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| how_to [2024/01/24 17:14] – [Measure memory used by GPUa?] habil | how_to [2025/01/28 14:27] (current) – [Write a scientific paper?] habil |
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| ==== Download files to where you cannot login or click using a GUI? ==== | ==== Download files to where you cannot login or click using a GUI? ==== |
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| Login using GUI on another computer. Click to start downloading. While it is downloading, right-click on the page and then click on "Inspect". Then, click on "Network" on the top of the panel and find the file. Get the cURL [[https://www.youtube.com/watch?v=udfCVWuobhc|command]] and run it in terminal to download the file in the other computer. | Login using GUI on another computer. Click to start downloading. While it is downloading, right-click on the page and then click on "Inspect". Then, click on "{{:screenshot2024-12-04at1.18.56pm.png?linkonly|Network}} " on the top of the panel and find the file. Get the cURL [[https://www.youtube.com/watch?v=udfCVWuobhc|command]] and run it in terminal to download the file in the other computer. |
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| ==== Supercharge your YouTube experience and minimize ads? ==== | ==== Supercharge your YouTube experience and minimize ads? ==== |
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| "[[https://chrome.google.com/webstore/detail/youtube-enhancer/ejcniippeghnejiodjkkmndlelbagmah|Enhancer]] for YouTube" is a popular browser extension that enhances the YouTube viewing experience by providing additional features and customization options. While it doesn't explicitly focus on blocking ads, it offers some options to minimize or hide them. Use [[https://chrome.google.com/webstore/detail/autoskip-for-youtube-ads/hmbnhhcgiecenbbkgdoaoafjpeaboine|Autoskip]] to automatically skip ads that pass the Enhancer filter. | "[[https://chrome.google.com/webstore/detail/youtube-enhancer/ejcniippeghnejiodjkkmndlelbagmah|Enhancer]] for YouTube" is a popular browser extension that enhances the YouTube viewing experience by providing additional features and customization options, but it may contains malware! While it doesn't explicitly focus on blocking ads, it offers some options to minimize or hide them. Use [[https://chrome.google.com/webstore/detail/autoskip-for-youtube-ads/hmbnhhcgiecenbbkgdoaoafjpeaboine|Autoskip]] to automatically skip ads that pass the Enhancer filter. \\ |
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| | The above solutions reduces the income of the person or the team who created and posted the YouTube video. Better than the above solutions is to use a YouTube **premium** account. In this way, you a) save your time and focus by avoiding ads and b) support the person who created the video. Youtube [[https://support.google.com/youtube/answer/7060016?hl=en#:~:text=How YouTube Premium supports creators,monthly membership fee with creators.|pays]] creators a little money for every minute we watch their video with a premium account. |
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| ==== Convert pdf to MS word? ==== | ==== Convert pdf to MS word? ==== |
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| Try whatever you can to avoid conversion! Instead, educate your team and your collaborators to use [[https://www.authorea.com/users/54336|Authorea]], [[https://www.overleaf.com/|Overleaf]] or at least Google Doc. In Google Doc, references can be easily handled using [[https://gsuite.google.com/marketplace/app/paperpile/894076725911|Paperpile]] add-on (NOT the extension), and figures can be automatically numbered using the the [[https://gsuite.google.com/marketplace/app/cross_reference/269114033347?pann=cwsdp&hl=en|Cross Reference]] add-on as suggested in these [[https://lcolladotor.github.io/2019/04/02/how-to-write-academic-documents-with-googledocs/#.Xjne6RNKjUI|guidelines]] on how to write academic documents with Google Docs. Add-ons are not available when editing .docx files. __Only__ if your biologist collaborators cannot [[http://www.dedoimedo.com/computers/latex.html|unfortunately]] edit the LaTeX source, consider using a conversion tool such as Adobe [[https://chrome.google.com/webstore/detail/adobe-acrobat/efaidnbmnnnibpcajpcglclefindmkaj|Acrobat]] Chrome extension or Acrobat Pro, which can export a .pdf as a .doc file. docs. The docs [[https://docs.zone/|zone]] and pdf [[https://www.freepdfconvert.com/|Converter]] are online