Introductory Synthetic Biology Assignments and
BIOC 313 is an ADVANCED laboratory course and requires greater
independence than BIOC 211. The experimental procedures may
be less demanding than those you performed in BIOC 211, and
you write just one short paper rather than three full-length
research papers. HOWEVER, just because the experiments may
be more "cookbook" does not mean the lab requires less effort.
I place a greater emphasis on analysis, interpretation, and
presentation of data; if you keep a "sloppy" notebook and slap
a proposal together at the last minute without really understanding "why" you
did a procedure and "what" the results mean, you will be disappointed
with your final grade.
Remember, the undergraduate program is a series of steps. Keep
in mind that a level of performance that would result in a
B/B+ or sometimes even an A at the introductory level, does
not (and should not) translate into a high grade at the advanced
We forgive a lot of mistakes early on but you must recall the
lessons learned from these mistakes when you conduct similar
work at an advanced level.
Additionally, the criteria we use to evaluate your performance in an advanced laboratory course are different from those we use in an introductory course.
"Fairness" in this course means everyone is evaluated on the same criteria.
Since everyone does not have the same ability, everyone does not get the same grade; this outcome is not "unfair" but rather is simply reality.
- Please read my Honor Code Policy.
- A total of 200 POINTS is available in this class.
Due dates are subject to change. Do not ask
for an individual extension to a due date because you
have a paper due, or three exams, or you lost your disk; due
dates are set so that you have plenty of time to complete your
work. Don't wait until the night before to start - there is
no penalty for starting early. Notebook pages are due at
the END of each lab session, including self-scheduled
time; the final notebook pages and Table of Contents must be
turned in with your project proposal. Please
read my policy concerning
Contributions of individual assignments are as follows:
- 50 points = Project Proposal (one per Team)
- 50 points = Journal Club Presentation (one per Pair)
- 30 points = Laboratory Notebook (Individual assignment:
graded ONCE, after the lab ends)
- 25 points = Laboratory Citizenship & Performance (Individual
- 10 points = Analysis/Conclusions for Functional
Analysis of Circuits: lab days 7 & 8: TEAM
as an "attachment" as an Assignment in OWL-Space)
- 10 points =
Team Project Presentation (last day of class)
- 10 points = Brainstorming:
TEAM assignment (submitted as an "attachment" as an Assignment
- 5 points = Homework Assignment: Journal Articles
in Synthetic Biology: TEAM assignment (submitted
an Assignment in OWL-Space)
- 5 points = Homework Assignment: Investigation of
Cloning Methods: TEAM assignment (submitted as an "attachment" as
an Assignment in OWL-Space)
- 5 points = Class Participation
(Questions/discussion during guest speakers and student presentations)
- The Project Proposal is 25% of your final
This proposal is a TEAM
project; each member
will receive the SAME grade.
Therefore, EACH of you is responsible for the ENTIRE proposal,
not just the part(s) you worked on.
Project proposals are due the last week of classes: please use
a paper clip (do NOT staple) and place your proposal in my Inbox
outside ABL 326.
- The Journal Club Presentation is
25% of your final grade. Student teams will present the findings
from a journal article in synthetic biology.
I will use the Presentation
Evaluation Form (see 313JClub_eval_F13.pdf in
OWL-Space Resources) to assess your presentation.
- The Lab Notebook is 15% of
your final grade.
You learned how to keep a research quality notebook in BIOC 111/211.
The SAME is expected of you in BIOC 313; it is YOUR responsibility
to review our guidelines for keeping a proper notebook. If
you have questions, please ask.
I will use the BIOC 313 Notebook
grade your lab notebook.
Notebook pages are turned in at the end of each lab meeting;
final notebook pages from AFTER the last day
of lab with your final analyses and conclusions and your Table
of Contents (make a photocopy of the cover page if necessary--do
not tear off the cover!) are due a few days after the last day
You will be graded on an absolute scale by percentage, as in the table. This means that you will not be graded relative to the performance of others in your class.
Grades posted on Esther are FINAL and cannot be changed.
