Difference between revisions of "Eval Sessions"

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<div id="BIO">
 
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<div class="b1">
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Self-Evaluation and Feedback
+
"Quizzes", Self-Assessment and Feedback
 
</div>
 
</div>
  
 
{{Vspace}}
 
{{Vspace}}
  
−
Our in-class evaluations will test your completion of the assignments and allow you to catch up with important concepts.  
+
<!-- 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).
−
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, and apply solution strategies. It may be useful to discuss your understanding with your classmates in person or on the mailing list. Also, at times, you may be asked to bring material to class (see below).
 
  
 
These evaluations (normally) consist of five integrated parts: collecting questions, review, quiz, take-up, and final assessment.
 
These evaluations (normally) consist of five integrated parts: collecting questions, review, quiz, take-up, and final assessment.
 +
-->
 +
 +
BCB420 will have a single quiz to test the specific preparation units assigned for weeks one and two, and general knowledge of introductory bioinformatics.
 +
 +
{{Vspace}}
 +
 +
__TOC__
 +
 +
{{Vspace}}
  
 
<table>
 
<table>
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</td>
 
</td>
 
<td style="padding:5px">
 
<td style="padding:5px">
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Prior to the evaluation session, we will '''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 assess the degree of understanding and ability to put the material 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 will 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.
+
<!-- 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)
  
−
I really need you to think along with the course, and designing your own quiz questions is an excellent way to do this.  remember: '''a part of your participation marks will depend on your contributions to these pages.''' On these pages I have provided a sample question for every week from previous quizzes so you can get an idea of what you may encounter.
 
  
 
</td>
 
</td>
 
</tr>
 
</tr>
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<tr>
 
<tr>
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2:
 
2:
 
</td>
 
</td>
−
<td style="padding:5px">
+
<td style="padding:5px">  
−
We start off each class 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.
+
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. -->
 +
 
 
</td>
 
</td>
 
</tr>
 
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</td>
 
</td>
 
<td style="padding:5px">
 
<td style="padding:5px">
−
'''Write the actual "Quiz"''', it will be about 20 minutes long. You write it with a black or blue pen. The rules are the same as for other academic evaluations: don't cheat. This is actually slightly more responsibility than you might think: it's not the intent that counts, but the action and this means that "not knowing you are committing an Academic Offence" does not mean none has been committed. If there are any questions about what that means for the practice of writing or marking the quiz, ask me for clarification<ref>This includes but is not limited to: 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 use unauthorized aids. Don't communicate with others while the quiz is being written.</ref>.
+
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>
 
</tr>
 
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</td>
 
</td>
 
<td style="padding:5px">
 
<td style="padding:5px">
−
Immediately afterwards you will '''mark your own Quiz''' while we discuss the answers. You will mark with a <span style="color:#DD0000;">'''red'''</span> pen and you will make sure the correct answers are recorded on your Quiz. This is crucial: at some point you need to have a (the?) correct answer written down, either at the outset, or while marking. If the answer still isn't clear to you, ask, ask again, until you understand.
+
'''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 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.
+
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.
  
−
I won't return the quizzes since I need them for reference when I assign final term grades. I also don't want to foster the misconception that you could prepare for the final exam by memorizing answers to quiz questions. Rather we should collaborate on the Quiz Questions section of the Student Wiki and make that a useful resource for intelligent questions and annotated solution strategies. But if you must have them as a record, you may of course take a picture of your quiz.
+
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.
  
 
</td>
 
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</td>
 
</td>
 
<td style="padding:5px">
 
<td style="padding:5px">
−
I will '''confirm your proposed marks''' 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, 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 quiz'''. However, 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 in general that won't be until shortly before grades are due.
+
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.
−
</td>
 
−
</tr>
 
  
−
</table>
+
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.
  
−
{{Vspace}}
+
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].
  
−
==Assigned material==
+
</td>
−
 
 
−
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.
 
−
 
 
−
;Grading
 
−
If the material includes workflow diagrams, concept maps or similar, the following grading rubrics will broadly apply:
 
