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for_members [2020/03/10 21:53]
admin [General guidelines for conducting research in the Oncinfo Lab]
for_members [2020/06/23 22:56] (current)
admin [Some references]
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   - Every member should upload their photo to his profile in the wiki. Todo this, click on your username at the top right, then, Account. In addition, everyone should have a photo and their updated CV in pdf format on their personal page. [[:​file_view_cv_template.zip_543305154_cv_template.zip|This]] is an optional LaTeX template. The permission of any lab notebook (lano) should be set to "​hidden"​and it is important that they be updated EVERY day. [[https://​civihosting.com/​|CiviHosting]] provides us with two edit modes: ckg and DW. Use the one that is more convenient for you. Write your posts in anti-chronological order so that the newest post comes at the top. For facilitating future reference, avoid sending data as attachments. Instead, upload files to your lano and link to them where needed.   - Every member should upload their photo to his profile in the wiki. Todo this, click on your username at the top right, then, Account. In addition, everyone should have a photo and their updated CV in pdf format on their personal page. [[:​file_view_cv_template.zip_543305154_cv_template.zip|This]] is an optional LaTeX template. The permission of any lab notebook (lano) should be set to "​hidden"​and it is important that they be updated EVERY day. [[https://​civihosting.com/​|CiviHosting]] provides us with two edit modes: ckg and DW. Use the one that is more convenient for you. Write your posts in anti-chronological order so that the newest post comes at the top. For facilitating future reference, avoid sending data as attachments. Instead, upload files to your lano and link to them where needed.
   - You can install Google Scholar [[https://​chrome.google.com/​webstore/​detail/​google-scholar-button/​ldipcbpaocekfooobnbcddclnhejkcpn?​hl=en|Button]] add-on for an easier way of searching Google Scholar. You select the paper title and then click on the little blue icon on the top right corner. For any paper which you want to cite on the lab wiki, find it on Google Scholar, click on "​More>​Cite"​ and copy the MLA format. Also, use [[https://​gsuite.google.com/​marketplace/​app/​paperpile/​894076725911|Paperpile]] for easy citation in Google doc, and Math [[https://​gsuite.google.com/​marketplace/​app/​math_equations/​825973477142|Equations]] for writing and manipulating equations on Google presentations.   - You can install Google Scholar [[https://​chrome.google.com/​webstore/​detail/​google-scholar-button/​ldipcbpaocekfooobnbcddclnhejkcpn?​hl=en|Button]] add-on for an easier way of searching Google Scholar. You select the paper title and then click on the little blue icon on the top right corner. For any paper which you want to cite on the lab wiki, find it on Google Scholar, click on "​More>​Cite"​ and copy the MLA format. Also, use [[https://​gsuite.google.com/​marketplace/​app/​paperpile/​894076725911|Paperpile]] for easy citation in Google doc, and Math [[https://​gsuite.google.com/​marketplace/​app/​math_equations/​825973477142|Equations]] for writing and manipulating equations on Google presentations.
-  - Create a Nature [[https://​idp.nature.com/​register/​natureuser?​redirect_uri=https://​www.nature.com/​my-account/​alerts|account]] for yourself. To get a monthly list of published papers ​in in Nature Methods, subscribe to the corresponding alert . This can help you get a sense of where the field is going. You can also create an [[https://​scholar.google.com/​intl/​en/​scholar/​help.html#​alerts|alert]] on the Google Scholar to get regular updates on what is being published on the specific topic of your study.+  - Create a Nature [[https://​idp.nature.com/​register/​natureuser?​redirect_uri=https://​www.nature.com/​my-account/​alerts|account]] for yourself. To get a monthly list of published papers in Nature Methods, subscribe to the corresponding alert . This can help you get a sense of where the field is going. You can also create an [[https://​scholar.google.com/​intl/​en/​scholar/​help.html#​alerts|alert]] on the Google Scholar to get regular updates on what is being published on the specific topic of your study.