Assessing Laboratory Citizenship and Performance
Created by David R. Caprette, Ph.D., Rice University
Modified by Beth Beason-Abmayr, Ph.D., Rice University
It is highly unlikely that in a real job you will be given
responsibilities that are so well defined that all you have
to do is follow instructions. It is equally unlikely that you
will be solely responsible for an outcome. Undergraduate laboratory
courses, laboratory components to lecture courses, independent
study, engineering design courses, and the like constitute
the experiential part of the curriculum. They give you the
opportunity to apply your cumulative knowledge and experience
to specific problems. In particular, experiential courses enable
you to polish up and apply teamwork skills and to exercise
critical thinking. Participation during the pre-lab discussions
and question/answer sessions after the presentations will be
crucial to your learning. Passive students who do not contribute
to discussions or problem solving are less likely to do well
on assignments and exams.
A completely satisfactory lab performance would be equivalent
to an A. A completely satisfactory performance requires
that the group's performance be satisfactory as well. For example,
if an "unknown individual" throws sharp glass or nondisposable
items in a wastebasket and nobody catches it, everyone loses
points. An exceptional performance will be rewarded with an increase
in score and may include bonus points. Punctuality, safe
conduct in the laboratory, and efficient completion of lab responsibilities
will enter into the evaluation of overall performance.
Expectations and Performance Criteria
You are expected to come on time, fully prepared and alert. You
should be engaged in the work itself and be aware of your surroundings.
You are expected to work efficiently, safely, and responsibly.
Most of the specific criteria listed here characterize an effective
member of a team.
All labs meet in ABL B03 and begin promoptly at 1:00 PM. Showing
up on time is a sign that you are fully engaged in a project,
are responsible, and that you respect your supervisor and coworkers.
When you are late your arrival is likely to be disruptive. For
example, you will interrupt the pre-lab talk for at least some
people if you come in after it starts. As you settle in you will
distract both the instructor and students in the vicinity. You
may miss key instructions and even become a liability, affecting
the efficiency with which your team works, and possibly compromising
Just showing up on time is a sign of courtesy. So is cleaning
up your lab station and keeping common areas such as sinks, balances,
bench tops, hoods, and side benches clean and neat. Be aware
that there are others working around you, and think before you
blurt out a question, possibly interrupting a conversation between
instructor and student. Think before you drop a backpack in the
middle of an aisle, take the last latex glove out of the box,
or pour something into a sink ignoring the fact that the drain
An exceptional performance might involve cleaning up a common
area such as sink or side bench, or pointing out a major safety
During pre-lab talks listen carefully for changes to a protocol,
for the locations of supplies and equipment, for pointers as
to use of equipment, and similar details. Conversing during a
pre-lab talk, fiddling with equipment, working on an assignment,
or sleeping are not recommended behavior. Above all, be awake
and alert. Occasionally a student shows up in lab nearly catatonic.
It is impossible to learn when you are fighting to stay awake.
Get a good night's sleep.
Know the objectives of the day's work and how you will achieve
them. Knowing how you will achieve them involves reviewing the
course web site as well as reading assigned scientific papers
(both for background preparation and for the presentations). Meet
with your team to discuss the lab and divide up tasks. Watch
for opportunities to apply a skill that you have learned in a
previous laboratory session. When the pre-lab work calls for
calculations, have them ready to go when you arrive to lab. If
you do have trouble with pre-lab planning or calculations, give
yourself time to work it out before you get to lab.
Students are considered to be exceptionally well prepared, for
example, when they respond to questions with informative answers,
ask especially relevant questions, or are readily able to adjust
to changes to a lab protocol or troubleshoot an experiment.
Responsibility and Teamwork
Responsible students work safely and are careful about discarding
materials such as broken glass. Responsible people double check
to make sure that they conduct procedures correctly and watch
for signs that something is wrong. They report when stocks are
getting low instead of simply taking the last of something. They
keep common areas clean, sinks and fume hoods clear of debris,
advise others of unsafe or wasteful practices or report such
practices. On the other hand, irresponsible people might waste
supplies or damage equipment, allow their lab partner to make
the same mistake they just made, throw away the samples that
they need the following week, forget to enter data for the team,
or enter data incorrectly.
