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| − | '''Boris Steipe''' <small>(course coordinator)</small>
| + | Bla bla bla |
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| − | :Medical Sciences Building, Room 5279<br>
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| − | :Toronto, Ontario M5S 1A8
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| − | :T: 416-946-7741<br>
| + | __NOTOC__ |
| − | :E: boris.steipe@utoronto.ca
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| − | __TOC__
| + | <table> |
| − | | + | <tr><td>=====this=====</td><td>NN</td> |
| − | | + | <td>12345</td><td>NN</td><td>yadda yadda yadda</td></tr> |
| − | ==Resources==
| + | <tr><td>=====this2=====</td><td>NN</td> |
| − | | + | <td>12345</td><td>NN</td><td>yadda yadda yadda</td></tr> |
| − | {{Vspace}}
| + | <tr><td>=====this3=====</td><td>NN</td> |
| − | | + | <td>12345</td><td>NN</td><td>yadda yadda yadda</td></tr> |
| − | ;[[Help:ABC_extensions_syntax|'''Extension and Template syntax''']]
| + | <tr><td>=====this4=====</td><td>NN</td> |
| − | | + | <td>12345</td><td>NN</td><td>yadda yadda yadda</td></tr> |
| − | {{Vspace}}
| + | <tr><td>=====this5=====</td><td>NN</td> |
| − | | + | <td>12345</td><td>NN</td><td>yadda yadda yadda</td></tr> |
| − | Original sidebar links;
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| − | <!-- *[[Main_Page]] --> | |
| − | <!-- *[[BCH441Hwiki:Community_portal]] --> | |
| − | <!-- *[[Current_events]] -->
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| − | *[[Special:RecentChanges]]
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| − | <!-- *[[Special:Random]] --> | |
| − | *[[Help:Contents]]
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| − | *What links here ... ctrl - option - j
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| − | *Related Changes ... ctrl- option - k
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| − | *[[Special:Upload]]
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| − | *[[Special:SpecialPages]]
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| − | | |
| − | ;Service pages
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| − | *[[MediaWiki:Common.css]]
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| − | *[[MediaWiki:Sidebar]]
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| − | *[[MediaWiki:Multiboilerplate|'''Multi Boiler Plate''' extension drop down menu]] (Copy Template location from there to edit.)
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| − | {{Vspace}}
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| − | ===Current===
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| − | *[[Workshops]]
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| − | *[[User:Boris/Temp]]
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| − | {{Cite web|title = NOX1 NADPH oxidase 1 [Homo sapiens (human)] - Gene - NCBI|url = http://www.ncbi.nlm.nih.gov/gene/27035|website = www.ncbi.nlm.nih.gov|accessdate = 2015-12-21}}
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| − | ==Test==
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| − | [[Media:Test.txt]]
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| − | ==Syllabus snips==
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| − | | |
| − | <section begin=Coordinator />
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| − | ===Coordinator===
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| − | | |
| − | :[mailto:boris.steipe@utoronto.ca '''Boris Steipe''']
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| − | {{Vspace}}
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| − | <section end=Coordinator />
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| − | <section begin=Office_hours />
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| − | ===Office hours===
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| − | Face to face meetings are by appointment, as required. You will find that meetings that we prepare by e-mail are both more efficient and effective than simply dropping in for a chat. Moreover e-mail discussions leave you with a document trail of what was discussed, can contain links to information sources, and we can share points of general interest more easily with the class.
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| − | {{Vspace}}
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| − | <section end=Office_hours />
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| − | | |
| − | | |
| − | <section begin=Student_Wiki />
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| − | ===Student Wiki===
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| − | Many of the class activities will take place interactively on a separate [http://steipe.biochemistry.utoronto.ca/abc/students/ Wiki site (the "Student Wiki")]. You will create a personalized user page there, and use it to submit materials as required.
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| − | This Wiki is not accessible to the general public, you need an account that we will register in the first class-session.
