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<div style="padding: 5px; background: #457DB5;  border:solid 1px #AAAAAA; font-size:300%;font-weight:bold; color:#FFFFFF">
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#REDIRECT [[Bioinformatics_Main_Page]]
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BCH441 - Bioinformatics
 
  
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<div style="font-size:50%;font-weight:normal;">
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{{Vspace}}
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Welcome to the BCH441 Course Wiki.
 
−
</div>
 
−
</div>
 
  
−
<small>'''This is our main tool to coordinate information, activities and projects in University of Toronto's bioinformatics course BCH441'''. If you are not one of our students, you can still browse this site, however only users with a login  account can edit or contribute or edit material. If you are here because you are interested in general aspects of bioinformatics or computational biology, you may want to review the [http://en.wikipedia.org/wiki/Bioinformatics Wikipedia article on bioinformatics], or visit [http://www.openwetware.org/wiki/Wikiomics Wikiomics]. Contact boris.steipe(at)utoronto.ca with any questions you may have.</small>
+
<div id="BIO">
 +
<div class="b1" style="padding-left:7%;">
  
 +
&nbsp;<br/>
  
−
== The Course ==
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<div style="font-size:150%;font-weight:bold;">
 +
[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">A&nbsp;&nbsp;B&nbsp;&nbsp;C</span>]]
 +
</div>
  
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<div style="padding: 5px; background: #A6AFD0;  border:solid 1px #AAAAAA; font-size:200%;font-weight:bold;">
+
[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Applying Bioinformatics Concepts</span>]]
−
We'll be back soon:
 
  
−
<span style="font-size:75%;">First class: Thursday, September 10. 2009</span>
+
<div style="font-size:50%;font-weight:bold;">
 +
[[Bioinformatics_Main_Page|<span style="color:#FFFFFF;">Boris Steipe&nbsp;&nbsp;(2006 – 2020)</span>]]
 
</div>
 
</div>
  
−
== Organization ==
+
&nbsp;<br/>
  
−
;Dates
+
</div>
−
:''Lectures'': Monday and Thursday, 12:00 to 13:00
+
</div>
−
:''Tutorial sessions'': Mondays, 13:00 to 14:00 <small>&nbsp;&nbsp;for in-class quizzes, quiz debriefings, exam preparation and other activities, as the need arises.</small>
 
−
 
 
−
;Location
 
−
:MSB 2173 (Medical Sciences Building)
 
−
 
 
−
See the [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/ Course Web page] for general information.
 
−
 
 
−
We are recommending '''[http://www.garlandscience.com/textbooks/0815340249.asp Understanding Bioinformatics]''', Zvelebil &amp; Baum, Garland 2008 as a background textbook for the course. <small>([http://www.amazon.ca/Understanding-Bioinformatics-Market-Zvelebil/dp/0815340249 amazon], [http://www.uoftbookstore.com/online/merchant.ihtml?pid=1051140&step=4 UofT Bookstore])</small>
 
−
 
 
−
== Grading and Activities ==
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="sh">
 
−
<td>'''Activity'''</td>
 
−
<td>'''Weight'''<br><small>(Undergraduates)</small></td>
 
−
<td>'''Weight'''<br><small>(Graduates)</small></td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>[[Assignments|'''5 Assignments''' (drop 1)]]</td>
 
−
<td>16 marks <small>(4 x 4)</small></td>
 
−
<td>12 marks <small>(4 x 3)</small></td>
 
−
</tr>
 
−
 
 
−
 
 
−
<tr class="s1">
 
−
<td>[[Quizzes|'''5 In-class quizzes''' (drop 1)]]</td>
 
−
<td>32 marks <small>(4 x 8)</small></td>
 
−
<td>20 marks <small>(4 x 5)</small></td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>'''[[Group project]]'''</td>
 
−
<td>10 marks</td>
 
−
<td>6 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>'''[[Participation]]'''</td>
 
−
<td>2 marks</td>
 
−
<td>2 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>'''[[Graduate project]]'''</td>
 
−
<td>&nbsp;</td>
 
−
<td>20 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>[[Exam questions|'''Final exam''']]</td>
 
−
<td>40 marks</td>
 
−
<td>40 marks</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>'''Total'''</td>
 
−
<td>100 marks</td>
 
−
<td>100 marks</td>
 
−
</tr>
 
−
 
 
−
</table>
 
−
 
 
−
I will not adjust marks towards a target average for the class ("Belling"). If your classmate gets a great mark because you helped him with a difficult concept, this will have no bearing whatsoever on your own mark. Collaborate as much as possible, it is a great way to learn. The only times I will consider adjusting marks is if we phrase questions ambiguously on quizzes or if I decide that the final exam was too long.
 
