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ANNOUNCEMENTS
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Final grades.
- Examples of good thesis proposals
(according to the Committee Members). These thesis proposals are posted with the
permission of the authors: I,
II,
and III.
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Lecture: Mondays from 1:00 PM to 1:50 PM - FA4-311
Lab: Mondays from 2:00
PM to 4:45 PM - FA1-206
Course Website (please, bookmark
it):
http://www.csulb.edu/~efernand/resmet/
Instructor: Esteban Fernández-Juricic
Phone:
562-985-7597 (but you can
reach me faster by e-mail)
E-mail:
efernand@csulb.edu
Instructor's website: http://www.csulb.edu/~efernand/
Office: PH1-226
Office hours:
Thursdays from 1:30 PM to 3:30 PM (or by
appointment)
This class does NOT require a textbook. However, if
students insist on buying a textbook, I recommend: Experimental Design
for the Life Sciences by Graeme D. Ruxton & Nick Colegrave. Oxford University
Press.
Course description:
Graduate students will learn the basic
aspects of research design, including statistics, literature searches, and
thesis proposal writing. The goal is to provide tools that will allow graduate
students to initiate their research projects. This course is required for all
graduate students in the first or second semester of the program.
My
expectations of students:
- attend classes
consistently,
- be prepared for class meetings
(read the papers/complete the assignments for each class),
- participate actively in class
discussions and group activities,
- be respectful of your peers
(including myself), and
- take advantage of this course as
an opportunity to learn and think!
What students can expect from the
Instructor:
- strive to create a positive
learning environment in the classroom,
- encourage you to be actively
engaged in your learning,
- bring enthusiasm about research
design in the life sciences,
- be respectful and
supportive,
- try to challenge you in positive
and constructive ways to improve your learning experience, and
- show up to each class on time and
well-prepared.
Evaluation:
1-
Attendance to classes (25 points)
2-
Involvement in class discussions/activities (25 points)
3-
Informal oral presentation (10 points)
4- Weekly assignments (140 points)
5-
Mid-term lecture exam (100
points)
4-
Final Exam (50 points)
TOTAL: 350 points.
Grading system:
A:
90-100% of the points
B:
80-90% of the points
C:
70-80% of the points
D:
60-70% of the points
F:
< 60% of the points
Slight
adjustments may be made at the end of the semester
according to the class curve.
Absences
Excused absences include: (a) illness or injury to the
student, (b) death, injury, or serious illness of an immediate family member,
(c) religious reasons, (d) jury duty or government obligation, and (e)
University sanctioned or approved activities. The instructor should be informed
about excused absences within 48
hours.
For more information, please read the CSULB
attendance policy carefully at:
http://www.csulb.edu/divisions/aa/grad_undergrad/senate/documents/policy/2001/01/
Make up exams
Make-up exams will ONLY be allowed for justified
absences. I must be informed within 24 hours of missing the exam due date.
Make-up exams may be oral exams.
Late work
Students will
be penalized for late work by deducting 15% per day of the total
point load of that activity for two days. Afterwards, the work will not be graded, and
students will not earn credits for that activity (= 0 points).
Policy on Withdrawals
It is
the student’s responsibility to withdraw from classes. Instructors
have no obligation to withdraw students who do not attend courses, and may
choose not to do so.
Please, check
this website
to find information about withdrawing from class:
http://www.csulb.edu/divisions/aa/grad_undergrad/senate/documents/policy/2002/02/
Accommodation
It is
the student’s responsibility to notify the
instructor in advance of the need
for accommodation of a disability.
Cheating and Plagiarism
Written work that you hand in is assumed to be original
unless your source material is documented appropriately. Using the ideas or
words of another person, even a peer, or a web site, as if it were your own,
is
plagiarism.
More specifically, the
following actions are considered plagiarism (this was taken verbatim from
http://www.plagiarism.org/learning_center/what_is_plagiarism.html): "(a)
turning in someone else's work as your own; (b) copying words or ideas from
someone else without giving credit; (c) failing to put a quotation in quotation
marks; (d) giving incorrect information about the source of a quotation; (e)
changing words but copying the sentence structure of a source without giving
credit; and (f) copying so many words or ideas from a source that it makes up
the majority of your work, whether you give credit or not (see our section on
"fair use" rules)"
Cheating and plagiarism are serious academic
offenses. Students should read the section on cheating and plagiarism in
the CSULB catalog.
