Difference between revisions of "Eval Sessions"

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<div id="BIO">
 
<div id="BIO">
 
<div class="b1">
 
<div class="b1">
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Quizzes
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"Quizzes", Self-Assessment and Feedback
 
</div>
 
</div>
  
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&nbsp;
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{{Vspace}}
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&nbsp;
 
  
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The in-class quizzes will test your completion of the assignments for last week. They will be 20 to 30 minutes long and given in class in the tutorial time slot. We will have twelve quizzes, one each week.  
+
<!-- Our in-class evaluations - or "Quizzes" - will test whether you completed the assignments and allow you to catch up with important concepts. They may also include questions about the broader context: concepts and methods, especially their computational aspects. Also, at times, you may be asked to bring material to class (see below).
  
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Typical questions will ask about your experiences while going through the assignments, and your basic understanding of concepts - what you where doing and why you were doing it. I try to make these questions easy for anyone who has completed the assignments with an active mind. It should be possible to get a perfect score on all of them. However there may be one question that requires a modicum of careful, structured thinking.
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These evaluations (normally) consist of five integrated parts: collecting questions, review, quiz, take-up, and final assessment.
 +
-->
  
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There may also be questions on the concepts and methods, especially their computational aspects. You may be asked to give your opinion on possible improvements or generalizations and to think through some "problem solving" questions. It may be useful to discuss your understanding with your classmates in person or on the mailing list.
+
BCB420 will have a single quiz to test the specific preparation units assigned for weeks one and two, and general knowledge of introductory bioinformatics.
  
−
You are welcome and encouraged to submit quiz questions to me or to the course mailing list. I always consider these carefully and often include such questions (in slightly modified fashion). It is a chance for me to better understand your background and expectations, and for you to think about the material in a structured way.
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{{Vspace}}
  
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We will pick up the quiz and mark it in class.
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__TOC__
  
 +
{{Vspace}}
  
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==Marking==
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<table>
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*You will mark your own quiz.
 
−
*You must bring a black or blue pen to write the quiz.
 
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*You must bring a <span style="color:red;">'''red'''</span> pen for marking.
 
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*You should write down and explain the right answer to yourself. Write legibly: if I like your explanation I may count the question as correct.
 
−
*You must not make mistakes in your marking. If I find errors in my spot-checks I will mark the quiz as a zero.
 
