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for_members [2019/07/12 20:10]
admin [General guidelines for conducting research in the Oncinfo Lab]
for_members [2019/07/19 17:57] (current)
admin [General guidelines for conducting research in the Oncinfo Lab]
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 ==== General guidelines for conducting research in the Oncinfo Lab ==== ==== General guidelines for conducting research in the Oncinfo Lab ====
  
-  - To join the Oncinfo Lab, you need to: \\ a) Be __organized and disciplined__,​ otherwise your efforts will be fruitless and lost even if you make important discoveries. Other lab members will enjoy working with you if your code is clean and you can clearly talk about your project. \\ b) __Hard working__, otherwise even a genius will not get to anywhere if they do not move. \\ c) __Talented__. Nobody knows everything that is needed to do multidisciplinary research.You should be able to learn many things that you were not thought in courses, and find novel solutions for small and big challenges that you face because you are the first person who is working on your specific study. ​ \\ d) __Knowledgeable__ ​ \\+  - To join the Oncinfo Lab, you need to: \\ a) Be __organized and disciplined__,​ otherwise your efforts will be fruitless and lost even if you make important discoveries. Other lab members will enjoy working with you if your code is clean and you can clearly talk about your project. \\ b) __Work hard__, otherwise even a genius will not get to anywhere if they do not move. \\ c) Be __talented__. Nobody knows everything that is needed to do multidisciplinary research.You should be able to learn many things that you were not thought in courses. You often need to find novel solutions for small and big challenges that you face because you are the first person who is working on your specific study. \\ d) Be __knowledgeable__ ​ because we are not interested in reinventing the wheel. ​\\ The above items are ordered based on importance. The most critical one is **discipline**.
   - All Google docs that need to be edited by lab members should be put in Oncinfo [[https://​drive.google.com/?​tab=mo&​authuser=0#​folders/​0B5Cpru0UXP0adTZTckg3aEd4SEE|folder]]. They should be kept confidential. Send your gmail address to Habil to get access to this folder. Remind him to add you his Oncinfo Google group. Then, create a subfolder with your name there, and create a google doc in your subfolder. Copy all items from this "For members"​ page to that google doc, and write "​**Done**",​ "​**Todo**",​ "​**Skip**"​ in front of each item.   - All Google docs that need to be edited by lab members should be put in Oncinfo [[https://​drive.google.com/?​tab=mo&​authuser=0#​folders/​0B5Cpru0UXP0adTZTckg3aEd4SEE|folder]]. They should be kept confidential. Send your gmail address to Habil to get access to this folder. Remind him to add you his Oncinfo Google group. Then, create a subfolder with your name there, and create a google doc in your subfolder. Copy all items from this "For members"​ page to that google doc, and write "​**Done**",​ "​**Todo**",​ "​**Skip**"​ in front of each item.
   - Pass the online training courses required by the University e.g., conflict of interest, safety, etc.   - Pass the online training courses required by the University e.g., conflict of interest, safety, etc.
   - 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?dl=0|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 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 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.