Furthermore, students should be aware that Faculty members
have a range of academic actions available to them in cases of cheating and
plagiarism from arranging a conference, to failing a student on that particular
work, to failing a student in a course, to referring the case to judicial
affairs.
Regular instructor-student communication out of class:
Announcements and messages to
the class may come by e-mail through
BeachBoard. If you do not
check your CSULB e-mail account regularly, but use another account instead,
please set your CSULB account in BeachBoard so that it will forward messages to your other
account.
Computer Help! The CSULB Technology Help Desk is now available for
students. You may check
the Help Desk
at:
http://www.csulb.edu/divisions/aa/academic_technology/thd/
or call
985-4959.
Selection of papers
(primary literature)
You
should select papers from primary literature (try to balance classic and recent
papers). You can search for these
papers in different databases (MY
RECOMMENDATION:
Web of Science).
IMPORTANT: If you do not find a copy of a paper at the Library, you
could request it from the Library (free service for CSULB students, but it takes about 10 days to get
the papers) or directly from the
author through e-mail.
Reading primary literature
While reading papers for class discussions or presentations,
focus on how the paper solves a problem /
answers a question / tests a hypothesis.
General assessment of a paper:
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Identify the novelty of the paper.
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Identify the hypothesis/es and
prediction/s.
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Identify a flaw in its design or in the analyses or in
the interpretation of data.
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Identify the relevance of the study to other areas.
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Identify the take-home message of the
paper.
Some specific questions you are expected to
ask/answer:
What are the
assumptions of the hypotheses being tested?
Do the
results support the hypotheses or more work is necessary?
Are the
results consistent with the conclusions of the paper?
Are the
experimental and statistical methods appropriate?
Are there
alternative ways of testing the same hypotheses using different methodologies
and data?
Does the
paper provide a novel insight? Why?
What are the
theoretical and practical implications?
Is the paper
difficult to understand because it is poorly presented or because you lack
sufficient background in the topic area?
Useful online general guidelines to
write up scientific papers (they apply to proposals as well):
http://abacus.bates.edu/~ganderso/biology/resources/writing/HTWtoc.html
Useful online guidelines to review
scientific papers:
http://www.bcl.hamilton.ie/~bap/how-to-review.html
http://advan.physiology.org/cgi/content/full/27/2/47/T1
http://esapubs.org/esapubs/reviewers.htm
Student informal
presentation:
A brief account of what
has led you to the decision of doing a Masters, why you have chosen CSULB to do
your Masters, why you have chosen a particular lab, and what your professional
goals are. These presentations are casual, but you may use Power Point to show
pictures or tell us funny anecdotes. Each presentation should not last more than
3-5 minutes. If you go over this allocated time, points will be deducted. Students will be assigned the first
class the order in which they will be presenting.
Assignments:
Assignments will be due at the end of the lab class
(4:45 PM) or at 4:45 PM the next day unless otherwise noted in the syllabus.
Format for assignments: Single spaced. Write down on the right hand top
corner your name (LAST, FIRST), your supervisor's name, and your e-mail.
Fall 2007: Class schedule
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Date |
Lecture topic/Assignments for the next class |
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Sept. 4th |
Labor day (campus closed) |
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Sept. 10th
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LECTURE:
Writing your thesis proposal (1): Guest lecture Dr. Judith Brusslan (Website,
E-mail).
Download lecture.
Download instructions on
how to cite the literature in your thesis proposal.
LAB: NO lab class (Instructor in a conference). HOWEVER,
students are expected to complete the following
assignments and turn them in on Sept. 17th (hard copies, one page per
assignment) at 1:00 PM.
Assignment 1:
Define your research
topic (not your specific research project) by talking with your advisor.
Justify the importance of your research topic. Summarize in maximum 100 words
(no minimum). (10
points)
Assignment 2:
What research areas
does your lab have? Summarize in maximum 200 words (no minimum).