  
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<tr>
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<td style="padding:5px; vertical-align: top;">
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1:
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</td>
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<td style="padding:5px">
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<!-- Many topics are relevant for quiz questions and while the questions will mostly be focussed on what we are currently '''doing''', the questions are certainly cumulative: material from previous classes is assumed to be known. Topics in approximate order of likelihood include:
 +
 +
# Questions related to assignments;
 +
# Contents of discussions on the mailing list;
 +
# Material discussed in class;
 +
# Information found in pre-reading;
 +
# Information contained in handouts or slides;
 +
# Current scientific breakthroughs;
 +
# ...
 +
-->
 +
 +
The topics that are relevant for this quiz include:
 +
 +
# Principles of R and R programming;
 +
# How to work with Wikis, in particular how to maintain a Lab Journal;
 +
# Configuring your computer for biocomputing;
 +
# General preparation including how to avoid academic offences, Netiquette and how to ask technical questions;
 +
# The genetic code, DNA, RNA and protein sequence and how to manipulate sequences;
 +
# Basic bioinformatics databases
 +
# Functional annotation of genes
 +
# Principles of expression data management and analysis
 +
# Local and global pairwise optimal sequence alignment, BLAST, PSI-BLAST and multiple sequence alignments
 +
# Genome data
 +
 +
 +
(Not: phylogenetic analysis and structural bioinformatics)
 +
 +
 +
</td>
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</tr>
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<tr>
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<td style="padding:5px; vertical-align: top;">
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2:
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</td>
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<td style="padding:5px">
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Prior to the quiz, we will hold a practice quiz. You are also encouraged to discuss preparatory contents on the mailing list or on Slack.<!--'''collect interesting questions''' on the [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/CurrentQuizzes Student Wiki]. A more detailed discussion on Quiz questions is [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/CurrentQuizzes '''there'''], we strive to identify checkpoints in the material that demonstrate your understanding and the ability to put what you have learned into practice. Pure memorization questions will probably not make it to the actual Quiz, good questions should stimulate you to think. Designing, writing, <u>editing, and improving</u> these questions can contribute to your participation mark. I will compile the actual Quiz largely from these questions, so if you know how to answer them, you will be well prepared.
 +
 +
I really need you to think along with the course, and designing your own quiz questions is an excellent way to do this.  -->
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</td>
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</tr>
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<tr>
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<td style="padding:5px; vertical-align: top;">
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3:
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</td>
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<td style="padding:5px">
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We start off the<!--each --> Quiz session with an open ended '''Question and Answer period''' to address and discuss any remaining questions. If you are able to guess what will be on the quiz, good on you: I'll answer every question in class to the best of my ability even if it's exactly what's on the quiz.
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</td>
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</tr>
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<tr>
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<td style="padding:5px; vertical-align: top;">
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4:
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</td>
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<td style="padding:5px">
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'''Take the actual "Quiz"''', it will be about 30 minutes long. I'll hand out the questions, you keep the page '''face down''' on your desk until you may start.
 +
 +
You write the quiz with a black or blue pen. The rules are the same as for other academic evaluations. This includes: Don't write after time is up. Don't look at your neighbour's work. Don't look at the work of the guy next to your neighbour either. Don't show your work to your neighbour. Don't use unauthorized aids. Don't communicate with others while the quiz is being written. Remember though: it's not the intent that counts, but the action. Not knowing you are committing an academic offence does not mean none has been committed, so ask if you are in doubt.
 +
 +
If you are done ahead of time, turn your sheet face-down and put your pen away. Then you can pull out a good book while you are waiting for the time to run down, catch some sleep, or pull out your phone, update your facebook, or see what Lior Pachter's up to. But don't write on your quiz paper again after you have put it away. That would be an academic offence.
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</td>
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</tr>
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<tr>
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<td style="padding:5px; vertical-align: top;">
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5:
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</td>
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<td style="padding:5px">
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Immediately after writing the quiz, you will '''assess how you did''' while we discuss the answers: you will mark your answers with a <span style="color:#DD0000;">'''red'''</span> pen and you will make sure the correct answers are recorded on your sheet: if you got it wrong, point out the error and write down the right answer. This is crucial: at some point you need to have the correct answer written down, either when you originally wrote it, or as you were marking. If the answer still isn't clear to you, ask, ask again, until you understand.
 +
 +
Let me repeat this. If you got something wrong, write down the correct answer (with a red pen).
 +
 +
You are responsible for marking your answers honestly, for prorating partially correct answers correctly, and for recording your final proposed "mark" without error. Please refer to further clarification below. <!-- '''Please understand that this is a trust-based process that requires a high level of academic integrity. If you fail to apply such integrity to your marking, you may be committing an Academic Offence.''' --> You should record your "mark" for your records and if done correctly this will be identical to the final mark that I will assign for the quiz. This will also give you some indication of where you stand, before the course drop date.
 +
 +
I won't return the quizzes since I need them to spot-check marks, and for reference when I assign final term grades. Take a picture for your records, and note down your marks. For all practical purposes, your noted down marks will serve as your guideline of how you did up to the [http://calendar.artsci.utoronto.ca/Sessional_Dates.html drop date].
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</td>
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</tr>
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<tr>
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<td style="padding:5px; vertical-align: top;">
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6:
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</td>
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<td style="padding:5px">
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I will '''confirm your self-assessed results''' while reviewing your work and spot-checking some quizzes in detail. If I find errors including but not limited to:
 +
*that the correct answer is missing,
 +
*that a wrong answer has been marked as correct,
 +
*that an inappropriately high partial mark has been recorded,
 +
*that errors have been made while adding the marks, or that the marks have not been added up at all ...
 +
then I will revise the Quiz mark. This may include further deduction of partial marks, full marks for a question, or for the entire quiz. To be very clear: '''if you mark incorrectly, you may receive zero marks for the entire quiz'''. In addition, if it appears that <!-- there is a pattern of incorrect marking or that --> the error indicates intent, I will consider whether an Academic Offence may have been committed.
 +
 +
If I need to change a mark for a quiz, I will e mail you<!--, but that may not be until shortly before grades are due-->.
 +
</td>
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</tr>
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</table>
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{{Vspace}}
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<!--
 +
==Assigned material==
 +
 +
At times the assignment will ask you to bring material to class and hand it in with your quiz. These materials will always be marked by me. Typically we will discuss this material in our pick-up session. Therefore I can't grant extensions on missing material. If it's not with you at the beginning of class, it's missing<ref>If the material ''replaces'' a quiz, we'll treat it like a missed quiz. If the material is worth ''part of a quiz'', we treat it like a wrong answer.</ref>.
 +
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{{Vspace}}
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-->
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<!--
 +
==Grading==
 +
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{{#lst:Grading|Grading}}
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{{Vspace}}
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-->
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==Changing marks?==
 +
 +
In all cases in which you believe a grade or partial mark is not correct, e-mail me. I will '''not''' adjust marks based on verbal discussions after class, in the corridors, or elsewhere. E-mail me with specifics, and back up your views with evidence. I will correct errors, but please note that marks are not "negotiable" merely on the basis of opinions.
 +
 +
{{Vspace}}
  