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| − | | |
| − | {{Vspace}}
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| − | <section end=Student_Wiki />
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| − | <section begin=Mailing_list />
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| − | ===Student Wiki=== | |
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| − | All course announcements and all course discussion (outside of class) will take place on a mailing list. We use Google Groups for this purpose. You will be subscribed to the list in the first class. You will not be able to participate fully in the course if you are not subscribed. Make sure you are subscribed '''with the email address you use most frequently''' and set your preferences to immediate delivery - "Digest" or "Web only" delivery won't allow you to participate actively in discussions and your participation mark will suffer.
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| − | {{Vspace}}
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| − | <section end=Mailing_list />
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| − | | |
| − | ====... under development==== | |
| − | | |
| − | ;CSB map 2
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| − | <table border="1">
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| − | <tr>
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| − | <th>Week</th>
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| − | <th>prereading</th>
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| − | <th>topic</th>
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| − | <th>exercise</th>
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| − | <th>quiz</th>
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| − | </tr>
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| − | <tr>
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| − | <td>00</td>
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| − | <td>-</td> | |
| − | <td>Intro; what is a system; topic for the term: extract systems from data; Organization; Prerequisites</td> | |
| − | <td>Exercise</td> | |
| − | <td>quiz</td> | |
| − | </tr> | |
| − | | |
| − | <tr> | |
| − | <td>00</td> | |
| − | <td>-</td> | |
| − | <td>A project: what do we need to solve this problem</td> | |
| − | <td>Exercise</td> | |
| − | <td>quiz</td> | |
| − | </tr> | |
| − | | |
| − | <tr> | |
| − | <td>00</td> | |
| − | <td>-</td> | |
| − | <td>A Software project; defining project; defining tasks; infrastructure</td> | |
| − | <td>Exercise</td> | |
| − | <td>quiz</td> | |
| − | </tr> | |
| − | | |
| − | <tr> | |
| − | <td>00</td> | |
| − | <td>-</td> | |
| − | <td>Biological entities</td> | |
| − | <td>Exercise</td> | |
| − | <td>quiz</td> | |
| − | </tr> | |
| − | | |
| − | <tr> | |
| − | <td>00</td> | |
| − | <td>-</td>
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| − | <td>Dynamics</td>
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| − | <td>Exercise</td>
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| − | <td>quiz</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>00</td>
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| − | <td>-</td>
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| − | <td>Annotations</td>
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| − | <td>Exercise</td>
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| − | <td>quiz</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>00</td>
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| − | <td>-</td>
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| − | <td>Relationships</td>
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| − | <td>Exercise</td>
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| − | <td>quiz</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>00</td>
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| − | <td>-</td>
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| − | <td>Systems discovery</td>
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| − | <td>Exercise</td>
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| − | <td>quiz</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>00</td>
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| − | <td>-</td>
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| − | <td>Visualization</td>
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| − | <td>Exercise</td>
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| − | <td>quiz</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>00</td>
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| − | <td>-</td>
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| − | <td>Interpretation</td>
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| − | <td>Exercise</td>
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| − | <td>quiz</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>00</td>
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| − | <td>-</td>
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| − | <td>Results</td>
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| − | <td>Exercise</td>
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| − | <td>quiz</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>00</td>
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| − | <td>-</td>
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| − | <td>Results</td>
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| − | <td>Exercise</td>
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| − | <td>quiz</td>
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| − | </tr>
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| − | | |
| − | | |
| − | </table>
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| − | | |
| − | <hr />
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| − | | |
| − | | |
| − | ;CSB map
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| − | <table border="1">
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| − | <tr>
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| − | <th>00</th>
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| − | <th>prereading</th>
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| − | <th>topic</th>
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| − | <th>exercise</th>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>01</td>
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| − | <td>-</td>
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| − | <td>Intro</td>
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| − | <td>Wiki</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>02</td>
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| − | <td>Annotation</td>
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| − | <td>Web</td>
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| − | <td>GO, GOSemSim</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>03</td>
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| − | <td>prereading</td>
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| − | <td>Gene lists</td>
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| − | <td>FAA, GSEA</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>04</td>
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| − | <td>prereading</td>
