Difference between revisions of "BIN-Info sources"

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<div id="BIO">
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Information Sources for Bioinformatics
 
Information Sources for Bioinformatics
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  </div>
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Wikipedia, NAR, Bioinformatics.ca, PubMed, Citation index)
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  {{Vspace}}
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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Wikipedia , NAR, Bioinformatics.ca, PubMed, Citation index
 
 
</div>
 
</div>
  
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{{Smallvspace}}
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__TOC__
 
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{{Vspace}}
 
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{{DEV}}
 
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{{Vspace}}
 
  
  
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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<section begin=abstract />
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This unit introduces key information sources for bioinformatics: journals, forums, and supporting sites.
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<section end=abstract />
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</div>
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<!-- ============================  -->
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<hr>
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<table>
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<tr>
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<td style="padding:10px;">
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<b>Objectives:</b><br />
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Get a sense for the academic field of bioinformatics and its community.
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</td>
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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You are familiar with the sites that facilitate much of the ongoing discussion in the field.
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</td>
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</tr>
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</table>
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<!-- ============================  -->
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<hr>
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<b>Deliverables:</b><br />
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<section begin=deliverables />
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<ul>
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<li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li>
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<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
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<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
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</ul>
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<section end=deliverables />
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<!-- ============================  -->
 
</div>
 
</div>
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<div id="ABC-unit-framework">
 
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== Abstract ==
 
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<!-- included from "../components/BIN-Info_sources.components.wtxt", section: "abstract" -->
 
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...
 
  
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{{Smallvspace}}
  
  
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== This unit ... ==
 
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=== Prerequisites ===
 
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<!-- included from "../components/BIN-Info_sources.components.wtxt", section: "prerequisites" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes-no_prerequisites" -->
 
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This unit has no prerequisites.
 
  
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{{Smallvspace}}
  
  
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=== Objectives ===
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__TOC__
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<!-- included from "../components/BIN-Info_sources.components.wtxt", section: "objectives" -->
 
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...
 
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{{Vspace}}
 
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=== Outcomes ===
 
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<!-- included from "../components/BIN-Info_sources.components.wtxt", section: "outcomes" -->
 
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...
 
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{{Vspace}}
 
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=== Deliverables ===
 
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<!-- included from "../components/BIN-Info_sources.components.wtxt", section: "deliverables" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
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*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
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*<b>Journal</b>: Document your progress in your [[FND-Journal|course journal]].
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|insights! page]].
 
  
 
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=== Evaluation ===
 
=== Evaluation ===
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<!-- included from "../components/BIN-Info_sources.components.wtxt", section: "evaluation" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "eval-none" -->
 
 
<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
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:This unit is not evaluated for course marks.
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
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</div>
 
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<div id="BIO">
 
 
== Contents ==
 
== Contents ==
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<!-- included from "../components/BIN-Info_sources.components.wtxt", section: "contents" -->
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{{Smallvspace}}
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{{Task|1=
 
{{Task|1=
 
* Read the introductory notes on {{ABC-PDF|FND-BIN-Concepts|'''bioinformatics concepts'''}} for some general observations on bioinformatics, to set the stage.
 
* Read the introductory notes on {{ABC-PDF|FND-BIN-Concepts|'''bioinformatics concepts'''}} for some general observations on bioinformatics, to set the stage.
 
* Read the introductory notes on {{ABC-PDF|BIN-Info_sources|information sources for bioinformatics}}.
 
* Read the introductory notes on {{ABC-PDF|BIN-Info_sources|information sources for bioinformatics}}.
 
}}
 
}}
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{{Vspace}}
 
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;Forums
 
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<div class="reference-box">'''[http://biostar.stackexchange.com BioStar]''': General bioinformatics, computational-, and systems biology questions <small>(timesink warning!)</small></div>
 
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<div class="reference-box">'''[https://www.reddit.com/r/bioinformatics/ Reddit]''': the bioinformatics "subreddit" <small>(timesink warning!)</small></div>
 
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<div class="reference-box">'''[https://stat.ethz.ch/mailman/listinfo/r-help R-help]''': The R programming language</div>
 
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<div class="reference-box">'''[http://stackoverflow.com/questions/tagged/r Stack Overflow]''': R-related questions</div>
 
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<div class="reference-box">'''[https://www.bioconductor.org/help/support/ BioConductor Support]''': for all questions about the BioConductor Project</div>
 
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<div class="reference-box">'''[http://stats.stackexchange.com/ Cross Validated]''': statistics related questions on ''Stack-exchange''</div>
 
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{{Vspace}}
 
{{Vspace}}
  
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=== Journals ===
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{{Smallvspace}}
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{{Task|1=
  
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== Further reading, links and resources ==
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* Visit the [https://academic.oup.com/nar Nucleic Acids Research Journal (NAR)] site and find the current database volume and the Web service volume.
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<!-- {{#pmid: 19957275}} -->
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* Task yourself to find at least one database and service that interests you, visit it and poke around. You should aim to develop an intuition for what to expect with such resources and how to use the services.
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<!-- {{WWW|WWW_GMOD}} -->
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
  
