below: 
  
-<​code>​ +==== Restore a file deleted in a local git directory? ====
-writeWorksheetToFile(data=matrix(1:​10,​2,​2),​file='​./​temp.xls',​sheet='​test1'​) +
-writeWorksheetToFile(data=matrix(1:​6,​2,​3),​file='​./​temp.xls',​sheet='​test2'​) +
-</​code>​ +
- +
-----+
  
-**Restore a file** **deleted ****in a local git directory?​** \\ 
 [[http://​stackoverflow.com/​questions/​9305326/​why-doesnt-git-pull-bring-back-directories-that-ive-deleted|Use]] git reset –hard to completely bring your working directory to HEAD state. However, this is a [[http://​stackoverflow.com/​questions/​5473/​how-can-i-undo-git-reset-hard-head1|dangerous]] command because you may loose some local files that are not pushed yet. [[http://​stackoverflow.com/​questions/​9305326/​why-doesnt-git-pull-bring-back-directories-that-ive-deleted|Use]] git reset –hard to completely bring your working directory to HEAD state. However, this is a [[http://​stackoverflow.com/​questions/​5473/​how-can-i-undo-git-reset-hard-head1|dangerous]] command because you may loose some local files that are not pushed yet.
  
 ---- ----
  
-**Get familiar with applications ​of machine learning in genetics ​and genomics?** \\ + 
-First read [[http://​www.nature.com/​nrg/​journal/​v16/​n6/​abs/​nrg3920.html|this]] 2015 review ​paper and then follow its references.+==== Get familiar with machine learning and its applications ​in computational biology? ==== 
 + 
 +- You can enroll in many online ​machine learning ​courses. Some of the best courses ​in ML can be found [[https://​docs.google.com/​spreadsheets/​d/​1AK8lqS-ztMhh8YoOaQ7ScIZmabrQ5AFxAyXKwYWiT04/​edit#​gid=0|here]]. 
 + 
 +- 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.
  
 ---- ----
  
-**Get access to the papers through the library when you are off-campus?** \\ + 
-First add the following to your browser (Chrome or Firefox) bookmarks.+==== Get access to the papers through the library when you are off-campus? ​==== 
 + 
 +In any of these two ways:\\ 
 +a) First add the following to your browser (Chrome or Firefox) bookmarks.
  
 <​code>​ <​code>​
-javascript:​void(location.href=%22http://​libproxy.txstate.edu/​login?​url=%22+location.href)+javascript:​void(location.href=%22http://​libproxy.uthscsa.edu/​login?​url=%22+location.href)
 </​code>​ </​code>​
  
 Then, on the journal page, click on the bookmark. Login and start reading. Then, on the journal page, click on the bookmark. Login and start reading.
 +
 +b) Use [[https://​infosec.uthscsa.edu/​two-factor-enrollment|GlobalProtect]],​ which is the University VPN.
  
 ---- ----
  
-**Convert pdf to MS word?** \\ + 
-Try whatever you can to avoid conversion! Instead, educate your team and your collaborators to use [[https://​www.authorea.com/​users/​54336|Authorea]],​ [[https://​www.overleaf.com/​|Overleaf]] or at least google ​doc. __Only__ if your biologist collaborators cannot [[http://​www.dedoimedo.com/​computers/​latex.html|unfortunately]] edit the LaTeX source, consider using a conversion tool such as docs.[[https://​docs.zone/​|zone]]. Alternatively,​ Acrobat Pro can export a .pdf as a .doc file. If Bibtex is not an option, use [[http://​www.easybib.com/​|EasyBib]].+==== Convert pdf to MS word? ==== 
 + 
 +Try whatever you can to avoid conversion! Instead, educate your team and your collaborators to use [[https://​www.authorea.com/​users/​54336|Authorea]],​ [[https://​www.overleaf.com/​|Overleaf]] or at least Google Doc. In Google Doc, references can be easily handled using [[https://​gsuite.google.com/​marketplace/​app/​paperpile/​894076725911|Paperpile]] add-on, and figures can be automatically numbered using the the [[https://​gsuite.google.com/​marketplace/​app/​cross_reference/​269114033347?​pann=cwsdp&​hl=en|Cross Reference]] add-on as suggested in these [[https://​lcolladotor.github.io/​2019/​04/​02/​how-to-write-academic-documents-with-googledocs/#​.Xjne6RNKjUI|guidelines]] on how to write academic documents with Google Docs . __Only__ if your biologist collaborators cannot [[http://​www.dedoimedo.com/​computers/​latex.html|unfortunately]] edit the LaTeX source, consider using a conversion tool such as docs.[[https://​docs.zone/​|zone]]. Alternatively,​ Acrobat Pro can export a .pdf as a .doc file. If Bibtex is not an option, use [[http://​www.easybib.com/​|EasyBib]].
  
 ---- ----
  
-**Enable spell check in Emacs on OS X?** \\+ 
 +==== Enable spell check in Emacs on OS X? ==== 
 The default Aquamacs spell checker has some issues. To replace it, first [[http://​stackoverflow.com/​questions/​19022015/​emacs-on-mac-os-x-how-to-get-spell-check-to-work|install]] Aspell, which is a [[https://​en.wikipedia.org/​wiki/​GNU_Aspell|replacement]] for Ispell: The default Aquamacs spell checker has some issues. To replace it, first [[http://​stackoverflow.com/​questions/​19022015/​emacs-on-mac-os-x-how-to-get-spell-check-to-work|install]] Aspell, which is a [[https://​en.wikipedia.org/​wiki/​GNU_Aspell|replacement]] for Ispell:
  
 <​code>​ <​code>​
-brew install aspell ​--with-lang-en+brew install aspell
 </​code>​ </​code>​
  
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 ---- ----
  
-**Do microaray analysis or anything else in Bioconductor?​** \\+==== Do microaray analysis or anything else in Bioconductor? ​==== 
 [[http://​manuals.bioinformatics.ucr.edu/​home/​R_BioCondManual#​TOC-Affy|This ]] is an excellent site with many well commented code examples and a lot of handy short-cuts. See also [[:​how_to|Functional analysis tools]]. [[http://​manuals.bioinformatics.ucr.edu/​home/​R_BioCondManual#​TOC-Affy|This ]] is an excellent site with many well commented code examples and a lot of handy short-cuts. See also [[:​how_to|Functional analysis tools]].
  
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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]].+ 
 +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]].
  
 ---- ----
  
-**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.
  
 ---- ----
  
-**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>​
  
 ---- ----
  
-**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.
  
 ---- ----
  
-**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.
  
 ---- ----
  
-**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.
  
 ---- ----
  
-**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]].
  
 ---- ----
  
-**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. If the package maintainer adds your public ssh [[https://​git.bioconductor.org/​BiocCredentials/​|key]],​ then 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>​
  
 ---- ----
  
-**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"​ of your mouse 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. 
 + 
 +---- 
 + 
 + 
 +===== 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. 
 + 
 +---- 
 + 
 +===== Work with screen session? ===== 
 + 
 +There are five main [[http://​www.pixelbeat.org/​lkdb/​screen.html|commands]] while working with screen session: 
 + 
 +  - Start and name a screen: ''​screen -S $NAME''​ 
 +  - Detach from a screen: ''​Ctrl+a d''​ 
 +  - See the list of active screens: ''​screen -ls''​ 
 +  - Reattach to a screen: ''​screen -r $NAME''​ 
 +  - Quit and [[https://​askubuntu.com/​questions/​356006/​kill-a-screen-session|kill]] your screen: ''​Ctrl+a then Ctrl+\''​ 
 + 
 +----