   - Code style in Oncinfo lab: We follow Hadley Wickhams’s R Style [[http://​r-pkgs.had.co.nz/​style.html|Guide]] unless another convention is mentioned below. The goal is to include as much code as possible on 1 page so that it is easier to skim while keeping the overall structure such as proper indentation. \\  When writing R code, use "x <- 5" for assigning a value to a variable. Do NOT use "x = 5" or "​x<​-5"​. **Do NOT use underscore, '​_',​ in variable or function names**. Instead of "​inverse_of",​ use "​inverseOf"​ as a variable name so that you can select it by 1 click. Use "​inverse.of"​ as a function name to indicate it is a function not a variable. Almost all functions must return a list so that extending them will be easy. Use "##"​ for comments NOT a single "#"​. Write the name of the loaded object in a comment in front of load(). Avoid long lines of code. Most lines should be < 90 characters, and all lines must be <100 characters . Thus, do NOT include space when using = in function calls. Good example: ''​average <- mean(feet[ ,"​real"​]/​12+inches,​ na.rm=TRUE) ## Spaces only around "<​-"​ and after ","''​. The space in "''​[ ,''"​ is OK, which refers to all rows. It is OK not to place a space before the parenthesis after "''​if(''",​ "''​for(''",​ and alike. \\ When the line is long, it usually means you need to extract some of it and define a new variable right above that line.Data structures in R can be ordered from simple to complex as follows: number , vector, matrix, and list. Always use the simplest possible data structure, e.i., do not use a list when you can use a matrix.   - Code style in Oncinfo lab: We follow Hadley Wickhams’s R Style [[http://​r-pkgs.had.co.nz/​style.html|Guide]] unless another convention is mentioned below. The goal is to include as much code as possible on 1 page so that it is easier to skim while keeping the overall structure such as proper indentation. \\  When writing R code, use "x <- 5" for assigning a value to a variable. Do NOT use "x = 5" or "​x<​-5"​. **Do NOT use underscore, '​_',​ in variable or function names**. Instead of "​inverse_of",​ use "​inverseOf"​ as a variable name so that you can select it by 1 click. Use "​inverse.of"​ as a function name to indicate it is a function not a variable. Almost all functions must return a list so that extending them will be easy. Use "##"​ for comments NOT a single "#"​. Write the name of the loaded object in a comment in front of load(). Avoid long lines of code. Most lines should be < 90 characters, and all lines must be <100 characters . Thus, do NOT include space when using = in function calls. Good example: ''​average <- mean(feet[ ,"​real"​]/​12+inches,​ na.rm=TRUE) ## Spaces only around "<​-"​ and after ","''​. The space in "''​[ ,''"​ is OK, which refers to all rows. It is OK not to place a space before the parenthesis after "''​if(''",​ "''​for(''",​ and alike. \\ When the line is long, it usually means you need to extract some of it and define a new variable right above that line.Data structures in R can be ordered from simple to complex as follows: number , vector, matrix, and list. Always use the simplest possible data structure, e.i., do not use a list when you can use a matrix.
   - **Never copy code**, instead generalize your code and write functions. If you are copying more than a line of code, most likely you are doing something wrong.   - **Never copy code**, instead generalize your code and write functions. If you are copying more than a line of code, most likely you are doing something wrong.
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   - Please cc Habil on any email that is related to scientific or logistic aspects of your research in the lab, your career development activities, and communications among lab members on issues related to the lab. When you send an email to multiple people, mention the primary addressee at the top. It helps drawing the attention of the addressee, and also shows your respect to others who do not need to read your whole message. Usually using "​reply-to-all"​ is preferred on emails with multiple recipients. When possible, reply to the previous email on a topic and avoid creating another thread unnecessarily,​ which will complicate future references. Emails should be receive some sort of reply within 24 hours even if it is short like "​I'​ll work on it". Otherwise, you will start your next email with "Sorry for the delay"​.   - Please cc Habil on any email that is related to scientific or logistic aspects of your research in the lab, your career development activities, and communications among lab members on issues related to the lab. When you send an email to multiple people, mention the primary addressee at the top. It helps drawing the attention of the addressee, and also shows your respect to others who do not need to read your whole message. Usually using "​reply-to-all"​ is preferred on emails with multiple recipients. When possible, reply to the previous email on a topic and avoid creating another thread unnecessarily,​ which will complicate future references. Emails should be receive some sort of reply within 24 hours even if it is short like "​I'​ll work on it". Otherwise, you will start your next email with "Sorry for the delay"​.
