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for_members [2019/08/22 00:12] – [General guidelines for conducting research in the Oncinfo Lab] adminfor_members [2019/10/23 20:01] – [General guidelines for conducting research in the Oncinfo Lab] admin
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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.
   - 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.
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   - 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.
   - Any file or data on this wiki that has restricted permissions, such as some paper pdfs or drafts, should not be shared with nonmembers unless authorized by the PI.   - Any file or data on this wiki that has restricted permissions, such as some paper pdfs or drafts, should not be shared with nonmembers unless authorized by the PI.
 +  - For future reference, please add the link to your presentations and drafts on the [[https://oncinfo.org/drafts|drafts]] page. At a minimum, please include: the author, the date, the audience, and the subject.
   - All members should read and follow [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424|Bill's]] guidelines, and organize their files and folders accordingly and to some extend. Start by making a "~/proj" directory in your home folder that will eventually contain a subfolder for each project you are working on. Major subfolders must have a readme file for example to describe where the data is coming from. Your code folder must include a runall.R script that sources other scripts. Avoid sourcing scripts in other scripts except for the runall because then following and debugging the pipeline would be difficult.   - All members should read and follow [[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424|Bill's]] guidelines, and organize their files and folders accordingly and to some extend. Start by making a "~/proj" directory in your home folder that will eventually contain a subfolder for each project you are working on. Major subfolders must have a readme file for example to describe where the data is coming from. Your code folder must include a runall.R script that sources other scripts. Avoid sourcing scripts in other scripts except for the runall because then following and debugging the pipeline would be difficult.
   - Your code and documents should be stored in a Bitbucket repository like [[https://bitbucket.org/habilzare/genetwork|https://bitbucket.org/habilzare/genetwork]]. Sign up for an [[https://bitbucket.org/account/signup/|account]] and add your photo. Do NOT sign in using your Google account. Only then, send your username to Habil. If you are new to Bitbucket, take [[https://guides.co/g/bitbucket-101/11146|Bitbucket 101]]. You can [[https://confluence.atlassian.com/bitbucket/use-the-ssh-protocol-with-bitbucket-cloud-221449711.html|avoid]] having to manually type a password each time you pull using ssh. To add a key, click on your photo at the top right corner of Bitbucket page, Bitbucket settings, SSH keys, Add key. This trick is not appropriate for TACC clusters because we should not change our .ssh folder there. On the cluster, use https to clone instead of ssh. Do NOT mess up with other's git folders on the cluster. You should //only//  clone, pull, and push in your own home or work directory. Do NOT skip this step. Before changing anything in a repository, read and abide to the conventions described in the main readme file.   - Your code and documents should be stored in a Bitbucket repository like [[https://bitbucket.org/habilzare/genetwork|https://bitbucket.org/habilzare/genetwork]]. Sign up for an [[https://bitbucket.org/account/signup/|account]] and add your photo. Do NOT sign in using your Google account. Only then, send your username to Habil. If you are new to Bitbucket, take [[https://guides.co/g/bitbucket-101/11146|Bitbucket 101]]. You can [[https://confluence.atlassian.com/bitbucket/use-the-ssh-protocol-with-bitbucket-cloud-221449711.html|avoid]] having to manually type a password each time you pull using ssh. To add a key, click on your photo at the top right corner of Bitbucket page, Bitbucket settings, SSH keys, Add key. This trick is not appropriate for TACC clusters because we should not change our .ssh folder there. On the cluster, use https to clone instead of ssh. Do NOT mess up with other's git folders on the cluster. You should //only//  clone, pull, and push in your own home or work directory. Do NOT skip this step. Before changing anything in a repository, read and abide to the conventions described in the main readme file.