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| − | <td>Genome, transcriptome</td>
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| − | <td>GEO (4+5)</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>05</td>
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| − | <td>prereading</td>
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| − | <td>Proteome, Metabolome</td>
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| − | <td>GEO 2?</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>06</td>
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| − | <td>prereading</td>
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| − | <td>Graph theory</td>
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| − | <td>exercise</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>07</td>
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| − | <td>prereading</td>
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| − | <td>Interactome</td>
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| − | <td>exercise</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>08</td> | |
| − | <td>prereading</td> | |
| − | <td>Networks</td> | |
| − | <td>exercise</td> | |
| − | </tr> | |
| − | | |
| − | <tr>
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| − | <td>09</td>
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| − | <td>prereading</td>
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| − | <td>Systems extraction</td>
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| − | <td>exercise</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>10</td>
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| − | <td>prereading</td>
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| − | <td>Dynamics</td>
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| − | <td>exercise</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>11</td>
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| − | <td>prereading</td>
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| − | <td>Modelling</td>
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| − | <td>exercise</td>
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| − | </tr>
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| − | | |
| − | <tr>
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| − | <td>12</td>
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| − | <td>prereading</td>
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| − | <td>Synthetic biology</td>
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| − | <td>exercise</td>
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| − | </tr>
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| | </table> | | </table> |
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| − | * [[User:Boris/Temp/APB]] - '''Applied Bioinformatics page hierarchy'''
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| − | *[[User:Boris/Temp]]
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| − | *[[User:Boris/Temp2|(Computing with PDB file, originally A4)]]
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| − | *[[User:Boris/Temp3|(Phylogenetic analysis, long version)]]
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| − |
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| − | *[[Cargo Cult Bioinformatics]]
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| − | *[[VMD]] tutorial(s)
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| − | *[[R tutorial]]
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| − | *[[Aminoacid tutorial]]
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| − | *[[Stereo Vision]] tutorial
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| − | *[[Database Identifiers]]
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| − | *[[Integrated_Exam_Questions]]
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| − | ====Additional BIO Topics====
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| − |
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| − | * Must make note to alert students who run LINUX boxes that some assignment tasks can be conveniently Perlified.
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| − | * http://www.biosolveit.de/PoseView/
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| − |
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| − | ====Additional CSB Topics====
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| − |
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| − | http://www.elsevier.com/wps/find/bookdescription.cws_home/707460/description
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| − | *Elsevier - Introducing Computational Systems Biology
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| − | *Elsevier - Enabling Information and Integration Technologies for Systems Biology:
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| − | **Elsevier - Databases for Systems Biology.
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| − | **Elsevier - Natural Language Processing and Ontology-enhanced Biomedical Literature Mining for Systems Biology
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| − | **Elsevier - Integrated Imaging Informatics
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| − | **Elsevier - Simpathica: A Computational Systems Biology Tool within the Valis Bioinformatics Environment
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| − | **Elsevier - Standards, Platforms and Applications
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| − | *Elsevier - Foundations of Biochemical Network Analysis and Modeling
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| − | **Elsevier - Introduction to Computational Models of Biochemical Reaction Networks
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| − | **Elsevier - Biological Foundations of Signal Transduction and the Systems Biology Perspective
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| − | **Elsevier - Reconstruction of Metabolic Network from Genome Information and Its Structural and Functional Analysis
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| − | **Elsevier - Integrated Regulatory and Metabolic Models
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| − | *Elsevier - Computer Simulations of Dynamic Networks
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| − | **Elsevier - A Discrete Approach to Network Modeling
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| − | **Elsevier - Gene Networks: Estimation, Modeling and Simulation
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| − | **Elsevier - Computational models for circadian rhythms: Deterministic versus stochastic approaches
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| − | *Elsevier - Multi-Scale Representations of Cells and Emerging Phenotypes
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| − | **Elsevier - Multistability and Multicellularity: Cell Fates as High-dimensional Attractors of Gene Regulatory Networks
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| − | **Elsevier - Spatio-Temporal Systems Biology
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| − | **Elsevier - Cytomics—from cell states to predictive medicine
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| − | **Elsevier - The IUPS Physiome Project: Progress and Plans.
