Difference between revisions of "CSB Assignment Week 1"

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<div id="CSB">
 
<div class="b1">
 
<div class="b1">
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Assignments for Week 1
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Assignments for Week 1<br/>
 +
<span style="font-size: 70%">Preparations: Wiki editing, "Systems" and introduction to R</span>
 
</div>
 
</div>
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<table style="width:100%;"><tr>
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<td style="height:30px; vertical-align:middle; text-align:left; font-size:80%;">&nbsp;</td>
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<td style="height:30px; vertical-align:middle; text-align:right; font-size:80%;">[[CSB_Assignment_Week_2|Assignment&nbsp;2&nbsp;&gt;]]</td>
 +
</tr></table>
  
 
{{Active}}
 
{{Active}}
  
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Assigned material will be reflected on next week's quiz. Please remember to contribute to [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/BCB420_Quiz_questions '''quiz questions'''] by Tuesday, 20:00.
+
Assigned material - concepts, exercises and reading - will be reflected in next week's evaluation and feedback session. Please remember to contribute to [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/BCB420_self-evaluation_questions '''self-evaluation questions'''] by Tuesday at noon.
  
  
 
__TOC__
 
__TOC__
  
−
 
−
;Special dates:
 
−
* Post your systems paper by Monday.
 
−
* Do the '''R''' task after Friday.
 
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* Post your quiz questions by Tuesday, 20:00.
 
−
* All other tasks are due by next week's class.
 
  
  
 
==Warm up==
 
==Warm up==
−
A farmer goes to the village pub after a hard day's work and takes his dog with him. The village is two kilometres away, and the farmer walks at a leisurely 4 km per hour. He takes his dog with him, who is impatient to get out and runs at a speed of 8 km per hour. The dog knows the way well and runs ahead to the pub. When the dog arrives, it turns around and runs back until it meets the farmer, then takes off again to the pub, back to the farmer, to the pub and so on until they both arrive. Good dog, the farmer says and gets a few bones for the dog from the innkeeper. How far in total did the dog run?
+
<section begin=warm-up />
 +
<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-01" style="border:solid 1px #000000;padding:10px;background-color:#F9F9FF">
 +
A farmer goes to the village pub after a hard day's work and takes his dog along. The village is two kilometres away, and the farmer walks at a leisurely 4 km per hour. The dog is impatient to get out, it knows the way well and it runs ahead to the pub at a constant speed of 8 km per hour. When the dog arrives, it turns around and runs back until it meets the farmer, then takes off again to the pub, back to the farmer, to the pub, and so on until they both arrive. "Good dog!" says the farmer and gets a few bones for the dog from the innkeeper.  
  
 +
'''How far in total did the dog run?''' <span class="mw-customtoggle-01" style="background:#F2F2FF;padding:5px;font-size:80%;margin-left:50px">[''I&nbsp;don't&nbsp;know...'']</span>
  
−
==Databases and Services==
+
<div class="mw-collapsible-content" style="padding:10px;">
−
Public databases store the raw material of our work and many Web services exist that process it. (Re)familiarize yourself with databases and services that are relevant for bioinformatics and computational systems biology on the Web.
 
−
{{task|
 
−
Access the [[CSB_Web_tools|'''Web tools page''']] on this Wiki, where many resources are listed. Browse the material. Spend some time with the resources in the "Further reading" section:
 
−
* The bionformatics.ca links directory;
 
−
* The NAR database issue;
 
−
* The NAR Web services issue.
 
  
−
* Visit the [http://ncbi.nlm.nih.gov '''NCBI home page'''] and browse the contents of the site.
+
<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-02" style="border:solid 1px #000000;padding:10px;background-color:#F2F2FF">
−
* Visit the [http://www.ebi.ac.uk/ '''EBI home page'''] and browse the contents of the site.
+
Seriously?<br />
 +
Have you thought about this for more than 5 minutes?<br />
 +
Or did you perhaps try to add up the path segments for the dog and get confused?<br />
 +
Maybe you need a hint ... <span class="mw-customtoggle-02" style="background:#EAEAFF;padding:5px;font-size:80%;margin-left:50px">[''Ok.&nbsp;A&nbsp;hint&nbsp;please...'']</span>
  
