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for_members [2020/02/10 21:07]
admin [General guidelines for conducting research in the Oncinfo Lab]
for_members [2020/02/18 21:05] (current)
admin [General guidelines for conducting research in the Oncinfo Lab]
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   - 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**.   - 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.
-  - If you have a lab computer, add the tag number written on the back of the laptop, your name, and the date you start using it in the [[https://​docs.google.com/​spreadsheets/​d/​1A6ouCCPov5VXt7xBCdTh7Cwc6jtPJGGJlekmGnKL5JY/​edit#​gid=441648294|table]] of computers.+  - If you have a lab computer, add the tag number written on the back of the laptop, your name, and the date you start using it in the [[https://​docs.google.com/​spreadsheets/​d/​1A6ouCCPov5VXt7xBCdTh7Cwc6jtPJGGJlekmGnKL5JY/​edit#​gid=441648294|table]] of computers. Your drive must be always encrypted. E.g., on macOS, you can make sure FileValut is on like {{:​screen_shot_2020-02-15_at_10.24.09_pm.png?​linkonly|this}}. Take a similar screenshot that shows your name at the upper right corner, and post it on your lab notebook.
   - 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 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.
-  - 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.+  - 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. Emails should be receive some sort of reply within 24 hours even if it is short like "​I'​ll work on it". Otherwise, you will start your next email with "Sorry for the delay".
   - 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.