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how_to [2019/02/12 18:49] – [Encrypt a folder?] admin | how_to [2019/09/19 22:37] – [Install Salmon on OSX?] admin |
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**Get familiar with applications of machine learning in genetics and genomics?** \\ | **Get familiar with machine learning and its applications in computational biology? ** \\ |
First read [[http://www.nature.com/nrg/journal/v16/n6/abs/nrg3920.html|this]] 2015 review paper and then follow its references. | - Most common ML techniques are very well explained in [[https://scikit-learn.org/stable/user_guide.html|Scikit learn]] with [[https://scikit-learn.org/stable/modules/decomposition.html|illustrations]] and example Python code. These techniques have been implemented in [[https://www.kaggle.com/getting-started/5243|R]] packages including mlr3 and tidymodels. |
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| -[[http://www.nature.com/nrg/journal/v16/n6/abs/nrg3920.html|This]] 2015 paper reviews applications of ML in genetics and genomics. Read it and follow its references. |
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<code> | <code> |
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> |
brew install aspell --with-lang-en | brew install aspell |
</code> | </code> |
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**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at Stanford is broad and covers the classic topics but it is not updated, and may become outdated.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]].\\ | ==== Begin learning bioinformatics? ==== |
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| 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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**Install Salmon on OSX?** \\ | ==== Install Salmon on OSX? ==== |
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If you do not have autoconf, [[http://mac-dev-env.patrickbougie.com/autoconf/|install]] it. Following the installation guidelines, for OSX you need to first [[http://stackoverflow.com/questions/3181468/how-do-you-install-intel-tbb-on-os-x|install]] Thread Building Blocks (TBB) (brew install tbb) and then check that the installation was successful (brew list). Download the latest [[https://github.com/COMBINE-lab/salmon/releases|version]] of Salmon source code and uncompress it. Follow Salmon's installation [[http://salmon.readthedocs.org/en/latest/building.html#installation|guidelines]]. The cmake command in the guidelines will be something like the following for OSX: | If you do not have autoconf, [[http://mac-dev-env.patrickbougie.com/autoconf/|install]] it. Following the installation guidelines, for OSX you need to first [[http://stackoverflow.com/questions/3181468/how-do-you-install-intel-tbb-on-os-x|install]] Thread Building Blocks (TBB) (brew install tbb) and then check that the installation was successful (brew list). Download the latest [[https://github.com/COMBINE-lab/salmon/releases|version]] of Salmon source code and uncompress it. Follow Salmon's installation [[http://salmon.readthedocs.org/en/latest/building.html#installation|guidelines]]. The cmake command in the guidelines will be something like the following for OSX: |
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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' 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]]. | [[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]], and add the following [[https://stackoverflow.com/questions/4879785/can-i-break-the-long-line-in-emacs-non-windows-to-the-next-line|line]]: |
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| <code> |
| (setq truncate-lines nil) |
| </code> |
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**Get older versions using git?** \\ | ==== Get older versions using git? ==== |
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[[https://githowto.com/getting_old_versions|Use]] "git log" to see the previous commits and the corresponding hashes, "git checkout <hash>" to get an older version, and "git checkout master" to get back. | [[https://githowto.com/getting_old_versions|Use]] "git log" to see the previous commits and the corresponding hashes, "git checkout <hash>" to get an older version, and "git checkout master" to get back. |
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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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==== Encrypt a folder? ==== | ==== Encrypt a folder? ==== |
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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". | {{: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 audience. |
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| ==== Disable scroll acceleration in macOS? ==== |
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| Install and [[https://www.reddit.com/r/osx/comments/6kx6zb/how_to_disable_mouse_scrolling_acceleration/|use]] USB [[http://www.usboverdrive.com/USBOverdrive/Information.html|Overdrive]] to set Wheel up and down "Speed" to say, 6 lines. The following [[https://apple.stackexchange.com/questions/253111/how-to-disable-scroll-acceleration-in-macos-sierra|command]] does NOT work: |
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| <code> |
| defaults write .GlobalPreferences com.apple.scrollwheel.scaling -1 |
| </code> |
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| Logitech Control Center may help on the [[https://support.logi.com/hc/en-gb/articles/360025297833-Logitech-Control-Center-for-Macintosh-OS-X|Logitech]] MX mice older than 2019. |
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