−
 
 
−
== Lecture Schedule ==
 
−
<small>This section is currently under construction.</small>
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="st">
 
−
<td colspan="7">'''I n t r o d u c t i o n'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sh">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
<td>'''Note'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>1</td>
 
−
<td>Mon. Sept 8</td>
 
−
<td>Steipe</td>
 
−
<td>Organisation and Orientation</td>
 
−
<td>[[Introduction]]</td>
 
−
<td>Ch 1, 2</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
<!--  ========= NEW TOPIC =========        -->
 
−
<tr class="s0"><td colspan="7">&nbsp;</td></tr>
 
−
<tr class="st">
 
−
<td colspan="7">'''A b s t r a c t i o n s'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sh">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
<td>'''Note'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="7" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>2</td>
 
−
<td>Thu. Sept 11</td>
 
−
<td>Steipe</td>
 
−
<td>Sequence abstraction and sequence databases</td>
 
−
<td>[[Sequence data]]</td>
 
−
<td>Ch 3</td>
 
−
<td>[[Assignment 1|Assignment 1 to be handed out]]</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>3</td>
 
−
<td>Mon. Sept 15</td>
 
−
<td>Steipe</td>
 
−
<td>Protein Structure Data</td>
 
−
<td>[[Structure data]]</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
<tr class="s2">
 
−
<td>3</td>
 
−
<td>Thu. Sept 18</td>
 
−
<td>Steipe</td>
 
−
<td>Sequence properties</td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/SequenceProperties.pdf Raw lecture PDF]</small></td>
 
−
<td>Ch 4.9, 11, 12</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
</table>
 
−
 
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on properties'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>4</td>
 
−
<td>Mon. Sept 22</td>
 
−
<td>Steipe</td>
 
−
<td> Sequence Analysis </td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/SequenceAnalysis.pdf Raw lecture PDF]</small></td>
 
−
<td>-</td>
 
−
 
 
−
 
 
−
<tr class="s1">
 
−
<td rowspan="4">5</td>
 
−
<td rowspan="4">Thu. Sept 25.</td>
 
−
<td colspan="4">[[Assignment 1]] due</td>
 
−
</tr>
 
−
<tr class="s1">
 
−
<td colspan="4">'''First quiz''' in class</td>
 
−
</tr>
 
−
<tr class="s1">
 
−
<td>Steipe</td>
 
−
<td>Lecture: Interpreting protein structure<br></td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/InterpretingProteinStructure.pdf Raw lecture PDF]</small></td>
 
−
<td>-</td>
 
−
</tr>
 
−
<tr class="s1">
 
−
<td colspan="4">[[Assignment 2]] handed out
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>6</td>
 
−
<td>Mon. Sept 29</td>
 
−
<td>Steipe</td>
 
−
<td>Homology I: the principles</td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Homology_I_Principles.pdf Raw lecture PDF]</small></td>
 
−
<td>Ch. 14</td>
 
−
 
 
−
<tr class="s1">
 
−
<td>7</td>
 
−
<td>Thu. Oct 2</td>
 
−
<td>Parkinson</td>
 
−
<td>Genome sequencing, genome browsers</td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Genome_sequencing.pdf Lecture slide PDFs (1.8 MB)]</small></td>
 
−
<td>Ch. 9, 10</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>8</td>
 
−
<td>Mon. Oct 6</td>
 
−
<td>Parkinson</td>
 
−
<td>Genomes and genome structure</td>
 
−
<td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Genomes.pdf Lecture slide PDFs (2.4 MB)]</td>
 
−
<td>-</td>
 
−
 
 
−
</table>
 
−
 
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on homology'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td rowspan="3">9</td>
 
−
<td rowspan="3">Thu. Oct 9.</td>
 
−
<td colspan="4">[[Assignment 2]] due</td>
 
−
</tr>
 
−
<tr class="s0">
 
−
<td>Steipe</td>
 
−
<td>Lecture: Homology II: Sequence alignment<br></td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/Homology_II_Alignment.pdf Raw lecture PDF]</small></td>
 
−
<td>-</td>
 
−
</tr>
 
−
<tr class="s0">
 
−
<td colspan="4">[[Assignment 3]] handed out
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>10</td>
 
