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for_members [2019/10/26 19:39]
admin [General guidelines for conducting research in the Oncinfo Lab]
for_members [2019/11/11 19:04] (current)
admin [General guidelines for conducting research in the Oncinfo Lab]
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   - [[http://​www.r-project.org/​|R]] is primarily used for statistical analysis and other scripting purposes in Oncinfo Lab. [[https://​www.coursera.org/​course/​rprog|This]] is a good online course on R which takes about 1 month to complete. A couple of days should be enough to read [[http://​cran.r-project.org/​doc/​manuals/​R-intro.pdf|this]] good guide for starters to get the basis ideas, or cover the [[http://​www.r-tutor.com/​r-introduction|introduction]] section from R-Tutorial. [[https://​www.datacamp.com/​|DataCamp]] facilitates reading about R and running examples at the same time using a browser . Those who know R to some extend can use the book Bioinformatics with R {{:​bioinformatics-r-cookbook.pdf|Cookbook}} ​ or [[http://​adv-r.had.co.nz/​|Advanced]] R by Hadley Wickham to gradually learn more as they proceed in a project. The next step after learning R is to learn [[http://​www.nature.com/​nmeth/​journal/​v12/​n2/​full/​nmeth.3252.html|Bioconductor]] .   - [[http://​www.r-project.org/​|R]] is primarily used for statistical analysis and other scripting purposes in Oncinfo Lab. [[https://​www.coursera.org/​course/​rprog|This]] is a good online course on R which takes about 1 month to complete. A couple of days should be enough to read [[http://​cran.r-project.org/​doc/​manuals/​R-intro.pdf|this]] good guide for starters to get the basis ideas, or cover the [[http://​www.r-tutor.com/​r-introduction|introduction]] section from R-Tutorial. [[https://​www.datacamp.com/​|DataCamp]] facilitates reading about R and running examples at the same time using a browser . Those who know R to some extend can use the book Bioinformatics with R {{:​bioinformatics-r-cookbook.pdf|Cookbook}} ​ or [[http://​adv-r.had.co.nz/​|Advanced]] R by Hadley Wickham to gradually learn more as they proceed in a project. The next step after learning R is to learn [[http://​www.nature.com/​nmeth/​journal/​v12/​n2/​full/​nmeth.3252.html|Bioconductor]] .
   - Using [[https://​en.wikipedia.org/​wiki/​Emacs|Emacs]] as a powerful, general purpose, text editor is [[https://​robertamezquita.github.io/​post/​2017-04-07-my-emacs-setup/​|encouraged]] ([[http://​www2.lib.uchicago.edu/​keith/​tcl-course/​emacs-tutorial.html|tutorial]]). In terminal, you can start it by typing emacs even in an SSH session. On Ubuntu you can simply install Emacs using Software Center, or by Package Synaptics, or by the following command: ''​sudo apt-get install emacs''​. On OS X, you can install [[https://​emacsformacosx.com/​|Emacs]] For MAC OS X, which is better than Aquamacs. A less recommended option is [[https://​vigou3.gitlab.io/​emacs-modified-macos/​|Emacs Modified for macOS]], which supports [[https://​ess.r-project.org/​|ESS]] and [[https://​www.gnu.org/​software/​auctex/​|AUCTeX]]. You can customize your emacs by editing .emacs file. Feel free to copy some, but not all, commands from Habil'​s .emacs file for [[https://​www.dropbox.com/​s/​pdt6fbho57k421d/​emacs_UTosx2018|macOS]]. As of 2019, his favorite packages include: tabbar, tabbar-ruler,​ rainbow-delimiters,​ idle-highlight-in-visible-buffers-mode,​ auto-highlight-symbol,​ auto-complete-auctex,​ auto-complete,​ and ess.   - Using [[https://​en.wikipedia.org/​wiki/​Emacs|Emacs]] as a powerful, general purpose, text editor is [[https://​robertamezquita.github.io/​post/​2017-04-07-my-emacs-setup/​|encouraged]] ([[http://​www2.lib.uchicago.edu/​keith/​tcl-course/​emacs-tutorial.html|tutorial]]). In terminal, you can start it by typing emacs even in an SSH session. On Ubuntu you can simply install Emacs using Software Center, or by Package Synaptics, or by the following command: ''​sudo apt-get install emacs''​. On OS X, you can install [[https://​emacsformacosx.com/​|Emacs]] For MAC OS X, which is better than Aquamacs. A less recommended option is [[https://​vigou3.gitlab.io/​emacs-modified-macos/​|Emacs Modified for macOS]], which supports [[https://​ess.r-project.org/​|ESS]] and [[https://​www.gnu.org/​software/​auctex/​|AUCTeX]]. You can customize your emacs by editing .emacs file. Feel free to copy some, but not all, commands from Habil'​s .emacs file for [[https://​www.dropbox.com/​s/​pdt6fbho57k421d/​emacs_UTosx2018|macOS]]. As of 2019, his favorite packages include: tabbar, tabbar-ruler,​ rainbow-delimiters,​ idle-highlight-in-visible-buffers-mode,​ auto-highlight-symbol,​ auto-complete-auctex,​ auto-complete,​ and ess.
