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how_to [2019/02/12 20:49]
admin [Encrypt a folder?]
how_to [2019/08/22 02:30] (current)
admin [Install R locally (e.g. on a cluster)?]
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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. 
 + 
 +-[[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at Stanford is broad and covers the classic topics but it is not updated, and may become outdated.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? ​  ==== 
 + 
 +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.\\
 \\ \\
 [[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?   ==== 
 + 
 +\\
 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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 **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"​.
 +
 +----
 +
 +==== Aks people'​s opinion? ====
 +
 +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.