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Computational Biology Seminar (Fall 2023)

Semester: Fall 2023
Website: pitt-biosc1630-2023f.oasci.org
Meeting time: Wednesdays 1:00 PM - 3:30 PM
Location: 206 Eberly Hall

Clear and efficient communication is a crucial—and often neglected—aspect of science. Intentional or unintentional miscommunication of research and data can result in adverse consequences; some examples include a flawed Challenger launch decision, inconsistent usage of units with the Mars Climate Orbiter, poor communication between experts and scientists with the public during the COVID-19 pandemic, and rampant misinformation. Lectures, assignments, and activities for this course are designed to teach you the tools to communicate effectively and comprehend scientific literature in computational biology.

What makes good written or visual communication? The answer is highly subjective. I argue that there is no “correct way” to communicate, and it depends on both the material’s producer and consumer. Some things could make papers or presentations incomprehensible, but everything else that turns “acceptable” into “excellent” is a matter of taste.

Furthermore, it’s essential to recognize that computational biology is a rapidly evolving landscape. To keep up-to-date, we must ensure our working knowledge is broad enough to comprehend and incorporate advancements quickly. We’ll look at many different topics in computational biology, exploring its complex details and the changes it leads to.

My principal goals for this course are to equip you with the tools to:

  • Engage in productive and positive learning experiences and growth;
  • Navigate and understand the various subfields of computational biology;
  • Organize, draft, revise, and finish preparing writing and presentations;
  • Recognize what aspects hamper written (e.g., grammar, organization, formatting) and visual (e.g., color, design, pace) communication;
  • Discover your voice and style of communication;
  • Process and digest information from a variety of different scientific sources.

Outcomes
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After successfully completing this course, students should be able to do the following.

C1. Efficiently search for and identify relevant scientific literature.
C2. Effectively summarize the motivation, methods, and key findings in scientific literature.
C3. Critically evaluate the robustness and validity of methods and analyses.
C4. Interpret and draw meaningful conclusions from biological data.
C5. Assess the transparency, reproducibility, and adherence to open science practices.
C6. Situate articles within the broader scientific literature, recognizing connections, gaps, and novel insights.
C7. Understand the interplay between computational and experimental corroboration.
C8. Communicate scientific ideas and data effectively through clear, concise, and well-structured writing.
C9. Deliver engaging and informative presentations on scientific literature.

Repository
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OASCI / 🏫 Courses / Pitt / biosc1630-2023f

0
0

Grade distribution
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A+ (33.3%)

A (33.3%)

A- (14.3%)

B+ (33.3%)

B (4.8%)

B- (0.0%)

C+ (4.8%)

C (0.0%)

C- (0.0%)

D+ (0.0%)

D (0.0%)

D- (0.0%)

F (0.0%)

Teaching evaluations
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Final
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The following passages are unmodified student responses (19 out of 21) to a Course Survey administered by OMET.

Results

Express your judgment of the instructor’s overall teaching effectiveness
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Mean: 4.37

Standard deviation: 0.76

The standards the instructor set for me were
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Too low: 0

Appropriate: 17

Too high: 2

How many hours per week did you usually spend working on this course outside of classroom time?
#

Less than one hour: 0

One to three hours: 10

Four to six hours: 9

Seven to nine hours: 0

Ten or more hours: 0

The instructor created an atmosphere that kept me engaged in course content
#

Strongly disagree: 0

Disagree: 1

Neutral: 0

Agree: 4

Strongly agree: 14

The instructor was prepared for class
#

Strongly disagree: 0

Disagree: 0

Neutral: 1

Agree: 5

Strongly agree: 13

The instructor treated students with respect
#

Strongly disagree: 0

Disagree: 0

Neutral: 0

Agree: 1

Strongly agree: 18

The instructor was available to me (in-person, electronically, or both)
#

Strongly disagree: 0

Disagree: 0

Neutral: 0

Agree: 3

Strongly agree: 16

The instructor evaluated my work fairly
#

Strongly disagree: 0

Disagree: 0

Neutral: 3

Agree: 5

Strongly agree: 11

The instructor provided feedback that was helpful to me
#

Strongly disagree: 0

Disagree: 0

Neutral: 1

Agree: 5

Strongly agree: 13

I learned a lot from this course. If there is no basis to judge or not applicable, answer N/A
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Strongly disagree: 0