−
* If you are aware of new resources that are relevant for our objectives, [mailto:bcb420_2015@googlegroups.com '''email the group'''] to share.
+
<div class="mw-collapsible-content" style="padding:10px;">
−
}}
 
  
 +
<div class="mw-collapsible mw-collapsed" id="mw-customcollapsible-03" style="border:solid 1px #000000;padding:10px;background-color:#EAEAFF">
 +
I wouldn't bother adding up the dog's path segments. Perhaps you can take a more global view. <span class="mw-customtoggle-03" style="background:#E2E2FF;padding:5px;font-size:80%;margin-left:50px">[''No.&nbsp;I&nbsp;still&nbsp;don't&nbsp;get&nbsp;it...'']</span>
  
−
&nbsp;
+
<div class="mw-collapsible-content" style="padding:5px;border:solid 1px #000000;background-color:#E2E2FF">
  
 +
It takes the farmer half an hour to reach the inn. The dog runs all this time at a speed of 8 km per hour. So the dog runs a total of 4 kilometres, regardless of the path it takes.
  
−
&nbsp;
+
</div>
 +
</div>
  
−
==Systems==
+
</div>
−
An overview of computational systems biology topics is given on the [[CSB_Introduction|'''introduction page''']] to this section of the Course Wiki.
+
</div>
 +
 
 +
</div>
 +
</div>
 +
<section end=warm-up />
  
−
{{task|
+
==Basic Bioinformatics==
−
* Browse through the material on the  [[CSB_Introduction|'''introduction page''']] after Thursday (I will be updating the page). Some of these papers may be suitable as examples for our project, or - via their pubmed link of related publications - they may be starting points to find other interesting examples.
+
{{vspace}}
 +
The BCH441 material is a course prerequisite. If you ''haven't'' taken the course, work through the assignments. If you ''have'' taken the course, review them briefly.
  
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As we have discussed in class, we are looking for others' work on examples for defining biological "systems" from data.
 
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* Identify a paper where this has been done;
 
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* Write a brief synopsis (one or two sentences);
 
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* Post a link to this paper on the [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/BCB420_2015_Project_Bibliography '''Project Bibliography page of the Student Wiki''']; follow the format of the first entry on that page.
 
−
;This task is due by Monday.
 
  
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* On Tuesday, browse the papers collected on that page so we can discuss the merits of various approaches in class on Wednesday. <small>Note: be prepared to summarize the key idea of ''your'' paper in Wednesday's quiz; be sufficiently familiar with others' papers to be able to contribute to the in-class discussion.</small>
+
{{task|
 +
Access the [[BIO_Assignment_Week_1|'''BCH441 Assignment 1 Page''']] on this Wiki, and begin working through the eleven assignments. There are forward- and back-links at the top and bottom of each page. Don't worry that they are labelled as ''inactive''. I may be editing the pages, but will try not to break anything while doing so. If in doubt, ask. Use your discretion regarding the level of detail that you work through, but don't fool yourself into going thorough this task superficially. Course evaluations will assume that you are are '''familiar and competent''' with the tools, resources, databases and concepts that are covered in these assignments.
  
 
}}
 
}}
  
 +
{{vspace}}
 +
 +
==Systems==
 +
An overview of computational systems biology topics is given on the [[CSB_Systems|'''"Systems" page''']]. In particular we have adopted the following "Systems" definition:
  
−
&nbsp;
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{{#lst:CSB Systems|systems_definition}}
  
 +
Navigate to the [[CSB_Systems|'''"Systems" page''']] to complete the following tasks:
  
−
&nbsp;
+
{{#lst:CSB Systems|exercises}}
  
−
==Student Wiki ==
+
{{vspace}}
−
;If you have taken BCH441, you have already done this task. Please take a moment however to add a category tag to your page: <code><nowiki>[[Category:BCB420_2015]]</nowiki></code>.
 
