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how_to [2019/07/03 16:24] – [Install R locally (e.g. on a cluster)?] adminhow_to [2019/09/19 22:37] – [Get older versions using git?] admin
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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at Stanford is broad and covers the classic topics but it is not updated, and may become outdated.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at Stanford is broad and covers the classic topics but it is not updated, and may become outdated.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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 **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.
  
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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.