 
==Missed quizzes==
 
==Missed quizzes==
−
You may miss as many quizzes as you want, I will initially score these as zero. For your final grade, I will record the marks of the (lower) 25% quartile of all your quizzes, to replace the zeros. You can easily figure out, since we are writing twelve quizzes, this means you will get partial marks for up to three missed quizzes. Conversely, if all your quizzes have perfect marks but you miss two, these two will be counted as perfect scores too.
+
 
 +
If you miss the quiz for documented medical reasons we will schedule a make-up quiz. Note that to preserve equitability, the difficulty of the makeup quiz will be adjusted to consider the added preparation time and knowledge of what was on the original quiz.
 +
 
 +
<!-- You may miss as many quizzes as you want, I will initially score these as zero. For your final grade, I will extrapolate missing marks by replacing them with the (lower) {{WP|quartile}} of all your evaluations. This replacement value is easily calculated with the '''R''' <code>summary()</code> function. If all your quizzes have perfect marks and you miss fewer than the quartile break, the missed quizzes will get perfect marks too.
 +
 
 +
 
 +
To illustrate:
 +
<source lang="R">
 +
 
 +
# some vector of quiz results. Three quizzes have been missed.
 +
x <- c(3.3, 0, 3.2, 3.6, 0, 2.8, 2.5, 4.0, 0, 2.9, 3.7)
 +
 
 +
sum(x)
 +
[1] 26    # 60% of 44
 +
 +
 
 +
 
 +
 +
summary(x)
 +
#  Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
 +
#  0.000  1.250  2.900  2.364  3.450  4.000
 +
 +
# Replace all zero values with 1st. quantile
 +
x[x==0] <- quantile(x, probs=c(0.25))
 +
 +
x
 +
[1] 3.30 1.25 3.20 3.60 1.25 2.80 2.50 4.00 1.25 2.90 3.70
 +
 
 +
sum(x)
 +
[1] 29.75  #68% of 44
 +
 +
 
 +
# Almost the same vector. But four quizzes have been missed.
 +
# I am removing the lowest mark: 2.5.
 +
x <- c(3.3, 0, 3.2, 3.6, 0, 2.8, 0, 4.0, 0, 2.9, 3.7)
 +
 
 +
summary(x)
 +
#  Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
 +
#  0.000  0.000  2.900  2.136  3.450  4.000
 +
 +
x[x==0] <- quantile(x, probs=c(0.25))
 +
x
 +
# [1] 3.3 0.0 3.2 3.6 0.0 2.8 0.0 4.0 0.0 2.9 3.7
 +
 +
# Note that in this case all zeros remain, since the lower quartile is zero.
 +
# You will probably want to avoid this situation and thus miss as few
 +
# quizzes as possible to have a buffer for unexpected situations.
 +
 
 +
sum(x)
 +
[1] 23.5  # Missing one additional quiz has dropped the marks to 53% of 44,
 +
          # down from 68%.
 +
 
 +
 
 +
</source>
 +
 
 +
-->
 +
 
 +
{{Vspace}}
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 +
==Notes==
 +
<references/>
 +
 
 +
 
  
 
[[Category: Bioinformatics]]
 
[[Category: Bioinformatics]]
 
</div>
 
</div>

Latest revision as of 15:54, 19 January 2018

"Quizzes", Self-Assessment and Feedback


 


BCB420 will have a single quiz to test the specific preparation units assigned for weeks one and two, and general knowledge of introductory bioinformatics.