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| − | ====Additional APB Topics====
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| − | ** GPU and Cloud computing
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| − | ** CSS ( http://www.csszengarden.com/ , http://en.wikipedia.org/wiki/Help:User_style , )
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| − | ** REST as API. Programming example: SADI or BOLD (Barcode of life).
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| − | ** GO annotation in http and R
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| − |
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| − | ==Practice to think==
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| − | ===Repository===
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| − | * Many hard logics questions [https://www.quora.com/What-are-some-fun-or-interesting-brain-teasers here at Quora]
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| − | * get to an island with two short planks.
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| − | *If two guns are pointed EXACTLY at each other, are mounted horizontally and the bullets leave the barrel at the same time then the bullets will collide regardless of muzzle velocity. The reason is that the vertical component of the acceleration will be equal.
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| − | * If you walk up and down a mountain, will you be at the same spot on the same hour?
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| − | * Three light switches: test which one switches with only one try.
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| − | * A scientist flies from his base ... what color is the bear?
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| − | * The three doors of the gameshow
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| − | * You are travelling down a road to a village. You reach a fork in the road and find a pair of identical twin brothers standing there. One of the brothers always tells the truth and the other always lies. If you are allowed to ask only one question to one of the brothers to find which is the correct road to the village, what is your question ?
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| − | * A boat has a ladder that has six rungs, each rung is one foot apart. The bottom rung is one foot from the water. The tide rises at 12 inches every 15 minutes. High tide peaks in one hour. When the tide is at its highest, how many rungs are under water?
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| − | * three glasses with OJ, three with water. Move only one glass so that full and empty alternate
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| − | *You are given two candles of equal size, which can burn 1 hour each. You have to measure 90 minutes with these candles. (There is no scale or clock). Also you are given a lighter.
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| − | *Can you name three consecutive days without using the words Wednesday, Friday, or Sunday?
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| − | *A murderer is condemned to death. He has to choose between three rooms. The first is full of raging fires. The second is full of assassins with loaded guns. The third is full of lions those haven't eaten in 3 years.
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| − | *If you were alone in a dark cabin, with a petroleum lamp, a fireplace, and a candle but you have only one match, which would you light first?
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| − | *You are driving along in your car on a wild, stormy night, it's raining heavily, when suddenly you pass by a bus stop, and you see three people waiting for a bus: an old lady who seems to be having a heart attack, an old friend who once saved your life, and the smart, handsome partner of your dreams. There can only be one passenger in your car. What is the best strategy? Give the car keys to my old friend and let him take the lady to the hospital; stay behind and wait for the bus with the partner of your dreams.
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| − | *The Zorganian Republic has some very strange customs. Couples only wish to have female children as only females can inherit the family's wealth, so if they have a male child they keep having more children until they have a girl. If they have a girl, they stop having children. What is the ratio of girls to boys in Zorgania? (Nice, because "a random string ending in a girl" is the wrong model! It's a string of boys, plus a girl. The right model is a random string, segmented to start with a boy and end with a girl.)
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| − | *Focus on one card ... 9/7/8 ... your card has been removed.
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| − | * In many London Underground tube stations there are two up escalators but only one going down. Why? People leave trains in a group, so all arrive at the escalators at the same time, but tend to go down to the trains in a more even flow, hence you need less down escalators.