(10
points)
Assignment
3: Find out the 1-2 most relevant
contributions to the literature that your advisor has made, read
the paper/s, cite it/them following the format: Authors. Year.
Title. Journal Volume: page numbers, and provide a brief comment about
the paper/s (goal, take-home message, scientific relevance). Maximum 200
words (no minimum).
(10
points)
Format for assignments: Single spaced. Write down on the right hand top
corner your name (LAST, FIRST), your supervisor's name, and your e-mail.
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Sept. 17th |
LECTURE:
Goals of the course and analysis of syllabus.
Writing your thesis proposal (2): (a) Writing for other scientists and
for reviewers. (b) Secrets of successful thesis proposal writing. (c)
Planning your writing realistically. Download
lecture.
LAB:
Download handout
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Why do experiments need to be
designed? (c) The costs of a poor experimental design. (d) The relationship between
experimental design and statistics. (e) What does it take to earn a
Masters at CSULB?
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Locating and using biological literature: (a) Differences between
primary and secondary sources. (b) Start by consulting general
references. (c) CSULB Library. (d) Scientific databases: Web of Science,
PubMed, Biosis. (e) Plan your search vocabulary carefully. (f) When is
Google acceptable? (g) How to read a scientific paper: tips.
Students’ informal presentations (3-5 min per student): Tom Thompson.
Colleen O'Rourke, Victor Kowalski, and Meghan
Rodela
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Students are expected to complete the following
assignments by the end of the lab session and turn them in the
next day as hard copies (one page per assignment) in
my mailbox (Biology Department Office) at 4:45 PM.
Assignment 1:
Search for 10 papers in the literature
relevant to your research topic, cite them following the format:
Authors. Year. Title. Journal Volume: page numbers. Additionally,
please justify why you chose each of the papers.
(10
points)
•
Assignment 2:
Subscribe to the TOC (Table of Contents) of (at least) 10 journals in your field.
Write down the names of those journals.
(10
points)
Format for assignments: Single spaced. Write down on the right hand top
corner your name (LAST, FIRST), your supervisor's name, and your e-mail.
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Sept. 24th |
LECTURE:
Introduction to experimental design: (a) The scientific method. (b) Scientific
questions. (c) Hypotheses and predictions. (d) Producing the strongest
evidence with which to challenge a hypothesis. (e) The importance of
pilot studies and preliminary data. (f) Experimental manipulation vs.
natural variation. Download lecture.
LAB:
- Dr.
Bryan Rourke: guest
speaker. Website.
E-mail.
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Students’ informal presentations (3-5 min per student):
Djekic, Kristina; Mace, Cristhian;
Pepo, Michael
- BEFORE CLASS:
(a) For a discussion of how to read a scientific paper refer
to guidelines to read primary literature papers in the syllabus. (b)
Read the INTRODUCTION only of the following papers:
paper 1 (supplemental
material), paper 2,
paper 3.
- Students are expected to complete the following
assignment by the end of the lab session and turn it in the
next day as a hard copy in my
mailbox (Biology Department Office) at 4:45 PM.
Assignment 1:
Based on the
INTRODUCTION sections
you read, produce a bulleted write-up
considering the following items FOR EACH PAPER: (1) main question the paper addressed, (2)
main goal of the
paper, (3) hypothesis/es, and (4) prediction/s.
(10
points) Format for assignments: Single spaced. Write down on the right hand top
corner your name (LAST, FIRST), your supervisor's name, and your e-mail.
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Oct.
1st |
LECTURE:
General Linear Model
Language. Download lecture
LAB:
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Students’ informal presentations (3-5 min per student):
Belanger, Eileen; Choi, Su Ji;
Corona, Emily
- General Linear
Models: examples and practice.
Download MINITAB files: file 1,
file 2.
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Students are expected to complete the following
assignment by the end of the lab session and turn it in the next
day as a hard copy in
my mailbox (Biology Department Office) at 4:45 PM.
Assignment 1: Think carefully and write up the question, hypothesis, and
prediction of your thesis proposal taking into account General Linear
Model Language. No word limit.
(10
points) Format for assignments: Single spaced. Write down on the right hand top
corner your name (LAST, FIRST), your supervisor's name, and your e-mail.