alternatives. If you need to to separate pages, use [[https://superuser.com/a/1584919|pdfjam]]. If Bibtex is not an option, use [[http://www.easybib.com/|EasyBib]]. | Try whatever you can to avoid conversion! Instead, educate your team and your collaborators to use [[https://www.authorea.com/users/54336|Authorea]], [[https://www.overleaf.com/|Overleaf]] or at least Google Doc. In Google Doc, references can be easily handled using [[https://gsuite.google.com/marketplace/app/paperpile/894076725911|Paperpile]] add-on (NOT the extension), and figures can be automatically numbered using the the [[https://gsuite.google.com/marketplace/app/cross_reference/269114033347?pann=cwsdp&hl=en|Cross Reference]] add-on as suggested in these [[https://lcolladotor.github.io/2019/04/02/how-to-write-academic-documents-with-googledocs/#.Xjne6RNKjUI|guidelines]] on how to write academic documents with Google Docs. Add-ons are not available when editing .docx files. __Only__ if your biologist collaborators cannot [[http://www.dedoimedo.com/computers/latex.html|unfortunately]] edit the LaTeX source, consider using a conversion tool such as Adobe [[https://chrome.google.com/webstore/detail/adobe-acrobat/efaidnbmnnnibpcajpcglclefindmkaj|Acrobat]] Chrome extension or Acrobat Pro, which can export a .pdf as a .doc file. docs. The docs [[https://docs.zone/|zone]] and pdf [[https://www.freepdfconvert.com/|Converter]] are online alternatives. If you need to to separate pages, use [[https://superuser.com/a/1584919|pdfjam]]. If Bibtex is not an option, use [[http://www.easybib.com/|EasyBib]]. |
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| | [[https://www.docx2latex.com/word-to-latex-converter/|Docx2LaTeX]] can convert simple Word or Google Docs to LaTeX. |
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| ==== Enable spell check in Emacs on OS X? ==== | ==== Enable spell check in Emacs on OS X? ==== |
| ===== Write a scientific paper? ===== | ===== Write a scientific paper? ===== |
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| 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]]. It might be easier to write the [[https://plos.org/resource/how-to-write-a-great-abstract/?utm_medium=email&utm_source=internal&utm_campaign=modnewsletters&utm_content=modnewsletter|abstract]]//after// other sections are drafted. You can use your [[https://www.nature.com/articles/d41586-018-02404-4|own]] voice. | 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]]. It might be easier to write the [[https://plos.org/resource/how-to-write-a-great-abstract/?utm_medium=email&utm_source=internal&utm_campaign=modnewsletters&utm_content=modnewsletter|abstract]] //after// other sections are drafted. You can use your [[https://www.nature.com/articles/d41586-018-02404-4|own]] voice. Explain in the [[https://www.springernature.com/gp/researchers/the-source/blog/blogposts-getting-published/boosting-your-acceptance-chances-as-an-author/24029788?sap-outbound-id=DC97DCEC6E137F198032918A1405F895E5D09A72&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030721_CONR_JRNLS_REP1_GL_PHSS_034NE_NATWINBRC5&utm_content=EN_56630_20250128&mkt-key=42010A0550671EEA9BA13B2C4609D4AD|cover]] letter how your work would be interesting to the journal audiance. |
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| Many journals require vectorized figures and different tweaks to the fonts and colors. So, make sure your figures are easily reproducible. At the submission stage, you can change to a [[https://docs.google.com/document/d/1L49DoVzBfhJaavIvW5CvrxmwV-RHNDJcuFIZy39dS2g/edit|vectorized]] format like eps or pdf using different tools including [[http://blog.linuxgrrl.com/2013/08/12/how-to-produce-vector-eps-with-cmyk-color-using-free-software/|Inkscape]]. | Many journals require vectorized figures and different tweaks to the fonts and colors. So, make sure your figures are easily reproducible. At the submission stage, you can change to a [[https://docs.google.com/document/d/1L49DoVzBfhJaavIvW5CvrxmwV-RHNDJcuFIZy39dS2g/edit|vectorized]] format like eps or pdf using different tools including [[http://blog.linuxgrrl.com/2013/08/12/how-to-produce-vector-eps-with-cmyk-color-using-free-software/|Inkscape]]. |
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| ===== Prepare or review computational biology papers for Nature methods? ===== | ===== Prepare or review computational biology papers for Nature methods? ===== |