 


 

1:

The topics that are relevant for this quiz include:

  1. Principles of R and R programming;
  2. How to work with Wikis, in particular how to maintain a Lab Journal;
  3. Configuring your computer for biocomputing;
  4. General preparation including how to avoid academic offences, Netiquette and how to ask technical questions;
  5. The genetic code, DNA, RNA and protein sequence and how to manipulate sequences;
  6. Basic bioinformatics databases
  7. Functional annotation of genes
  8. Principles of expression data management and analysis
  9. Local and global pairwise optimal sequence alignment, BLAST, PSI-BLAST and multiple sequence alignments
  10. Genome data


(Not: phylogenetic analysis and structural bioinformatics)


2:

Prior to the quiz, we will hold a practice quiz. You are also encouraged to discuss preparatory contents on the mailing list or on Slack.

3:

We start off the Quiz session with an open ended Question and Answer period to address and discuss any remaining questions. If you are able to guess what will be on the quiz, good on you: I'll answer every question in class to the best of my ability even if it's exactly what's on the quiz.

4:

Take the actual "Quiz", it will be about 30 minutes long. I'll hand out the questions, you keep the page face down on your desk until you may start.

You write the quiz with a black or blue pen. The rules are the same as for other academic evaluations. This includes: Don't write after time is up. Don't look at your neighbour's work. Don't look at the work of the guy next to your neighbour either. Don't show your work to your neighbour. Don't use unauthorized aids. Don't communicate with others while the quiz is being written. Remember though: it's not the intent that counts, but the action. Not knowing you are committing an academic offence does not mean none has been committed, so ask if you are in doubt.

If you are done ahead of time, turn your sheet face-down and put your pen away. Then you can pull out a good book while you are waiting for the time to run down, catch some sleep, or pull out your phone, update your facebook, or see what Lior Pachter's up to. But don't write on your quiz paper again after you have put it away. That would be an academic offence.

5:

Immediately after writing the quiz, you will assess how you did while we discuss the answers: you will mark your answers with a red pen and you will make sure the correct answers are recorded on your sheet: if you got it wrong, point out the error and write down the right answer. This is crucial: at some point you need to have the correct answer written down, either when you originally wrote it, or as you were marking. If the answer still isn't clear to you, ask, ask again, until you understand.

Let me repeat this. If you got something wrong, write down the correct answer (with a red pen).

You are responsible for marking your answers honestly, for prorating partially correct answers correctly, and for recording your final proposed "mark" without error. Please refer to further clarification below. You should record your "mark" for your records and if done correctly this will be identical to the final mark that I will assign for the quiz. This will also give you some indication of where you stand, before the course drop date.

I won't return the quizzes since I need them to spot-check marks, and for reference when I assign final term grades. Take a picture for your records, and note down your marks. For all practical purposes, your noted down marks will serve as your guideline of how you did up to the drop date.

6:

I will confirm your self-assessed results while reviewing your work and spot-checking some quizzes in detail. If I find errors including but not limited to:

  • that the correct answer is missing,
  • that a wrong answer has been marked as correct,
  • that an inappropriately high partial mark has been recorded,
  • that errors have been made while adding the marks, or that the marks have not been added up at all ...

then I will revise the Quiz mark. This may include further deduction of partial marks, full marks for a question, or for the entire quiz. To be very clear: if you mark incorrectly, you may receive zero marks for the entire quiz. In addition, if it appears that the error indicates intent, I will consider whether an Academic Offence may have been committed.

If I need to change a mark for a quiz, I will e mail you.


 

Changing marks?

In all cases in which you believe a grade or partial mark is not correct, e-mail me. I will not adjust marks based on verbal discussions after class, in the corridors, or elsewhere. E-mail me with specifics, and back up your views with evidence. I will correct errors, but please note that marks are not "negotiable" merely on the basis of opinions.


 

Missed quizzes

If you miss the quiz for documented medical reasons we will schedule a make-up quiz. Note that to preserve equitability, the difficulty of the makeup quiz will be adjusted to consider the added preparation time and knowledge of what was on the original quiz.


 

Notes

Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=Eval_Sessions&oldid=10735"