Exceptionally responsible students focus on the overall goals
of the teaching laboratory and not just their own work. People
who can organize a group and keep the team on track are especially
Students who finish earlier than most while successfully completing
their lab work are usually noted as being exceptionally efficient.
Students who take an exceptionally long time usually do so because
of some omission in a procedure, unfamiliarity with the protocol,
inattention to a pre-lab talk, or in some cases simply being
too meticulous. In any case we will take the effectiveness
of a team into account. One important way to be efficient is
to divide responsibilities so that one team member is working
on one part of a study while the others focus on other parts.
Efficiency requires that you take notes as you go along. Once
you complete your lab work, you should not take more than five
minutes to make the last entry and write a brief summary.
It is especially inefficient to "trade" notes when
your team has finished the lab work--and in fact, it's an honor
code violation. Such practice suggests that you've missed the
whole point of timely recordkeeping. You are all equally responsible
for a complete laboratory record. If you simply copy your teammates'
notes you miss the opportunity to ensure that the notes are complete
and accurate. Communicating with each other during the lab session
allows you to catch each other's mistakes and helps you keep
up with the recordkeeping as you go along.
ADDITIONAL COMMENTS ABOUT LABORATORY PERFORMANCE: We
expect students to follow explicit instructions and to recall
and apply previous training to each experimental procedure.
- You will be assessed each week in the following areas:
- Preparation (e.g., pre-lab calculations) and
familiarity with procedures (you're not expected
to know how to do the procedures already, but you are
expected to have read over the procedures and be familiar
with the "big picture" for the day)
- Lab Citizenship (showing up on time, cleaning
up your area as well as common areas, adhering to
safety instructions, using and storing equipment
properly, handling lab reagents and solutions sensibly,
helping your classmates)
- Proper lab notebook (i.e., updating Table of
Contents BEFORE coming to lab each week, recording
notes DURING experiments, NOT writing on scrap paper
and copying or catching up at the end of lab or exchanging
notebooks with your team at the end of lab)
- Teamwork (collaboration, division of labor, troubleshooting,
and time management)
- Ability to function independently (troubleshooting
and time management)
- Experimental technique (did you obtain reasonable
- You are expected to function both as a member of a TEAM
and as an INDEPENDENT investigator.
Follow the experimental procedures, record the results,
and analyze/interpret your findings.
Accomplishment of the laboratory goals requires contributions
from EACH team member.
If a team member does not carry his/her weight, focuses
only on his/her own work, or is not competent in the
lab please bring this matter to our attention; be honest
and objective (your comments will remain confidential).
A conscientious evaluation of your peers will be appreciated
and will be considered when determining the laboratory
- You do not necessarily earn a high grade in
lab performance by obtaining the expected results (i.e.,
performing the experiment properly); likewise, you do not
necessarily lower your grade if you don't obtain
the expected results. You are evaluated on HOW you get
the results, not the results themselves. And, there are
many factors besides experimental technique (see the list
above) that contribute to the evaluation of your lab performance. In
other words, even if you are unsuccessful in producing
GFP, you can still earn an "A" in lab performance.
You will likely make mistakes, especially with a procedure
that is brand new and strange--that's ok when that happens.
I will help you troubleshoot so you can decide what steps
to take next. Many times when I've made mistakes or something
just didn't work the way it was supposed to I actually
learned more and understood the procedure better than when/if
it worked as expected.
Sometimes experiments fail, or the results don't make sense,
or your findings are at odds with published studies. Because
of time constraints and limited materials you may not be
able to repeat the procedure in a lab course; however,
you should recognize that in a research setting you would
perform the experiment again.
****Come to lab prepared and learn to work effectively
as a TEAM. Focus on learning and you should do fine.****
and Intended Use
Created by B. Beason (firstname.lastname@example.org),
Rice University, 10 January 2008
Updated 22 November 2013