  
 +
{{#lst:MediaWiki|wiki_assignment}}
  
−
Collaboration is a common theme for modern lab work and a Wiki is a great way to share and seamlessly update information in groups - or just for yourself. Probably the most sophisticated Wiki software is MediaWiki, a set of PHP scripts that is under continuous development by the Wikimedia foundation; it is the same software that runs Wikipedia. This is open source, free software that is easy to install, is well documented and requires very little resources other than a machine that runs a MySQL database server and an Apache Web server. Numerous extensions exist (and extensions are not hard to write); they enhance the already rich functionality. But let's start with small steps. By now, you should already have an account on the Student Wiki, and I have configured the Wiki so that
+
=='''R'''==
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* only logged in users can view the pages;
+
Please work through the introductory '''[[R tutorial]]''' on this Wiki.
−
* all logged in users can create and edit pages at will.
 
  
−
This means you could edit pages that don't "belong" to you. Respect the "House Rules" I have posted on the Main Page and don't edit other's things without permission, even if you can think of a particularly witty comment or hilarious prank. If you want to comment on a page: every page has an associated "Discussion" page that you can freely edit. Remember to "sign your name" to discussion entries.
+
<section begin=assignment_footer />
 +
{{vspace}}
  
−
{{task|
+
;That is all.
  
−
* Access the [http://steipe.biochemistry.utoronto.ca/abc/students '''Student Wiki];
+
{{Vspace}}
−
* log in and navigate to your user page;
 
−
* open the "Help" link in the left-hand sidebar in a separate tab;
 
−
* follow the link to the "Editing" page on the Student Wiki;
 
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* try and learn basic editing syntax by editing your User Page:
 
−
** enter your name,
 
−
** your major(s), specialist program, year of study - or your lab and thesis theme if you are a graduate student;
 
−
** your special interests and/or skills in the field;
 
−
** enter your eMail address.
 
−
** Add a category tag to your User page (see above) . <small>All pages with this tag are accessible via the link in the sidebar.</small>
 
  
−
Feel free to look at my User Page for code examples: clicking on the edit link will show you the source text. <small>How do you find my User Page? Good question ... </small>
+
== Footnotes and references  ==
  
−
* Create a '''subpage to your User Page'''; call it "Resources" or something similar. <small>Note: the link '''MUST''' be in your "User space". If you don't add the prefix <code>User:''yourname''/...</code> before your page name, the new page will end up in the main "namespace". I'll then have to delete it. That's not good because you have then failed this part of the assignment. Make sure you know what you are doing, for example by looking at the code on my User Page, asking someone who knows, or asking on the mailing list.</small> 
+
{{Vspace}}
−
* Put some text on your new page - perhaps a link to a Wikipedia article, or to PubMed, or to the NCBI. Make sure you understand the difference between an internal link and an external link (they have slightly different formats), and you understand the concept of namespace and categories. Also add a category link to that page.
 
−
* Play around some more. Feel free to ask how to go about achieving a particular effect that you may have seen elsewhere.
 
  
−
Before you are done, you should be comfortable with the following mark-up conventions and concepts:
+
<references />
−
* Login and accessing your user page;
 
−
* viewing a page's history;
 
−
* basic text formatting;
 
−
* "signing" your name;
 
−
* creating internal and external links;
 
−
* creating sections headers on a page on multiple levels;
 
−
* reverting a changed page to an earlier version;
 
−
* creating a new page (as a subpage of an existing page);
 
−
* the concept of namespaces - especially the default ("main") and <code>User:</code> namespace;
 
−
* the concept of categories.
 
  
−
I expect that there may be aspects of the Wiki you find puzzling, it is after all a complex piece of software that supports the world's largest collaborative project and one of the busiest sites on the Internet. Do ask about these things on the mailing list. My first encounter with Wikis is a while back and I can't remember everything I was initially confused about.
+
{{Vspace}}
  
−
}}
+
----
  
 +
{{Vspace}}
  
−
&nbsp;
+
;Ask, if things don't work for you!
 +
: If anything about the assignment is not clear to you, please ask on the mailing list. You can be certain that others will have had similar problems. Success comes from joining the conversation.
  
 +
* Do consider how to ask your questions so that a meaningful answer is possible. the following two links:
 +
** [http://stackoverflow.com/help/mcve ''How to create a Minimal, Complete, and Verifiable example''] on stack'''overflow''' and ...
 +
** [http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example ''How to make a great <b>R</b> reproducible example'']
  
−
&nbsp;
+
:... are <u>required</u> reading.
−
=='''R'''==
 
−
An introductory task regarding the statistical workbench and programming language '''R''' will be posted here by Friday afternoon. A separate announcement will follow.
 