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| Read their "Reviewing computational methods" ([[http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3686.html|2015]]) and "Guidelines for algorithms and software in Nature Methods" ([[http://blogs.nature.com/methagora/2014/02/guidelines-for-algorithms-and-software-in-nature-methods.html|2014]]) articles. Provide source code, pseudocode, compiled executables, and the mathematical description. Softwares must be accompanied with documentation, sample data and the expected output, and a license (e.g., GPL≥2). Have a look at [[:the_list_of_computational_biology_papers_in_nature_methods|The list of computational biology papers in Nature Methods]] published in 2015, and the [[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&cad=rja&uact=8&ved=0ahUKEwic2Oum3dvJAhUGeSYKHWurD-EQFghQMAg&url=http%3A%2F%2Ford.ntu.edu.tw%2Ftc%2Fincludes%2FGetFile.ashx%3FmID%3D253%26id%3D1744%26chk%3De15262f3-87bf-4a7e-be6a-4103cbc61968&usg=AFQjCNHfNXyryLDQMWBRrInOpJVKIL0LCA&sig2=8C9UE1arY4vi2q_CUdsdiQ|hints]] by an editor of Nature Communications. | Read their "Reviewing computational methods" ([[http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3686.html|2015]]) and "Guidelines for algorithms and software in Nature Methods" ([[http://blogs.nature.com/methagora/2014/02/guidelines-for-algorithms-and-software-in-nature-methods.html|2014]]) articles. Provide source code, pseudocode, compiled executables, and the mathematical description. Softwares must be accompanied with documentation, sample data and the expected output, and a license (e.g., GPL≥2). Have a look at [[:the_list_of_computational_biology_papers_in_nature_methods|The list of computational biology papers in Nature Methods]] published in 2015, and the [[https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&cad=rja&uact=8&ved=0ahUKEwic2Oum3dvJAhUGeSYKHWurD-EQFghQMAg&url=http%3A%2F%2Ford.ntu.edu.tw%2Ftc%2Fincludes%2FGetFile.ashx%3FmID%3D253%26id%3D1744%26chk%3De15262f3-87bf-4a7e-be6a-4103cbc61968&usg=AFQjCNHfNXyryLDQMWBRrInOpJVKIL0LCA&sig2=8C9UE1arY4vi2q_CUdsdiQ|hints]] by an editor of Nature Communications. Several [[https://en.wikipedia.org/wiki/Computational_biology#Research|journals]] publish papers in this field. |
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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? ===== |
| </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. | Also, read the packages instructions to learn how to [[https://www.emacswiki.org/emacs/InstallingPackages#toc4|configure]] and use them.\\ |
| | Update 2024-08-14: tabbar can take 50%-90% CPU usage! Use ''tab-bar-mode'' in Emacs >=27. |
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| ==== Test an R function that you have extracted from a script? ==== | ==== Test an R function that you have extracted from a script? ==== |
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| ==== Review a paper? ==== | ==== Review a paper? ==== |
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| Read the journal guidelines, and the Nature's quick and concise [[https://www.springer.com/gp/authors-editors/authorandreviewertutorials/howtopeerreview?utm_source=hybris&utm_medium=email&utm_content=internal&utm_campaign=AEXS_1_PF_ReviewerThankYou_tutorial&sap-outbound-id=37A4EBB275E142189BFB59083911E79615029EBE|tutorial]]. The PLOS Open Reviewer [[https://genweb.plos.org/RR/PLOSOpenReviewerGatewayInfosheet.pdf|Gateway]] can be helpful if you are interested in becoming a reviewer for PLOS journals. | Read the journal guidelines, and the Nature's quick and concise [[https://www.springer.com/gp/authors-editors/authorandreviewertutorials/howtopeerreview?utm_source=hybris&utm_medium=email&utm_content=internal&utm_campaign=AEXS_1_PF_ReviewerThankYou_tutorial&sap-outbound-id=37A4EBB275E142189BFB59083911E79615029EBE|tutorial]]. The PLOS Open Reviewer [[https://genweb.plos.org/RR/PLOSOpenReviewerGatewayInfosheet.pdf|Gateway]] can be helpful if you are interested in becoming a reviewer for PLOS journals. Read [[https://www.biomedcentral.com/getpublished/peer-review-process?sap-outbound-id=96A0B5635C39747973E5643D05210092E64D31E6&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030108_CONR_JRNLS_REP1_GL_PHSS_034NC_NATMAINRC2&utm_content=EN_56237_20240820&mkt-key=42010A0550671EEA9BA13B2C4609D4AD|BMC]] or [[https://www.springernature.com/gp/authors/campaigns/how-to-peer-review?sap-outbound-id=96A0B5635C39747973E5643D05210092E64D31E6&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030108_CONR_JRNLS_REP1_GL_PHSS_034NC_NATMAINRC2&utm_content=EN_56237_20240820&mkt-key=42010A0550671EEA9BA13B2C4609D4AD|Nature]] introduction, and take the Nature's Focus on Peer Review [[https://masterclasses.nature.com/focus-on-peer-review-online-course/16605550?sap-outbound-id=96A0B5635C39747973E5643D05210092E64D31E6&utm_source=automation&utm_medium=email&utm_campaign=000_WANJ01_0000030108_CONR_JRNLS_REP1_GL_PHSS_034NC_NATMAINRC2&utm_content=EN_56237_20240820&mkt-key=42010A0550671EEA9BA13B2C4609D4AD|course]].\\ |
