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for_members [2024/04/30 22:14] – [General guidelines for conducting research in the Oncinfo Lab] adminfor_members [2024/05/14 14:37] – azad
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   - When possible, give and use **column and row names**  to the matrixes. Also, give and use names for vectors as well as lists.   - When possible, give and use **column and row names**  to the matrixes. Also, give and use names for vectors as well as lists.
   - When sharing the results with biologists collaborator, make your **xlsx**  tables fancy e.g., by using bold and slightly larger fonts in the first row and column and also freezing the first row and column.   - When sharing the results with biologists collaborator, make your **xlsx**  tables fancy e.g., by using bold and slightly larger fonts in the first row and column and also freezing the first row and column.
-  - Do’s and don’ts when**[[http://www.sicb.org/students/Dos_and_Donts.pdf|submitting]] papers**.+  - Do’s and don’ts when **[[https://web.archive.org/web/20181123152529/https://sicb.org/students/Dos_and_Donts.pdf|submitting]] papers**.
   - Make sure that your home, work, and scratch directories on the cluster are at least **readable to the group, and not readable to others**. E.g., in your .bashrc, set umask 007 and do the following: \\ ''chmod -R g+rwX,o-rwx $HOME $WORK $SCRATCH \\ chmod 600 ~/.ssh/id_rsa ## If you have this file, it **MUST**  be private. \\ chmod g-w ~ ## Home must NOT be writable by the group otherwise submiting jobs will not be allowed. \\ chmod 700 ~/.ssh ## Nobody other than you is allowed to change the sensative .ssh folder. \\ chmod 644 ~/.ssh/id_rsa.pub ~/.ssh/authorized_keys ~/.ssh/known_hosts '' \\ There might be some [[https://unix.stackexchange.com/questions/37164/ssh-and-home-directory-permissions|exceptions]] like your private ssh key at ''~/.ssh/id_rsa'', which must be readable only by you. On Ranch, adding umask in .bashrc. does not work. Instead, create or modify ~/.cshrc. You need to do the above modifications on ALL clusters you use including Lonestar and Ranch.   - Make sure that your home, work, and scratch directories on the cluster are at least **readable to the group, and not readable to others**. E.g., in your .bashrc, set umask 007 and do the following: \\ ''chmod -R g+rwX,o-rwx $HOME $WORK $SCRATCH \\ chmod 600 ~/.ssh/id_rsa ## If you have this file, it **MUST**  be private. \\ chmod g-w ~ ## Home must NOT be writable by the group otherwise submiting jobs will not be allowed. \\ chmod 700 ~/.ssh ## Nobody other than you is allowed to change the sensative .ssh folder. \\ chmod 644 ~/.ssh/id_rsa.pub ~/.ssh/authorized_keys ~/.ssh/known_hosts '' \\ There might be some [[https://unix.stackexchange.com/questions/37164/ssh-and-home-directory-permissions|exceptions]] like your private ssh key at ''~/.ssh/id_rsa'', which must be readable only by you. On Ranch, adding umask in .bashrc. does not work. Instead, create or modify ~/.cshrc. You need to do the above modifications on ALL clusters you use including Lonestar and Ranch.
   - If you are unfamiliar with prior, **posterior**, and likelihood, read about [[https://en.wikipedia.org/wiki/Bayesian_inference|Bayesian inference]].   - If you are unfamiliar with prior, **posterior**, and likelihood, read about [[https://en.wikipedia.org/wiki/Bayesian_inference|Bayesian inference]].
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   - 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, Science Careers, and [[https://docs.google.com/document/d/1tRVpO0eFzYfl0f95X_X8YvE9DeQVX3vYBkmw4smRJLU/edit#|other]] 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, Science Careers, and [[https://docs.google.com/document/d/1tRVpO0eFzYfl0f95X_X8YvE9DeQVX3vYBkmw4smRJLU/edit#|other]] 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 {{:second-ad-knowledge-portal-controlled-access-duc-march2022-v7.3-signed.pdf|this}}  file, and upload it again to Oncinfo without changing the file name. Let Habil know so that he uploads it on the Synapse [[https://help.adknowledgeportal.org/apd/Data-Use-Certificates.2623373330.html|website]]. Then, accept Terms of Use through this [[https://www.synapse.org/#!AccessRequirements:ID=syn2910256&TYPE=ENTITY|link]].   - If you want to use **ROSMAP**  data, please create a Synapse [[https://www.synapse.org/#!RegisterAccount:0|account]], add your information to {{:second-ad-knowledge-portal-controlled-access-duc-march2022-v7.3-signed.pdf|this}}  file, and upload it again to Oncinfo without changing the file name. Let Habil know so that he uploads it on the Synapse [[https://help.adknowledgeportal.org/apd/Data-Use-Certificates.2623373330.html|website]]. Then, accept Terms of Use through this [[https://www.synapse.org/#!AccessRequirements:ID=syn2910256&TYPE=ENTITY|link]].
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 ==== Some references ==== ==== Some references ====
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   - [[http://stephenturner.us/edu.html|Lists 1]] and [[https://www.r-bloggers.com/2013/04/list-of-bioinformatics-workshops-and-training-resources/|2]] of bioinformatics workshops.   - [[http://stephenturner.us/edu.html|Lists 1]] and [[https://www.r-bloggers.com/2013/04/list-of-bioinformatics-workshops-and-training-resources/|2]] 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 ====