−
 
 
−
<table cellpadding="5">
 
−
<tr class="sh">
 
−
<td>Category</td>
 
−
<td>Excellent</td>
 
−
<td>Good</td>
 
−
<td>Adequate</td>
 
−
<td>Marginal</td>
 
−
<td>Inadequate</td>
 
 
</tr>
 
</tr>
  
−
<tr><td colspan="6" class="sp"></td></tr>
 
  
−
<tr class="s2">
+
<tr>
−
<td>General<ref>Principles based on the University of Toronto's [http://www.artsci.utoronto.ca/newstudents/transition/academic/grading Grading Policies] (with extensions).</ref></td>
+
<td style="padding:5px; vertical-align: top;">
−
<td>'''Advances the field''': strong evidence of original thinking; good organization; material is understood in broader context; capacity to analyze and synthesize; superior grasp of subject matter with sound critical evaluations; evidence of extensive knowledge base.</td>
+
6:
−
<td>'''Knowledgeable and competent''': evidence of fundamental understanding and operational grasp of subject matter; awareness of context; some evidence of critical capacity and analytic ability; evidence of familiarity with literature.</td>
+
</td>
−
<td>'''Basic understanding''': able to reproduce a majority of facts; basic understanding of the subject matter; ability to develop solutions to simple problems in the material; evidence of exposure to the literature.</td>
+
<td style="padding:5px">
−
<td>'''Significant gaps''': some evidence of familiarity with subject matter; not fully able to reproduce factual knowledge; some evidence that critical and analytic skills have been developed; vague knowledge of literature.</td>
+
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:
−
<td>'''No evidence of competence''': little evidence of even superficial understanding of subject matter; weakness in critical and analytic skills; limited or irrelevant use of literature.</td>
+
*that the correct answer is missing,
−
</tr>
+
*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-->.
−
<tr class="s1">
+
</td>
−
<td>Concepts</td>
 
−
<td>Adds to expected concepts; well balanced between broad perspective and crucial detail.</td>
 
−
<td>All required concepts present; granularity appropriate.</td>
 
−
<td>Contains most main concepts; too broad or too deep in parts.</td>
 
−
<td>Contains a few of the main concepts; granularity appears somewhat arbitrary.</td>
 
−
<td>Contains a limited number of concepts and/or irrelevant ones; haphazard granularity.</td>
 
 
</tr>
 
</tr>
  
 +
</table>
  
−
<tr class="s2">
+
{{Vspace}}
−
<td>Relationships</td>
+
<!--
−
<td>Meaningful and original insights; precise representation of relationships; no ambiguities.</td>
+
==Assigned material==
−
<td>Expected relationships largely complete; relationships meaningful and accurate</td>
 
−
<td>Missing some important relationships; generally correct.</td>
 
−
<td>Many omissions; existing ones not fully thought through; meaning vague.</td>
 
−
<td>Trivial connections only and/or erroneous connections; meaning not clear.</td>
 
−
</tr>
 
  
 +
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>.
  
−
<tr class="s1">
+
{{Vspace}}
−
<td>Organization</td>
+
-->
−
<td>Clear and compelling; cuts through superficial complexity but all essential relationships present; discovers unexpected associations; independently finds appropriate level of abstractions.</td>
+
<!--
−
<td>Thoughtful; clusters and pathways clear; expected relationships present.</td>
+
==Grading==
−
<td>Mostly represents topic adequately; some higher-order relationships shown.</td>
 
−
<td>Not all parts coherent; missing significant structure.</td>
 
−
<td>Choppy; confusing; with erroneous application of principles.</td>
 
−
</tr>
 
  
 +
{{#lst:Grading|Grading}}
  
−
<tr class="s2">
+
{{Vspace}}
−
<td>Form</td>
+
-->
−
<td>Inspiring</td>
+
==Changing marks?==
−
<td>Effective</td>
 
−
<td>Adequate</td>
 
−
<td>Hasty</td>
 
−
<td>Careless</td>
 
−
</tr>
 
  
−
</table>
+
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}}
 
{{Vspace}}
−
----
 
−
 
−
Note: in general, marks will be "holistic" in the sense that a high-level achievement in one category can not simply compensate for an inferior achievement in another category. It is the overall, integrated quality that counts. Therefore it would not make sense to attempt a "marks-breakdown" for these items and in general rubric-based marks negotiations will be pointless.
 
  
 +
==Missed quizzes==
  
−
{{Vspace}}
+
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.
  
−
==Missed quizzes==
+
<!-- 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.
−
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) {{WP|quartile}} of all your quizzes to replace the zeros. This value is easily calculated with the '''R''' <code>summary()</code> function. If all your quizzes have perfect marks and you miss less than the quartile break, the missed quizzes will get perfect marks too.
 
  
  
Line 162: Line 163:
 
# some vector of quiz results. Three quizzes have been missed.
 
# 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)
 
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)
 
summary(x)
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sum(x)
 
sum(x)
−
# [1] 29.75
+
[1] 29.75 #68% of 44
 
   
 
   
  
Line 194: Line 201:
  
 
sum(x)
 
sum(x)
−
[1] 23.5  # Missing an additional quiz has dropped the total marks by 6.25 points.
+
[1] 23.5  # Missing one additional quiz has dropped the marks to 53% of 44,
 +
          # down from 68%.
  
  
 
</source>
 
</source>
  
 +
-->
 +
 +
{{Vspace}}
  
 
==Notes==
 
==Notes==

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"