  
 +
<span id="myAnchor"></span>
  
−
&nbsp;
+
{{Vspace}}
  
 +
<section end=assignment_footer />
  
−
&nbsp;
+
<table style="width:100%;"><tr>
 +
<td style="height:30px; vertical-align:middle; text-align:left; font-size:80%;">&nbsp;</td>
 +
<td style="height:30px; vertical-align:middle; text-align:right; font-size:80%;">[[CSB_Assignment_Week_2|Assignment&nbsp;2&nbsp;&gt;]]</td>
 +
</tr></table>
  
 
[[Category:Computational_Systems_Biology]]
 
[[Category:Computational_Systems_Biology]]
−
 
 
</div>
 
</div>

Latest revision as of 19:49, 19 January 2016

Assignments for Week 1
Preparations: Wiki editing, "Systems" and introduction to R

  Assignment 2 >

Note! This assignment is currently active. All significant changes will be announced on the mailing list.

 
 

Assigned material - concepts, exercises and reading - will be reflected in next week's evaluation and feedback session. Please remember to contribute to self-evaluation questions by Tuesday at noon.



Warm up

A farmer goes to the village pub after a hard day's work and takes his dog along. The village is two kilometres away, and the farmer walks at a leisurely 4 km per hour. The dog is impatient to get out, it knows the way well and it runs ahead to the pub at a constant speed of 8 km per hour. When the dog arrives, it turns around and runs back until it meets the farmer, then takes off again to the pub, back to the farmer, to the pub, and so on until they both arrive. "Good dog!" says the farmer and gets a few bones for the dog from the innkeeper.

How far in total did the dog run? [I don't know...]

Seriously?
Have you thought about this for more than 5 minutes?
Or did you perhaps try to add up the path segments for the dog and get confused?
Maybe you need a hint ... [Ok. A hint please...]

I wouldn't bother adding up the dog's path segments. Perhaps you can take a more global view. [No. I still don't get it...]

It takes the farmer half an hour to reach the inn. The dog runs all this time at a speed of 8 km per hour. So the dog runs a total of 4 kilometres, regardless of the path it takes.


Basic Bioinformatics

 

The BCH441 material is a course prerequisite. If you haven't taken the course, work through the assignments. If you have taken the course, review them briefly.


Task:

Access the BCH441 Assignment 1 Page on this Wiki, and begin working through the eleven assignments. There are forward- and back-links at the top and bottom of each page. Don't worry that they are labelled as inactive. I may be editing the pages, but will try not to break anything while doing so. If in doubt, ask. Use your discretion regarding the level of detail that you work through, but don't fool yourself into going thorough this task superficially. Course evaluations will assume that you are are familiar and competent with the tools, resources, databases and concepts that are covered in these assignments.



 

Systems

An overview of computational systems biology topics is given on the "Systems" page. In particular we have adopted the following "Systems" definition:


S Y S T E M

A set of collaborating entities with functional relationships that are more specific between members of the set than they are with other entities .


Navigate to the "Systems" page to complete the following tasks:


Task:

  • Can you improve on our current systems definition? Can you identify gaps in the definition? Problems? Ambiguities? Tautologies? Other issues? If you can, discuss this on the course mailing list.
  • Browse through the material on the "Systems" page. Some of the papers referenced there may be suitable as starting points for our project, or - via their pubmed link of related publications - they may be starting points to find other interesting examples.
  • If you are aware of interesting recent papers - both conceptual, or examples of good, recent work - e-mail me to add them or post a note about the paper on our course mailing list.



 


Wiki Assignment

This page is part of my Course Wiki which contains the syllabi and other course resources that (usually) only I edit. To actively collaborate, host students' contributions and submit assignments, I have provided a second, independent Wiki, the Student Wiki. This is a reasonably private environment: only users who have accounts on the system[1] and are logged in can view and edit pages. This means in order to participate in the course you must have an account on the Student Wiki and that should have been set up at the first lecture. Contact me if you still need an account.