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Oct.
8th |
LECTURE:
General Linear Model
Language II. Download lecture
LAB:
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No student informal presentations today.
- General Linear
Models: examples and practice.
Download handout.
Download MINITAB files: file 1
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Students are expected to complete the following
assignment by the end of the lab session and turn it in the next
day as a hard copy in
my mailbox (Biology Department Office) at 4:45 PM.
No assignments accepted by e-mail, please.
Assignment 1: Think AGAIN carefully and write up the
question, hypothesis,
prediction, at least one GLM model, the sample size, and the main
aspects of your sampling procedures of your thesis proposal. No word limit.
(10
points) Format for assignments: Single spaced. Write down on the right hand top
corner your name (LAST, FIRST), your supervisor's name, and your e-mail.
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Oct.
15th |
LECTURE:
Sampling: (a) Between-individual variation. (b) Replication. (c) Pseudoreplication. (d) Randomization. (e) Choosing the 'right' sample
size. Download lecture.
LAB:
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Students’ informal presentations (3-5 min per student):
Hoiness,
Robert; Espinoza, Mario; Farrugia, Thomas
- Practice on how
to estimate sample size. Download material. Please, download the following
program and install it in your computer (it is free):
http://www.psycho.uni-duesseldorf.de/aap/projects/gpower/
Students are expected to complete the following
assignment by the end of the lab session and turn it in the next
day as a hard copy in
my mailbox (Biology Department Office) at 4:45 PM.
Assignment 1:
Summarize in text or schematically the details of
the sampling procedures of your thesis proposal keeping in mind the
ideas of replication, treatments, randomization, and sample size.
(10
points)
Format for assignments: Single spaced. Write down on the right hand top
corner your name (LAST, FIRST), your supervisor's name, and your e-mail.
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Oct. 22th |
LECTURE: -
Different experimental designs I: (a) Controls. (b) Completely
randomized and factorial experiments. Download
lecture.
LAB:
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Different experimental designs II: (c) Blocking. (d) Within-subject
designs. (e) Split-plot designs.
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Students’ informal presentations (3-5 min per student):
Flores, Daisy; Hall, Wendy; Cuellar,
Danny
- Students are expected to complete the following
assignment by the end of the lab session and turn it in the next
day as a hard copy in my mailbox (Biology Department Office) at 4:45 PM.
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Assignment 1: Summarize in text or
schematically the whole experimental design of your
thesis.
(10
points)
Format for assignments: Single spaced. Write down on the right hand top
corner your name (LAST, FIRST), your supervisor's name, and your e-mail.
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October 29th |
LECTURE:
Presenting your ideas with Power
Point: myths and recommendations.
LAB:
- Dr. Kevin Sinchak:
guest speaker.
Website. E-mail.
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Mid-term exam. Duration: 1:45 min. Download
sample questions.
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Nov.
5th |
LECTURE:
Learning to criticize
constructively and receive constructive criticism in science. Student
examples. Discussion class. Download: (a)
handout, (b) example of Intro
without and
with corrections, and (c)
journal guidelines regarding
how to write a scientific paper.
LAB:
- Dr. Kelly Young:
guest speaker.
Website. E-mail. Download her
lecture.
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Students’ informal presentations (3-5 min per student):
Joseph, Alton; Kantak, Sangeeta;
Kimoto, Maryann
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Students are expected to complete the following
assignment by the end of the lab session and turn it in the next
day as a hard copy in my mailbox (Biology Department Office) at 4:45 PM.
-
Assignment 1:
Produce a bulleted outline of your thesis proposal,
describing the main ideas of the different paragraphs that will be in
the Introduction. No word limit. Second semester students will be
allowed to produce an outline of the Power Point presentations for their
thesis defense.
(10
points)
Format for assignments: Single spaced. Write down
on the right hand top corner your name (LAST, FIRST), your supervisor's
name, and your e-mail.
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Nov. 12th |
Veteran's Day (campus closed) |
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Nov.
19th |
LECTURE:
Taking measurements: (a) Calibration. (b) Inaccuracy and imprecision.