-  - Using proprietary file formats is not professional when you are sharing information (e.g., your CV) with others. The pdf and png formats are OK and portable. Use Google Docs instead of .docx, ​and Google Presentation instead of .ppt.+  - Using proprietary file formats is not professional when you are sharing information (e.g., your CV) with others. The pdf and png formats are OK and portable. Use Google Docs instead of .docx, Google Presentation instead of .ppt, .zip or tar.gz instead of rar, etc.
   - [[https://​www.youtube.com/​watch?​v=WsofH466lqk|This]] video illustrates transcription ([[https://​en.wikipedia.org/​wiki/​Transcription_(genetics)|wikipedia]],​ [[https://​www.youtube.com/​watch?​v=5MfSYnItYvg|video 2]]), more videos on [[https://​www.youtube.com/​watch?​v=OEWOZS_JTgk|gene expression]] ([[https://​en.wikipedia.org/​wiki/​Gene_expression|wikipedia]]),​ [[https://​www.youtube.com/​watch?​v=TfYf_rPWUdY|translation]] ([[https://​www.youtube.com/​watch?​v=5bLEDd-PSTQ|detailed]]),​ etc.   - [[https://​www.youtube.com/​watch?​v=WsofH466lqk|This]] video illustrates transcription ([[https://​en.wikipedia.org/​wiki/​Transcription_(genetics)|wikipedia]],​ [[https://​www.youtube.com/​watch?​v=5MfSYnItYvg|video 2]]), more videos on [[https://​www.youtube.com/​watch?​v=OEWOZS_JTgk|gene expression]] ([[https://​en.wikipedia.org/​wiki/​Gene_expression|wikipedia]]),​ [[https://​www.youtube.com/​watch?​v=TfYf_rPWUdY|translation]] ([[https://​www.youtube.com/​watch?​v=5bLEDd-PSTQ|detailed]]),​ etc.
   - All members should know about central [[https://​en.wikipedia.org/​wiki/​Central_dogma_of_molecular_biology|dogma]] of biology which is almost enough biological knowledge to start the majority of projects [[:​dogma.pdf?​media=dogma.pdf|pdf]]]. Familiarity with some basic concepts such as [[https://​en.wikipedia.org/​wiki/​Exon|exon]],​ intron, etc. is helpful. Watch [[https://​www.dnalc.org/​resources/​3d/​|animations]] from DNA Learning Center.   - All members should know about central [[https://​en.wikipedia.org/​wiki/​Central_dogma_of_molecular_biology|dogma]] of biology which is almost enough biological knowledge to start the majority of projects [[:​dogma.pdf?​media=dogma.pdf|pdf]]]. Familiarity with some basic concepts such as [[https://​en.wikipedia.org/​wiki/​Exon|exon]],​ intron, etc. is helpful. Watch [[https://​www.dnalc.org/​resources/​3d/​|animations]] from DNA Learning Center.