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how_to [2019/01/01 16:54]
admin
how_to [2019/05/31 16:26] (current)
admin [Install R locally (e.g. on a cluster)?]
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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at Stanford is broad and covers the classic topics but it is not updated, and may become outdated.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at Stanford is broad and covers the classic topics but it is not updated, and may become outdated.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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 **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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-**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? ====
 +
 +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]],​
 +
 +<​code>​
 +7z a -tzip -mem=AES256 -p super-secret.7z super-secret_folder
 +
 +7z x super-secret.7z ## Decrypt and uncomperess
 +</​code>​
 +
 +----
 +
 +==== 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"​.
 +
 +----
 +
 +==== 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.