(c) Recording data. (d) Keeping a carefully organized notebook.
Download
lecture.
LAB:
-
Students’ informal presentations (3-5 min per student): Loke, Kerri;
Meas, Rithy; Nguyen, Tien
- Problems and solutions
regarding observer bias.
Repeatability
index: download material.
-
Students are expected to complete the following
assignment by the end of the lab session and turn it in the next
day as a hard copy in my mailbox (Biology Department Office) at 4:45 PM.
Assignment 1: Produce a new version of the outline of your thesis proposal,
describing the main ideas of the different paragraphs that will be in
the Introduction, including the hypothesis/prediction, and in the Methods.
If you have time, please, write up the draft of the first paragraph of
the Introduction section. No word limit.
Second semester students will be allowed to work on
their Power Point presentations for their thesis defense.
(10
points)
Format for assignments: Single spaced. Write down
on the right hand top corner your name (LAST, FIRST), your supervisor's
name, and your e-mail.
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Nov. 26th |
LECTURE:
Managing and curating data: (a) Managing raw data. (b) Storing and
curating the data. (c) Checking the data. (d) Transforming the data. Download
lecture.
LAB:
-
Transforming the data. Data management flow chart:
download. How to get a
dataset ready for analysis. Exercise on data
entry. Methods to detect outliers and extreme values. Producing a
"random" dataset of your thesis. Download
handout.
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Students’ informal presentations (3-5 min per student):
Passarelli, Bruno; Sanathara, Nayna;
Tai, Yu-Tou
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Students are expected to complete the following
assignment by the end of the lab session and turn it in the next
day as a hard copy in my mailbox (Biology Department Office) at 4:45 PM.
Assignment 1:
Produce a random dataset of your thesis data in Excel. Print it out and
turn it in. Additionally, justify the different columns in a separate
document in Word.
(10
points)
Format for assignments: Write down on the right
hand top corner your name (LAST, FIRST), your supervisor's name, and
your e-mail.
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Dec. 3rd
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LECTURE: Challenges in experimental design in the molecular sciences.
Guest lecture: Dr.
Flora Banuett.
Website. E-mail.
LAB:
- BEFORE CLASS:
Read the "Useful online guidelines to review
scientific papers" presented in the syllabus
-
Students’ informal presentations (3-5 min per student):
Valinluck, Michael; Vu, Nam
-
Students are expected to complete the following
assignment by the end of the lab session and turn it in the next
day as a hard copy in my mailbox (Biology Department Office) at 4:45 PM.
Assignment 1:
Produce the draft of the summary of your thesis
proposal (maximum 400 words, but you do NOT have to write that many
words).
Second semester students will be allowed to work on
their Power Point presentations for their thesis defense.
Share it with a student in a field different from yours and get
some constructive criticism. Revise the summary based on the reviewer's
comments. Write down the name of the student who revised your abstract/Power
Point presentation.
(10
points)
Format for assignments: Single spaced. Write down
on the right hand top corner your name (LAST, FIRST), your supervisor's
name, and your e-mail.
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Dec.
10th |
LECTURE: How does science really work?: (a) publication
expectations, (b) the tournament model, (c) scientific misconduct, (d)
Impact Factors (definition, scope, biases), (e) peer-review process, (f)
new variations of the peer-review process.
Download lecture.
LAB:
-
Students’ informal presentations (3-5 min per student):
Wingard, Claire; Zemel, Hayley
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Students are expected to complete the following
assignment.
Assignment 1:
Work on your final exam! However, in doing so, please, pay attention to
the review of your abstract.
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Dec. 18th
Final exam |
Final exam: Full-length Introduction of your thesis proposal plus a
bulleted outline of the Methods. This outline should include reference
citations.
The
final exam is due at 4 PM in the Department office. Please, turn in a
hard copy and an electronic copy (CD). Furthermore, you are asked to
send an electronic copy of this document to your Thesis Advisor the same
day and explain to him/her the file is the final exam for the Research
Design class.
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Please, note
that occasionally
adjustments in the course schedule or the course
assignments may be necessary. Students will
be notified about changes, if any, and, whenever possible, students will be
consulted in advance about any changes.
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