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for_members [2020/02/18 15:56] – [General guidelines for conducting research in the Oncinfo Lab] adminfor_members [2020/02/18 19:05] – [General guidelines for conducting research in the Oncinfo Lab] admin
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   - All experiments and analysis are done on Unix. That is a __real__  Unix system like Linux, OS X, etc., NOT a virtual machine. Start with a [[http://www.ee.surrey.ac.uk/Teaching/Unix/|tutorial]] for beginners or the [[http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf|introduction]] to Bio-Linux.   - All experiments and analysis are done on Unix. That is a __real__  Unix system like Linux, OS X, etc., NOT a virtual machine. Start with a [[http://www.ee.surrey.ac.uk/Teaching/Unix/|tutorial]] for beginners or the [[http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf|introduction]] to Bio-Linux.
   - [[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 these books: Computational [[https://compgenomr.github.io/book/|Genomics]] with R, Bioinformatics with R {{:bioinformatics-r-cookbook.pdf|Cookbook}}, and [[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 these books: Computational [[https://compgenomr.github.io/book/|Genomics]] with R, Bioinformatics with R {{:bioinformatics-r-cookbook.pdf|Cookbook}}, and [[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. For guidelines on installing these packages and other emacs customizations, see the notes on [[:how_to|How to]] page.
   - 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.   - 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.
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   - When possible, give and use column and row names to the matrixes. Also, give and use names for vectors.   - When possible, give and use column and row names to the matrixes. Also, give and use names for vectors.
   - Do’s and don’ts when s[[http://www.sicb.org/students/Dos_and_Donts.pdf|ubmitting]] papers.   - Do’s and don’ts when s[[http://www.sicb.org/students/Dos_and_Donts.pdf|ubmitting]] papers.
-  - Make sure that your home directory and also your work directory on the cluster are at least readable to the group. E.g., In your .bashrc, set [[http://www.cyberciti.biz/tips/understanding-linux-unix-umask-value-usage.html|umask]] 007 and do the following: \\  chmod -R g+rwX ~ ; cdw; chmod -R g+rwX; cds; chmod -R g+rwX+  - Make sure that your home directory and also your work directory on the cluster are at least readable to the group. E.g., In your .bashrc, set umask 007 and do the following: \\ ''chmod -R g+rwX ~ ; cdw; chmod -R g+rwX; cds; chmod -R g+rwX \\ chmod 600 ~/.ssh/id_rsa'' \\ There might be some exceptions like your private ssh key at ''~/.ssh/id_rsa''  which must be readable only by you.
   - If you are unfamiliar with prior, posterior, and likelihood, read about [[http://%5Bhttp://en.wikipedia.org/wiki/Bayesian_inference|Bayesian inference]].   - If you are unfamiliar with prior, posterior, and likelihood, read about [[http://%5Bhttp://en.wikipedia.org/wiki/Bayesian_inference|Bayesian inference]].
   - To use ref.bib bibliography in bibtex, do the following: \\ a) cd proj \\ b) git clone [[mailto:git@bitbucket.org:habilzare/refs.git|git@bitbucket.org:habilzare/refs.git]] \\  c) At the bottom of your LaTeX document, write: \\  \bibliography{\detokenize{~/proj/refs/refs}} \\  d) To add a new entry, find the appropriate format using "Google Scholar Button" (see above, click on the quotation mark at the to right, and then BibTeX at the bottom) copy the entry and see if it is already in the refs.bib file. If not, add it in "**its right location"**  (i.e., key are alphabetically ordered) and push. Use the key with the \cite command in your LaTeX file. To compile, use pdflatex, bibtex (without .tex), and pdflatex *2.   - To use ref.bib bibliography in bibtex, do the following: \\ a) cd proj \\ b) git clone [[mailto:git@bitbucket.org:habilzare/refs.git|git@bitbucket.org:habilzare/refs.git]] \\  c) At the bottom of your LaTeX document, write: \\  \bibliography{\detokenize{~/proj/refs/refs}} \\  d) To add a new entry, find the appropriate format using "Google Scholar Button" (see above, click on the quotation mark at the to right, and then BibTeX at the bottom) copy the entry and see if it is already in the refs.bib file. If not, add it in "**its right location"**  (i.e., key are alphabetically ordered) and push. Use the key with the \cite command in your LaTeX file. To compile, use pdflatex, bibtex (without .tex), and pdflatex *2.