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how_to [2018/12/28 00:21] – admin | how_to [2019/05/31 13:26] – [Install R locally (e.g. on a cluster)?] admin |
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javascript:void(location.href=%22http://libproxy.txstate.edu/login?url=%22+location.href) | javascript:void(location.href=%22http://libproxy.uthscsa.edu/login?url=%22+location.href) |
</code> | </code> |
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</code> | </code> |
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And then add the following line to your emacs [[http://www.emacswiki.org/emacs/InitFile|initialization]] file, ~/Library/Preferences/Aquamacs Emacs/Preferences.el | And then add the following line to your emacs [[http://www.emacswiki.org/emacs/InitFile|initialization]] file, e.g., ~/Library/Preferences/Aquamacs Emacs/Preferences.el, or ~/.emacs |
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<code> | <code> |
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**Begin learning bioinformatics?** \\ | **Begin learning bioinformatics?** \\ |
Take a course from the [[http://research.omicsgroup.org/index.php/List_of_free_online_bioinformatics_courses|list]] of free online bioinformatics courses e.g., the Computational Molecular Biology [[http://cmgm.stanford.edu/biochem218/index.html|Course]] at Stanford is broad and covers the classic topics but it is not updated, and may become outdated. The same is true for PLOS Translational Bioinformatics [[http://collections.plos.org/translational-bioinformatics|Collection]] of articles, which are more advanced. Most central topics are covered in some course from the European Bioinformatics Institute ([[https://www.ebi.ac.uk/training/online/course-list|EBI]]). Very useful training materials are available from [[https://www.mygoblet.org/|GOBLET]].\\ | Take a course from the [[http://research.omicsgroup.org/index.php/List_of_free_online_bioinformatics_courses|list]] of free online bioinformatics courses e.g., the Computational Molecular Biology [[http://cmgm.stanford.edu/biochem218/index.html|Course]] at Stanford is broad and covers the classic topics but it is not updated, and may become outdated. The same is true for PLOS Translational Bioinformatics [[http://collections.plos.org/translational-bioinformatics|Collection]] of articles, which are more advanced. Most central topics are covered in some course from the European Bioinformatics Institute ([[https://www.ebi.ac.uk/training/online/course-list|EBI]]). Very useful training materials are available from [[https://www.mygoblet.org/|GOBLET]]. Videos from the Models, Inference & Algorithms Initiative ([[https://www.broadinstitute.org/scientific-community/science/mia/models-inference-algorithms|MIA]]) at Broad are relatively advanced.\\ |
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[[http://bioconductor.org/help/course-materials/|Bioconductor]] course material provides a walkthrough in specific areas. Also, you can find valuable resources from the [[http://stephenturner.us/edu.html|list]] of bioinformatics workshops and [[http://www.engr.uconn.edu/~mukul/cbc.htm|conferences]]. Following the "Bioinformatics for biologists [[:bioinformatics_for_biologist_workshop|workshop]]" does not require expertise in computer programing. Bio-Linux team prepared a good [[http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf|introduction]], which can be used as a reference too. If machine learning is new to you, [[http://www.nature.com/nrg/journal/v16/n6/full/nrg3920.html|read]] about its applications in genetics and genomics. You need to have some basic knowledge in [[https://www.coursera.org/learn/biostatistics?recoOrder=9&utm_medium=email&utm_source=recommendations&utm_campaign=recommendationsEmail~recs_email_2016_06_26_17%3A57|mathematics]] and statistics too. | [[http://bioconductor.org/help/course-materials/|Bioconductor]] course material provides a walkthrough in specific areas. Also, you can find valuable resources from the [[http://stephenturner.us/edu.html|list]] of bioinformatics workshops and [[http://www.engr.uconn.edu/~mukul/cbc.htm|conferences]]. Following the "Bioinformatics for biologists [[:bioinformatics_for_biologist_workshop|workshop]]" does not require expertise in computer programing. Bio-Linux team prepared a good [[http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf|introduction]], which can be used as a reference too. If machine learning is new to you, [[http://www.nature.com/nrg/journal/v16/n6/full/nrg3920.html|read]] about its applications in genetics and genomics. You need to have some basic knowledge in [[https://www.coursera.org/learn/biostatistics?recoOrder=9&utm_medium=email&utm_source=recommendations&utm_campaign=recommendationsEmail~recs_email_2016_06_26_17%3A57|mathematics]] and statistics too. |
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**Write a scientific paper?** \\ | **Write a scientific paper?** \\ |