−
<td>'''Thu. Oct 16'''</td>
 
−
<td>Steipe</td>
 
−
<td>Lecture: Homology III: Fast sequence database searches</td>
 
−
<td>[[BLAST]]</td>
 
−
<td>Ch. 4</td>
 
−
 
 
−
<tr class="s0">
 
−
<td rowspan="3">11</td>
 
−
<td rowspan="3">Mo. Oct 20</td>
 
−
<td>Steipe</td>
 
−
<td>Homology IV: Multiple sequence alignment</td>
 
−
<td>[[Multiple Sequence Alignment]]</td>
 
−
<td>Ch. 5</td>
 
−
</tr>
 
−
<tr class="s0">
 
−
<td colspan="4">'''Second quiz''' in class (13:00 tutorial time slot)</td>
 
−
</tr>
 
−
<tr class="s0">
 
−
<td>Steipe</td>
 
−
<td><!-- Lecture: Bioinformatics methods --></td>
 
−
<td>-</td>
 
−
<td>Ch 6</td>
 
−
 
 
−
 
 
−
<tr class="s1">
 
−
<td rowspan="3">12</td>
 
−
<td rowspan="3">Thu. Oct 23.</td>
 
−
<td colspan="4">[[Assignment 3]] due</td>
 
−
</tr>
 
−
<tr class="s1">
 
−
<td>Steipe</td>
 
−
<td>Lecture: Structural domains<br></td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/StructuralDomains.pdf Raw lecture PDF]</small></td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
</table>
 
−
 
 
−
 
 
−
 
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on conservation'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecture'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>13</td>
 
−
<td>Mon. Oct 27</td>
 
−
<td>(Steipe) Phylogenetic analysis I (Book: Ch. 7,8)<br><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PhylogeneticAnalysis_I.pdf Raw lecture PDF]</small>
 
−
<hr>
 
−
'''Third quiz''' in class, 13:00 in tutorial time-slot
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>14</td>
 
−
<td>Thu. Oct 30</td>
 
−
<td>(Steipe) Phylogenetic analysis II (Book: Ch. 7,8)<br>
 
−
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PhylogeneticAnalysis_II.pdf Raw lecture PDF]</small>
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>15</td>
 
−
<td>Mon. Nov 3</td>
 
−
<td>(Parkinson) Comparative genomics (Book: Ch. Ch. 9.8, 10.8)<br>
 
−
[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/ComparativeGenomics.pdf Lecture slide PDFs (1.6 MB)]
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>16</td>
 
−
<td>Thu. Nov 6</td>
 
−
<td>(Steipe) Quiz pickup, Human population genomics (Part 1)<br>
 
−
</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>17</td>
 
−
<td>Mon. Nov 10</td>
 
−
<td>(Steipe) Human population genomics (Part 2)<br>
 
−
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/HumanPopulationGenomics.pdf Raw lecture PDF]</small><hr>
 
−
[[Assignment 4]] to be posted.
 
−
</td>
 
−
</tr>
 
−
 
 
−
 
 
−
<tr class="s1">
 
−
<td>18</td>
 
−
<td>Thu. Nov 13</td>
 
−
<td>(Steipe) Homology modeling and structure prediction (Part 1)<br>
 
−
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PredictingProteinStructure_I.pdf Raw lecture PDF]</small></td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>19</td>
 
−
<td>Mon. Nov 17</td>
 
−
<td>(Steipe) Homology modeling and structure prediction (Part 2)<br>
 
−
<small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PredictingProteinStructure_II.pdf Raw lecture PDF]</small><hr>
 
−
[[Assignment 4]] due.
 
−
<hr>
 
−
'''Fourth quiz''' in class: 13:00 in tutorial time slot.
 
−
<hr>
 
−
[[Assignment 5]] to be posted.
 
−
</td>
 
−
</tr>
 
−
 
 
−
</table>
 
−
 
 
−
 
 
−
<table cellpadding="5">
 
−
 
 
−
<tr class="s0">
 
−
<td colspan="6">'''Analysis based on context'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>'''#'''</td>
 
−
<td>'''Date'''</td>
 
−
<td>'''Lecturer'''</td>
 
−
<td>'''Topic'''</td>
 
−
<td>'''Handout'''</td>
 
−
<td>'''Book'''</td>
 
−
</tr>
 
−
 
 
−
<tr class="sp"><td colspan="3" style="height: 5px;"></td></tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>20</td>
 
−
<td>Thu. Nov 20</td>
 
−
<td> Wodak </td>
 
−
<td>Gene regulation I</td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/GeneRegulation.pdf Lecture slide PDFs (2.1 MB)]</small></td>
 