| | Get credit for your reviews via Web of Science Reviewer [[https://authorservices.wiley.com/Reviewers/journal-reviewers/recognition-for-reviewers/publons.html|Recognition]] Service (publons). |
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| ==== Adjust the acceleration and speed of a Logitec mouse? ==== | ==== Adjust the acceleration and speed of a Logitec mouse? ==== |
| ==== Encrypt a folder? ==== | ==== Encrypt a folder? ==== |
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| Encrypt a ''largeFolder'' folder using [[https://www.cyberciti.biz/tips/linux-how-to-encrypt-and-decrypt-files-with-a-password.html|tar]] and compress it using ''gpg'' based on the AES-256 encrypting algorithm. You will obtain the [[https://crypto.stackexchange.com/a/71078|strongest]] security with these options: | Encrypt a ''largeFolder'' folder using [[https://www.cyberciti.biz/tips/linux-how-to-encrypt-and-decrypt-files-with-a-password.html|tar]] and compress it using ''gpg'' based on the AES-256 encrypting algorithm. You will obtain the [[https://crypto.stackexchange.com/a/71078|strongest]] security with these options: |
| <code> | <code> |
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| tar -cvz largeFolder | gpg --s2k-mode 3 --s2k-count 65011712 --s2k-digest-algo SHA512 --s2k-cipher-algo AES256 --symmetric --no-symkey-cache -o largeFolder.tgz.gpg | tar -cvz largeFolder | gpg --s2k-mode 3 --s2k-count 65011712 --s2k-digest-algo SHA512 --s2k-cipher-algo AES256 --symmetric --no-symkey-cache -o largeFolder.tgz.gpg |
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| </code> | </code> |
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| The ''–no-symkey-cache'' option is available in [[https://unix.stackexchange.com/a/557051|version]] >=2.2.7. On macOS, you need to first install [[https://sourceforge.net/p/gpgosx/docu/Download/|GnuPG]]. An alternative approach is to use [[http://www.dzhang.com/blog/2018/03/11/using-7-zip-create-aes-256-encrypted-zip-files-command-line|7z]], which can be installed using [[http://molecularsciences.org/content/installing-and-running-7-zip-from-mac-terminal/|homebrew]], however, 7z is windows based and thus not recommended. \\ \\ | The ''–no-symkey-cache'' option is available in [[https://unix.stackexchange.com/a/557051|version]] >=2.2.7. On macOS, you need to first install [[https://sourceforge.net/p/gpgosx/docu/Download/|GnuPG]]. An alternative approach is to use [[http://www.dzhang.com/blog/2018/03/11/using-7-zip-create-aes-256-encrypted-zip-files-command-line|7z]], which can be installed using [[http://molecularsciences.org/content/installing-and-running-7-zip-from-mac-terminal/|homebrew]], however, 7z is windows based and thus not recommended.\\ |
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| To decrypt and uncomperess, | To decrypt and uncomperess, |
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| <code> | <code> |
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| gpg --decrypt --no-symkey-cache largeFolder.tgz.gpg | tar -xv | gpg --decrypt --no-symkey-cache largeFolder.tgz.gpg | tar -xv |
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| </code> | </code> |
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| | ''tar'' may need ''-z --no-same-owner''. |
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| A good password should have at least 12 characters, include both small and capital letters, and at least one digit and one special character such as !@#$%^&*(). Do not use dictionary words in your password, instead, use a [[https://cybernews.com/best-password-managers/how-to-create-a-strong-password/|passphrase]] "to create strong passwords". | A good password should have at least 12 characters, include both small and capital letters, and at least one digit and one special character such as !@#$%^&*(). Do not use dictionary words in your password, instead, use a [[https://cybernews.com/best-password-managers/how-to-create-a-strong-password/|passphrase]] "to create strong passwords". |
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| ==== Upload a file to Oncinfo and link to it? ==== | ==== Upload a file to Oncinfo and link to it? ==== |