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}}
  
  
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== Notes ==
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Incidentally: you can subscribe to regular Table of Contents updates from any journal. [https://www.nature.com/ '''nature'''] and [http://science.sciencemag.org/ '''Science'''] should for sure be in your inbox, but subscribe to some of the bioinformatics journal alerts too =  such as [https://academic.oup.com/bioinformatics '''Bioinformatics'''] - at least for this term.
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<!-- included from "../components/BIN-Info_sources.components.wtxt", section: "notes" -->
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<ul>
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<!-- included from "ABC-unit_components.wtxt", section: "notes" -->
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<!-- li>[https://jcr-clarivate-com.myaccess.library.utoronto.ca/JCRJournalHomeAction.action?pg=JRNLHOME&categoryName=MATHEMATICAL%20%26%20COMPUTATIONAL%20BIOLOGY&year=2019&edition=SCIE&categories=MC Journals by Impact Factor] (ISI Category "Mathematical & Computational Biology") <small>Unfortunately the library's sign-on mechanism is broken...</small></li -->
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<references />
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<li> Among the top ranked journals (according to ISI), we have [https://journals.plos.org/ploscompbiol/ PLoS Computational Biology], [https://bmcbioinformatics.biomedcentral.com/ BMC Bioinformatics], [https://www.nature.com/npjsba/ Nature Systems Biology and Applications], and [https://academic.oup.com/bib Briefings in Bioinformatics]. Explore.
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<li>{{WP|List of bioinformatics journals|Wikipedia: Bioinformatics journals}}</li>
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</ul>
  
 
{{Vspace}}
 
{{Vspace}}
  
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=== Forums ===
  
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</div>
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Much current, active exchange of bioinformatics knowledge happens in non-traditional platforms:
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<div id="ABC-unit-framework">
 
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== Self-evaluation ==
 
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<!-- included from "../components/BIN-Info_sources.components.wtxt", section: "self-evaluation" -->
 
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<!--
 
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=== Question 1===
 
  
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Question ...
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{{Task|1=
  
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<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
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Visit each of the forums below and find (at least) one item that interests you.
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Answer ...
 
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<div class="mw-collapsible-content">
 
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Answer ...
 
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</div>
 
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  </div>
 
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  {{Vspace}}
 
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-->
 
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{{Vspace}}
 
  
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<div class="reference-box">'''[http://www.biostars.org BioStars]''': General bioinformatics, computational-, and systems biology questions <small>(timesink warning!)</small></div>
 +
<div class="reference-box">'''[https://www.reddit.com/r/bioinformatics/ Reddit]''': the bioinformatics "subreddit" <small>(timesink warning!)</small></div>
 +
<div class="reference-box">'''[https://stat.ethz.ch/mailman/listinfo/r-help R-help]''': The R programming language</div>
 +
<div class="reference-box">'''[http://stackoverflow.com/questions/tagged/r Stack Overflow]''': R-related questions</div>
 +
<div class="reference-box">'''[https://www.bioconductor.org/help/support/ BioConductor Support]''': for all questions about the BioConductor Project</div>
 +
<div class="reference-box">'''[http://stats.stackexchange.com/ Cross Validated]''': statistics related questions on ''Stack-exchange''</div>
  
 +
}}
  
 
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<!-- included from "ABC-unit_components.wtxt", section: "ABC-unit_ask" -->
 
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----
 
  
 
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<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-08-05
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:2020-09-15
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:0.1
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:1.2
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*0.1 First stub
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*1.2 Removed bioinformatics.ca link. Maintenance updates.
 +
*1.1 Bioinformatics.ca links database no longer exists
 +
*1.0.1 Update Biostars link
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*1.0 Completed to first live version
 +
*0.1 Material collected from previous tutorial
 
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[[Category:ABC-units]]
 
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Latest revision as of 09:26, 25 September 2020

Information Sources for Bioinformatics

(Wikipedia, NAR, Bioinformatics.ca, PubMed, Citation index)


 


Abstract:

This unit introduces key information sources for bioinformatics: journals, forums, and supporting sites.

Objectives:
Get a sense for the academic field of bioinformatics and its community.

Outcomes:
You are familiar with the sites that facilitate much of the ongoing discussion in the field.

Deliverables:

  • Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.


 



 



 


Evaluation

Evaluation: NA

This unit is not evaluated for course marks.

Contents

 

Task:


 

Journals

 

Task:

  • Visit the Nucleic Acids Research Journal (NAR) site and find the current database volume and the Web service volume.
  • Task yourself to find at least one database and service that interests you, visit it and poke around. You should aim to develop an intuition for what to expect with such resources and how to use the services.


Incidentally: you can subscribe to regular Table of Contents updates from any journal. nature and Science should for sure be in your inbox, but subscribe to some of the bioinformatics journal alerts too = such as Bioinformatics - at least for this term.


 

Forums

Much current, active exchange of bioinformatics knowledge happens in non-traditional platforms:

Task:
Visit each of the forums below and find (at least) one item that interests you.

BioStars: General bioinformatics, computational-, and systems biology questions (timesink warning!)
Reddit: the bioinformatics "subreddit" (timesink warning!)
R-help: The R programming language
Stack Overflow: R-related questions
BioConductor Support: for all questions about the BioConductor Project
Cross Validated: statistics related questions on Stack-exchange


 


 


About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2020-09-15

Version:

1.2

Version history:

  • 1.2 Removed bioinformatics.ca link. Maintenance updates.
  • 1.1 Bioinformatics.ca links database no longer exists
  • 1.0.1 Update Biostars link
  • 1.0 Completed to first live version
  • 0.1 Material collected from previous tutorial

CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-Info_sources&oldid=11684"