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| − | * The amount of water flowing into a tank doubles every minute. The tank is full in an hour. When was the tank half full?
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| − | * There are three boxes, one contains only apples, one contains only oranges, and one contains both apples and oranges. The boxes have been incorrectly labeled such that no label identifies the actual contents of the box it labels. Opening just one box, and without looking in the box, you take out one piece of fruit. By looking at the fruit, how can you immediately label all of the boxes correctly? Open the box that is labeled "Apples and Oranges". You know that since none of the labels are correct, the box must either contain only apples, or only oranges.Suppose that you remove an apple from that box. Therefore, that box must be the "Apples Only" box.One of the two remaining boxes must be the "Oranges Only" box. However, one is labeled "Apples Only", and the other is labeled "Oranges Only". Therefore, the one labeled "Apples Only" is the box that contains only oranges, and the box labeled "Oranges Only" is the box that contains both kinds of fruit.
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| − | * A boy and a girl are sitting on the porch. "I'm a boy," says the child with black hair. "I'm a girl," says the child with red hair. If at least one of them is lying, who is which?
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| − | * You have a 10-gallon jug and a 3-gallon jug. Neither jug is labeled. You need exactly 5 gallons of water. You have a working water faucet right next to you. How can you get exactly 5 gallons of water?
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| − | * You are in the dark, and on the floor there are six shoes of three colors, and a heap of twenty-four socks, which are either black or brown. How many socks and shoes must you take into the light to be certain that you have a matching pair of socks and a matching pair of shoes?
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| − | * There are 27 gold coins. All of them are fake except for one. All of them appear exactly the same, and there is no way to tell them apart - except that the real gold coin is slightly heavier than the others. Using a balance scale, how can you determine which is the fake coin, with only three weighings?
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| − | * Janice and Marge were roommates in college, and meet again after many years. What are the ages of each of the children? Here is their discussion:
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| − | :Janice: I have three children.
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| − | :Marge: That's nice! How old are they?
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| − | :Janice: Well, the product of their ages is 36.
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| − | :Marge: Ah - I need more information.
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| − | :Janice: The sum of their ages is the number of coins I have in my wallet.
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| − | :Marge: That’s still not enough information.
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| − | :Janice: The oldest one has blue eyes.
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| − | :Marge: Now I know their ages!
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| − | *How can you arrange 6 identical pencils in such as way as to form 4 identical triangles whose sides area are all equal, without modifying the pencils in any way?
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| − | *Divide an L-shaped plot into four equal parts.
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| − | *Someone did a survey to see how many siblings people had. He carried out his statistical research by stopping people at random in the street and asking them how many brothers and sister they had. To his surprise he found that the average number of siblings people had on the street were much higher than the average from a door to door household survey. Unfortunately he hadn't realised that large families are disproportionately over represented on the streets as each family has more siblings out and about.
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| − | *A blind man is all alone in a mountain hut. He has to take two different pills before nightfall today and tomorrow - the pills are identical in shape, weight and size, but one is red and the other one blue. He has two pills of each. But unfortunately he drops them on the floor. While he manages to find all four, they are now all jumbled up. And if he takes two of the same type by accident, he will overdose and die. What should he do?
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| − | ===Questions used===
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| − | {{#lst:CSB_Assignment_Week_1|warm-up}}
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| − | {{#lst:CSB_Assignment_Week_2|warm-up}}
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| − | {{#lst:CSB_Assignment_Week_3|warm-up}}
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| − | {{#lst:CSB_Assignment_Week_4|warm-up}}
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| − |
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| − | ==Utilities==
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| − |
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| − | [http://pediapress.com/code/ PediaPress mwlib] mediaWiki → eBook extension/software.
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| − | <span style="display:none"><section begin=pdf_repository_path />biochemistry.utoronto.ca/steipe/abc/376CEB52AF96EA94<section end=pdf_repository_path /></span>
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