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for_members [2020/06/23 00:18] – adminfor_members [2020/08/28 15:16] – [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. You need to do this on ALL clusters including Lonestar and Ranch. On Ranch, adding umask in .bashrc. does not work. Instead, create or modify ~/.cshrc.
   - 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. 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".   - 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 computational 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]].   - 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]].
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 ==== Some references ==== ==== Some references ====
  
-  - Two machine learning bibles: Bishop ({{:bishop-pattern_recongnition_and_machine_learning-1.pdf|1}},{{:bishop-pattern_recongnition_and_machine_learning-2.pdf|2}}  ) and [[http://statweb.stanford.edu/~tibs/ElemStatLearn/download.html|Hasite et al.]].+  - Two machine learning bibles, which summarize important topics in the field up to 2005: Bishop ({{:bishop-pattern_recongnition_and_machine_learning-1.pdf|1}},{{:bishop-pattern_recongnition_and_machine_learning-2.pdf|2}}  ) and [[http://statweb.stanford.edu/~tibs/ElemStatLearn/download.html|Hasite et al.]].
   - [[https://www.biostars.org/|Biostars]] is a good forum, similar to Stack Overflow in structure, but focused on bioinformatics and Computational Biology.   - [[https://www.biostars.org/|Biostars]] is a good forum, similar to Stack Overflow in structure, but focused on bioinformatics and Computational Biology.
   - [[http://www.wikiwand.com/en/List_of_free_online_bioinformatics_courses|List]] of free online bioinformatics courses and some interesting [[http://bioconductor.org/help/events/|events]] in Bioconductor.   - [[http://www.wikiwand.com/en/List_of_free_online_bioinformatics_courses|List]] of free online bioinformatics courses and some interesting [[http://bioconductor.org/help/events/|events]] in Bioconductor.
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   - [[http://stephenturner.us/edu.html|List]] of bioinformatics workshops.   - [[http://stephenturner.us/edu.html|List]] of bioinformatics workshops.
   - A 5-minutes introduction to next-generation sequencing [[https://www.youtube.com/watch?annotation_id=annotation_228575861&feature=iv&src_vid=womKfikWlxM&v=fCd6B5HRaZ8|video]].   - A 5-minutes introduction to next-generation sequencing [[https://www.youtube.com/watch?annotation_id=annotation_228575861&feature=iv&src_vid=womKfikWlxM&v=fCd6B5HRaZ8|video]].
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 ==== Fun stuff ==== ==== Fun stuff ====