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| for_members [2019/01/14 19:52] – admin | for_members [2019/01/25 15:38] – [General guidelines for conducting research in Oncinfo lab] SSH to lab machines admin |
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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. |
| - If you need to ssh into the lab machine you will need to have an account on the machine already. Then you will follow the following commands: ssh <user name>@10.102.163.212 | - Usually, the latest version of Ubuntu is missing some dependencies for the R packages Pigengene, WGCNA, and GEOquery. To easily install these dependencies, download [[:file_view_ubuntuinstall.sh_614871151_ubuntuinstall.sh|this]] script, as well as [[:file_view_pigengeneubuntuinstall.r_614318347_pigengeneubuntuinstall.r|pigengeneUbuntuInstall.R]] to a local directory. Navigate to that directory and then run: |
| - Usually, the latest version of Ubuntu is missing some dependencies for the R packages Pigengene, WGCNA, and GEOquery. To easily install these dependencies, download [[:file_view_ubuntuinstall.sh_614871151_ubuntuinstall.sh|this]] script, as well as [[:file_view_pigengeneubuntuinstall.r_614318347_pigengeneubuntuinstall.r|pigengeneUbuntuInstall.R]] to a local directory. Navigate to that directory and then run: \\ $ chmod +x ubuntuInstall.sh \\ $ ./ubuntuInstall.sh \\ $ Rscript pigengeneUbuntuInstall.R | - $ chmod +x ubuntuInstall.sh \\ $ ./ubuntuInstall.sh \\ $ Rscript pigengeneUbuntuInstall.R |
| - 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. | - 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. |
| - 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. |
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| ==== Some references ==== | ==== Some references ==== |
