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for_members [2020/02/18 19:02] – [General guidelines for conducting research in the Oncinfo Lab] adminfor_members [2020/03/10 19:53] – [General guidelines for conducting research in the Oncinfo Lab] admin
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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 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.+  - 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.
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   - 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.
 +  - If you want to use ROSMAP data, please create a Synapse [[https://www.synapse.org/#!RegisterAccount:0|account]], add your information to {{:dua_sagebionetworks_zare_ros-map_fe.pdf|this}}  file, and upload it again to Oncinfo without changing the file name. Then, let Habil know so that he uploads it on the Synapse [[https://www.synapse.org/#!AccessRequirements:ID=syn3219045&TYPE=ENTITY|website]].