Put the figures together and then [[http://www.scidev.net/global/publishing/practical-guide/how-do-i-write-a-scientific-paper-.html|draft]] different [[https://www.nature.com/articles/nmeth.4532?WT.ec_id=NMETH-201712&spMailingID=55474826&spUserID=MTIyMzczNjc4MDI2S0&spJobID=1285409878&spReportId=MTI4NTQwOTg3OAS2|sections]]. Focus the [[http://www.grantcentral.com/strategies-for-avoiding-common-problems-with-research-manuscripts/|Discussion]]. | Put the figures together and then [[http://www.scidev.net/global/publishing/practical-guide/how-do-i-write-a-scientific-paper-.html|draft]] different [[https://www.nature.com/articles/nmeth.4532?WT.ec_id=NMETH-201712&spMailingID=55474826&spUserID=MTIyMzczNjc4MDI2S0&spJobID=1285409878&spReportId=MTI4NTQwOTg3OAS2|sections]]. Focus the [[http://www.grantcentral.com/strategies-for-avoiding-common-problems-with-research-manuscripts/|Discussion]]. Be careful about [[http://colah.github.io/posts/2019-05-Collaboration/index.html|authorship]]. |
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**Set the default width of fill mode (line length) in emacs?** \\ | **Set the default width of fill mode (line length) in emacs?** \\ |
[[http://stackoverflow.com/questions/3566727/how-to-set-the-default-width-of-fill-mode-to-80-with-emacs|Use]] 'M-x customize-variable' on 'fill-column'. DejaVu Sans Mono size 18 is an [[http://ergoemacs.org/emacs/emacs_unicode_fonts.html|appropriate]] font for programming in Emacs. | [[http://stackoverflow.com/questions/3566727/how-to-set-the-default-width-of-fill-mode-to-80-with-emacs|Use]] 'M-x customize-variable' to set 'fill-column' (100 in Oncinfo). Use DejaVu Sans Mono (~[[http://www.leancrew.com/all-this/2009/10/the-compleat-menlovera-sans-comparison/|Menlo]] on MacOS) size 18-20 is an [[http://ergoemacs.org/emacs/emacs_unicode_fonts.html|appropriate]] font for programming in Emacs. To do so, you may need to manually edit your .emacs in [[https://stackoverflow.com/questions/4821984/emacs-osx-default-font-setting-does-not-persist|macOS]]. |
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(global-auto-complete-mode t) | (global-auto-complete-mode t) |
</code> | </code> |
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| Also, read the packages instructions to learn how to [[https://www.emacswiki.org/emacs/InstallingPackages#toc4|configure]] and use them. |
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**Rescue US biomedical research from its systemic flaws?** \\ | **Rescue US biomedical research from its systemic flaws?** \\ |
[[http://www.pnas.org/content/111/16/5773|Hypercompetition]] has damaging effects. Reduce the number of PhD students and postdocs. Revise funding mechanisms to encourage "path-breaking ideas that, by definition," are risky. Support [[https://nexus.od.nih.gov/all/2018/05/04/the-issue-that-keeps-us-awake-at-night/|early]]-stage investigators. | [[http://www.pnas.org/content/111/16/5773|Hypercompetition]] has damaging effects. Reduce the number of PhD students and postdocs. Revise funding mechanisms to encourage "path-breaking ideas that, by definition," are [[https://www.nature.com/articles/426389a|risky]]. Support [[https://nexus.od.nih.gov/all/2018/05/04/the-issue-that-keeps-us-awake-at-night/|early]]-stage investigators. |
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**Adjust the acceleration and speed of a Logitec mouse?** \\ Install and [[https://apple.stackexchange.com/questions/253111/how-to-disable-scroll-acceleration-in-macos-sierra|use]] the Logitech Control Center. | **Adjust the acceleration and speed of a Logitec mouse?** \\ \\ Install and [[https://apple.stackexchange.com/questions/253111/how-to-disable-scroll-acceleration-in-macos-sierra|use]] the Logitech Control Center. |
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| ==== Encrypt a folder? ==== |
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| Compress the folder in 7z format using the AES-256 encrypting algorithm. [[https://www.dzhang.com/blog/2018/03/11/using-7-zip-create-aes-256-encrypted-zip-files-command-line|E.g]], |
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| <code> |
| 7z a -tzip -mem=AES256 -p super-secret.7z super-secret_folder |
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| 7z x super-secret.7z ## Decrypt and uncomperess |
| </code> |
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| ==== Upload a file to Oncinfo and link to it? ==== |
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| {{:screen_shot_2019-02-12_at_12.38.39_pm.png?linkonly|Set}} the link type to "internal media", click on "Browse Server", and then on "Choose File" and "Update". |
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| ==== Aks people's opinion? ==== |
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| Create a [[https://doodle.com/|Doodle]] to find a common time for scheduling events. For longer surveys, use [[https://www.surveymonkey.com/|SurveyMonkey]] for offline, and [[https://www.pollev.com/|Poll]] Everywhere for online interaction with audiance. |
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