If you have previously worked through this task for a different course, take a few moments to review the points anyway. Then add a correct, current category tag to your user page[2]


 
For BCH441/BCH1441: [[Category:BCH441_2016]]
For BCB410: [[Category:BCB410_2016]]
For BCB420/JTB2020: [[Category:BCB420_2016]]


 

Collaboration is a common theme for modern lab work and a Wiki is a great way to share and seamlessly update information in groups - or just for yourself. Probably the most sophisticated Wiki software is MediaWiki, a set of PHP scripts that is under continuous development by the Wikimedia foundation; it is the same software that runs Wikipedia. This is open source, free software that is easy to install, is well documented and requires very little resources other than a machine that runs a MySQL database server and an Apache Web server. Numerous extensions exist (and extensions are not hard to write); they enhance the already rich functionality. But let's start with small steps. By now, you should already have an account on the Student Wiki, and I have configured the Wiki so that

  • only logged in users can view the pages;
  • all logged in users can create and edit pages at will.

This means you could edit pages that don't "belong" to you. Respect the "House Rules" that are posted on the Main Page of the Student Wiki and don't edit other's things without permission, even if you can think of a particularly witty comment or hilarious prank. If you want to comment on a page: every page has an associated "Discussion" page (sometimes this is called the "talk page") that you can freely edit. It is accessible via a tab at near the top of each page. Remember to "sign your name" to discussion entries.

Task:


  • Access the Student Wiki;
  • log in and navigate to your user page;
  • open the "Help" link in the left-hand sidebar in a separate tab;
  • follow the link to the "Editing" page on the Student Wiki;
  • learn and practice basic editing syntax by editing your User Page:
    • enter your name,
    • your major(s), specialist program, year of study - or your lab and thesis theme if you are a graduate student;
    • your special interests and/or skills in the field;
    • enter your eMail address.
    • Add a category tag to your User page (see above).
    • I propose adding a small, recognizable picture of yourself to the page. There's probably a regulation somewhere that says I can't require this due to "privacy" considerations. But (a) it doesn't have to be a formal portrait, something like a Facebook profile is fine as long as we can begin recognizing each other in class, and (b) if we collaborate with each other in class, on the mailing list, on the Wiki and elsewhere, it's really important that we can associate a name with a person. it actually helps me a lot when I define participation marks.

Feel free to look at my User Page for code examples: clicking on the edit link will show you the source text. How do you find my User Page? Good question ...

  • Create a subpage to your User Page; call it "Resources" or something similar. Note: the link MUST be in your "User space". If you don't add the prefix User:yourname/... before your page name, the new page will end up in the main "namespace". I'll then have to delete it. That's not good because you have then failed this part of the assignment. Make sure you know what you are doing, for example by looking at the code on my User Page, asking someone who knows, or asking on the mailing list.
  • Put some text on your new page - perhaps a link to a Wikipedia article, or to PubMed, or to the NCBI. Make sure you understand the difference between an internal link and an external link (they have slightly different formats), and you understand the concept of namespace and categories. Also add a category link to that page.
  • Play around some more. Feel free to ask how to go about achieving a particular effect that you may have seen elsewhere.

Before you are done, you should be comfortable with the following mark-up conventions and concepts:

  • Login and accessing your user page;
  • viewing a page's history;
  • reverting a changed page to an earlier version;
  • basic text formatting;
  • "signing" your name;
  • creating internal and external links;
  • creating sections headers on a page on multiple levels;
  • creating a new page (as a subpage of an existing page);
  • the concept of namespaces - especially the default ("main") and User: namespace;
  • the concept of categories.

I expect that there may be aspects of the Wiki you find puzzling, it is after all a complex piece of software that supports the world's largest collaborative project and one of the busiest sites on the Internet. Do ask about these things on the mailing list. My first encounter with Wikis is a while back and I can't remember everything I was initially confused about.



 


R

Please work through the introductory R tutorial on this Wiki.


 
That is all.


 

Footnotes and references

 
  1. ↑ All users on the student wiki are current or former UofT students, these pages are not accessible to the general public.
  2. ↑ The tag is typically added to the bottom of the page, though it can realy appear anywhere. It's fine to have more than one category tag, pages can belong to more than one category.


 


 
Ask, if things don't work for you!
If anything about the assignment is not clear to you, please ask on the mailing list. You can be certain that others will have had similar problems. Success comes from joining the conversation.
... are required reading.


 


  Assignment 2 >
Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=CSB_Assignment_Week_1&oldid=8429"