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for_members [2019/07/19 14:57] – [General guidelines for conducting research in the Oncinfo Lab] adminfor_members [2019/08/22 00:12] – [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 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 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. Another 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, and auto-complete.+  - 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, and Google Presentation instead of .ppt.
   - [[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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   - 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.
-  - Please cc Habil on any email that is related to scientific or logistic aspects of your research in the lab, your career development activities, and communications among lab members on issues related to the lab. When you send an email to multiple people, mention the primary addressee at the top. It helps drawing the attention of the addressee, and also shows your respect to others who do not need to read your whole message. Usually using "reply-to-all" is preferred on emails with multiple recipients.+  - Please cc Habil on any email that is related to scientific or logistic aspects of your research in the lab, your career development activities, and communications among lab members on issues related to the lab. When you send an email to multiple people, mention the primary addressee at the top. It helps drawing the attention of the addressee, and also shows your respect to others who do not need to read your whole message. Usually using "reply-to-all" is preferred on emails with multiple recipients. When possible, reply to the previous email on a topic and avoid creating another thread unnecessarily, which will complicate future references.
   - As employees of UT Health, we can get facilitated appointments with UT Health primary care physicians (call: 210-450-9090).   - As employees of UT Health, we can get facilitated appointments with UT Health primary care physicians (call: 210-450-9090).
   - If you are considering ultimately getting jobs in computation biology or bioinformatics, have a look at postings at the [[http://bioinformatics.org|bioinformatics.org]] website __within the first week__  after joining the lab. For academic positions, see the Nature Jobs and Science Careers websites. Read the articles on "[[http://oncinfo.org/how_to|How to]] rescue US biomedical research from its systemic flaws?" if you are, or want to be, a PhD student.   - If you are considering ultimately getting jobs in computation biology or bioinformatics, have a look at postings at the [[http://bioinformatics.org|bioinformatics.org]] website __within the first week__  after joining the lab. For academic positions, see the Nature Jobs and Science Careers websites. Read the articles on "[[http://oncinfo.org/how_to|How to]] rescue US biomedical research from its systemic flaws?" if you are, or want to be, a PhD student.