   - As employees of UT Health, we can get facilitated appointments with UT Health primary care physicians (call: 210-450-9090).   - As employees of UT Health, we can get facilitated appointments with UT Health primary care physicians (call: 210-450-9090).
-  - If you are considering ultimately getting jobs in computation ​biology or bioinformatics,​ have a look at postings at the [[http://​bioinformatics.org|bioinformatics.org]] website __within the first week__ ​ after joining the lab. For academic positions, see the Nature Jobs and Science Careers websites. Read the articles on "​[[http://​oncinfo.org/​how_to|How to]] rescue US biomedical research from its systemic flaws?"​ if you are, or want to be, a PhD student.+  - If you are considering ultimately getting jobs in computational ​biology or bioinformatics,​ have a look at postings at the [[http://​bioinformatics.org|bioinformatics.org]] website __within the first week__ ​ after joining the lab. For academic positions, see the Nature Jobs and Science Careers websites. Read the articles on "​[[http://​oncinfo.org/​how_to|How to]] rescue US biomedical research from its systemic flaws?"​ if you are, or want to be, a PhD student.
   - If you want to use ROSMAP data, please create a Synapse [[https://​www.synapse.org/#​!RegisterAccount:​0|account]],​ add your information to {{:​dua_sagebionetworks_zare_ros-map_fe.pdf|this}} ​ file, and upload it again to Oncinfo without changing the file name. Then, let Habil know so that he uploads it on the Synapse [[https://​www.synapse.org/#​!AccessRequirements:​ID=syn3219045&​TYPE=ENTITY|website]].   - If you want to use ROSMAP data, please create a Synapse [[https://​www.synapse.org/#​!RegisterAccount:​0|account]],​ add your information to {{:​dua_sagebionetworks_zare_ros-map_fe.pdf|this}} ​ file, and upload it again to Oncinfo without changing the file name. Then, let Habil know so that he uploads it on the Synapse [[https://​www.synapse.org/#​!AccessRequirements:​ID=syn3219045&​TYPE=ENTITY|website]].
- 
  
 ==== Some references ==== ==== Some references ====
  
-  - Two machine learning bibles: Bishop ({{:​bishop-pattern_recongnition_and_machine_learning-1.pdf|1}},​{{:​bishop-pattern_recongnition_and_machine_learning-2.pdf|2}} ​ ) and [[http://​statweb.stanford.edu/​~tibs/​ElemStatLearn/​download.html|Hasite et al.]].+  - Two machine learning bibles, which summarize important topics in the field up to 2005: Bishop ({{:​bishop-pattern_recongnition_and_machine_learning-1.pdf|1}},​{{:​bishop-pattern_recongnition_and_machine_learning-2.pdf|2}} ​ ) and [[http://​statweb.stanford.edu/​~tibs/​ElemStatLearn/​download.html|Hasite et al.]].
   - [[https://​www.biostars.org/​|Biostars]] is a good forum, similar to Stack Overflow in structure, but focused on bioinformatics and Computational Biology.   - [[https://​www.biostars.org/​|Biostars]] is a good forum, similar to Stack Overflow in structure, but focused on bioinformatics and Computational Biology.
   - [[http://​www.wikiwand.com/​en/​List_of_free_online_bioinformatics_courses|List]] of free online bioinformatics courses and some interesting [[http://​bioconductor.org/​help/​events/​|events]] in Bioconductor.   - [[http://​www.wikiwand.com/​en/​List_of_free_online_bioinformatics_courses|List]] of free online bioinformatics courses and some interesting [[http://​bioconductor.org/​help/​events/​|events]] in Bioconductor.
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   - [[http://​stephenturner.us/​edu.html|List]] of bioinformatics workshops.   - [[http://​stephenturner.us/​edu.html|List]] of bioinformatics workshops.
   - A 5-minutes introduction to next-generation sequencing [[https://​www.youtube.com/​watch?​annotation_id=annotation_228575861&​feature=iv&​src_vid=womKfikWlxM&​v=fCd6B5HRaZ8|video]].   - A 5-minutes introduction to next-generation sequencing [[https://​www.youtube.com/​watch?​annotation_id=annotation_228575861&​feature=iv&​src_vid=womKfikWlxM&​v=fCd6B5HRaZ8|video]].
 +
  
 ==== Fun stuff ==== ==== Fun stuff ====