−
<td>Ch. 15</td>
 
−
</tr>
 
−
 
 
−
<tr class="s1">
 
−
<td>21</td>
 
−
<td>Mon. Nov 24</td>
 
−
<td>Wodak</td>
 
−
<td>Gene regulation II</td>
 
−
<td>-</td>
 
−
<td>-</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>22</td>
 
−
<td>Thu. Nov 27</td>
 
−
<td>Wodak</td>
 
−
<td>Functional annotation</td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/FunctionalAnnotations.pdf Lecture slide PDFs ('''10.6 MB''')]</small></td>
 
−
<td>Appendix A</td>
 
−
</tr>
 
−
 
 
−
 
 
−
<tr class="s1">
 
−
<td rowspan="2">23</td>
 
−
<td rowspan="2">Mon. Dec 1</td>
 
−
<td>Wodak</td>
 
−
<td>Metabolic networks</td>
 
−
<td><small>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/PathwaysAndNetworks.pdf Lecture slide PDFs (3.1 MB)]</small></td>
 
−
<td>Ch. 17.1</td>
 
−
</tr>
 
−
<tr class="s1">
 
−
<td colspan="4">[[Assignment 5]] due<br>
 
−
<hr>
 
−
'''Fifth quiz''' in class: 13:00 in tutorial time slot</td>
 
−
</tr>
 
−
 
 
−
<tr class="s0">
 
−
<td>24</td>
 
−
<td>Thu. Dec 4</td>
 
−
<td>Parkinson</td>
 
−
<td>Computational systems biology</td>
 
−
<td>[http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/resources/ComputationalSystemsBiology.pdf Lecture slide PDFs (3.4 MB)]</td>
 
−
<td>Ch. 17</td>
 
−
</tr>
 
−
 
 
−
 
 
−
</table>
 
−
 
 
−
==In depth...==
 
−
 
 
−
* [[Glossary]]
 
−
* [[Mutation Data Matrices]]
 
−
* [http://en.wikipedia.org/wiki/List_of_standard_amino_acids Amino acids]
 
−
 
 
−
<!-- * [[Database Identifiers]] -->
 
−
 
 
−
&nbsp;
 
−
 
 
−
== Resources ==
 
−
;Course related
 
−
*The [http://biochemistry.utoronto.ca/undergraduates/courses/BCH441H/ Course Web site].
 
−
*The [http://groups.google.com/group/bch441_2008 Course Google Group].
 
−
*[[Netiquette]] for the Group mailing list
 
−
*Previous [[Exam_questions]]
 
−
*[[Feedback_2007|2007 course feedback]]
 
−
*[[Feedback_2008|2008 course feedback]]
 
−
 
 
−
 
 
−
&nbsp;<br>
 
−
;Contents related
 
−
*The '''[[VMD]]''' tutorial
 
−
*A '''[[Stereo Vision]]''' tutorial
 
−
*[http://biodatabase.org/index.php/Main_Page MetaDatabase]
 
−
*[http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl NAR January-2008 '''Database''' issue]
 
−
*[http://nar.oxfordjournals.org/content/vol36/suppl_2/index.dtl NAR July-2008 '''Web server''' issue]
 
−
&nbsp;<br>
 
−
 
 
−
 
 
−
 
 
−
<!--
 
−
;Course Wiki
 
−
*[[Help:Introduction|Introduction:]] Concept and contents of the Course Wiki
 
−
*[[Soapbox]]: A page to commmunicate. Do you want to leave a message? Alert the course members? Voice an opinion? Praise or flame? Use this page.
 
−
*[[Help:Editing| Editing:]] Editing principles and Wiki markup syntax for the Course Wiki pages
 
−
*[[Sandbox]]: A page for your editing experiments. Content added to this page will not stay permanently.
 
−
*[[Feedback]]: Share your views on the course, suggest improvements.
 
−
-->
 
−
 
 
−
 
 
−
 
 
−
&nbsp;<br>
 
−
 
 
−
 
 
−
 
 
−
<!--- Color schemes
 
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<div style="padding: 3px; background: #457DB5;  border:solid 1px #AAAAAA;">Level 1</div>
 
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<div style="padding: 3px; background: #6F9BD0;  border:solid 1px #AAAAAA;">Level 2</div>
 
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<div style="padding: 3px; background: #9CC86F;  border:solid 1px #AAAAAA;">Level 3</div>
 
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<div style="padding: 3px; background: #F0F07A;  border:solid 1px #AAAAAA;">Alert</div>
 
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<div style="padding: 3px; background: #FF4560;  border:solid 1px #AAAAAA;">Warning!</div>
 
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Latest revision as of 08:17, 8 September 2020

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