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how_to [2019/02/06 05:50] – [Install R locally (e.g. on a cluster)?] adminhow_to [2019/07/08 17:56] – [Install R locally (e.g. on a cluster)?] 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. 
 + 
 +-[[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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-**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at Stanford is broad and covers the classic topics but it is not updated, and may become outdated.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.\\
 \\ \\
 [[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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 +
 +==== Upload a file to Oncinfo and link to it? ====
 +
 +{{: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? ====
 +
 +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.