Disagree: 1

Neutral: 2

Agree: 10

Strongly agree: 6

The instructor creates an inclusive learning environment for all students
#

Strongly disagree: 0

Disagree: 0

Neutral: 0

Agree: 4

Strongly agree: 15

Classroom activities made a valuable contribution to my learning
#

Strongly disagree: 0

Disagree: 0

Neutral: 3

Agree: 11

Strongly agree: 5

Class discussion contributed positively to learning in this course
#

Strongly disagree: 0

Disagree: 0

Neutral: 1

Agree: 8

Strongly agree: 10

Assignments contributed to my learning experience in this course
#

Strongly disagree: 0

Disagree: 0

Neutral: 3

Agree: 8

Strongly agree: 8

Grading policies were fair
#

Strongly disagree: 0

Disagree: 1

Neutral: 2

Agree: 4

Strongly agree: 12

Useful feedback was provided
#

Strongly disagree: 0

Disagree: 0

Neutral: 1

Agree: 7

Strongly agree: 11

Instructor conveyed knowledge of the subject matter
#

Strongly disagree: 0

Disagree: 0

Neutral: 1

Agree: 4

Strongly agree: 14

The online course materials were easy to use
#

Strongly disagree: 0

Disagree: 1

Neutral: 0

Agree: 6

Strongly agree: 12

The instructor required an appropriate amount of work for the credits received
#

Strongly disagree: 0

Disagree: 1

Neutral: 1

Agree: 12

Strongly agree: 5

The instructor was well prepared for each day’s class
#

Strongly disagree: 0

Disagree: 0

Neutral: 0

Agree: 8

Strongly agree: 11

The presentations provided a meaningful learning experience
#

Strongly disagree: 0

Disagree: 0

Neutral: 2

Agree: 6

Strongly agree: 11

This class made a valuable contribution to my professional development
#

Strongly disagree: 0

Disagree: 2

Neutral: 1

Agree: 4

Strongly agree: 12

Group work contributed to my understanding of the course material
#

Strongly disagree: 0

Disagree: 0

Neutral: 4

Agree: 11

Strongly agree: 4

This course helped me communicate clearly about this subject
#

Strongly disagree: 0

Disagree: 0

Neutral: 1

Agree: 10

Strongly agree: 8

This course enabled me to critically evaluate research in this field
#

Strongly disagree: 0

Disagree: 0

Neutral: 0

Agree: 13

Strongly agree: 6

The instructor actively engaged students in the learning process
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Strongly disagree: 0

Disagree: 0

Neutral: 1

Agree: 5

Strongly agree: 13

What did you like best about how the course was taught?
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  • Alex adapted to the feedback and took action fairly early and quickly.
  • I appreciated and valued how prepared the professor was for each and every class. Having everything set and laid out on a Github website made it clear and easy for me to find where and what we were doing beforehand. I thought especially in a writing class, it was extremely helpful to have all sorts of resources in an organized fashion.
  • I liked how for the final paper we had multiple drafts to gain feedback
  • I liked how the entire course was structured, from start to finish learning how to effectively read scientific papers. Then on to researching and picking our topics. To then write our final paper. While it was an over two–hour class having a break every hour made it much easier to concentrate and learn while in the classroom as well.
  • I loved the open and honestness of the classroom teaching style. There was a lot of information provided for every assignment, and we had an ample amount of help and resources.
  • I liked that a lot of the activities were more conversational and that the entire class was in a conversational format.
  • I liked how non rigid it was. There was certainly a lot of preset assignments however I really liked being able to give feedback that altered the content covered in the class.
  • I liked the structure of this course a lot. In the beginning, we learned about how to read and critique research articles, which set us up for our presentations and final papers later on. the paper was broken up by drafts and not just one big grade at the end
  • I liked the fact that the course and instructor were adaptable and listened to what the students needed
  • I liked the presentations and paper that we had to write, I feel that it has developed my skills in those areas
  • I enjoyed the interactive coursework in class. The programs helped me gain more insight into the course itself.
  • I liked the way the presentations were done. I felt liked I was able to comprehend and actually understand what was being thought in the class.
  • I liked the smaller class size because it gave me opportunities to ask questions and really be involved in the discussions
  • I like this class because it can urge me to read the research paper. And each part can be analyzed, which is very helpful in the future work or continue to study.
  • I liked how the assignments were clearly outlined at the start of the course, and how the class itself is more–so spent doing group activities and supplemental.
  • Alex was very open to suggestions and ran the class based on feedback given during the class.
  • Generally, I liked how the course was laid out with the giant paper over the semester along with the presentation.

If you were teaching this course, what would you do differently?
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  • I would probably not include such a large volume of papers to read, but instead focus on one paper. This way the analysis process becomes much easier and it doesn’t feel like time was wasted reading multiple papers that were not particularly useful. Techniques can always be demonstrated with one paper.
  • We did end up doing a variation of this, but I wish we could have a set in stone lecture on graduate school/professional career advice earlier in the semester. Most of the class was applying to graduate schools or jobs and it was honestly super helpful being able to hear from someone in the field who has gone through what we had.
  • I would dedicate a whole class to working on paper/presentation so that we can ask questions. It was very hard for me to figure out how to get started
  • I cannot think of anything I would change, Alex formatted the class amazingly well.
  • I have no input! I though it was taught very well, the class was definitely long and hard to focus in, but the instructor did as much as possible to help.
  • I did not enjoy all of the group activities at the start of the semester. I feel as though a broader discussion format or more tophat/canvas discussion posts would be more engaging for everyone.
  • Maybe more smaller group discussions about papers.
  • I think I would spend a little time teaching students where to find credible research papers and also talk about the many different fields that these research papers can cover. I know that this class is computational biology, but it would be interesting to talk about papers pertaining to computational neuroscience, chemistry, immunology, etc., since they have some degree of overlap.
  • include some mini hw presentations to practice and get used to presenting.
  • I do not think there is anything I would do differently for this class
  • Maybe break it up into two different days
  • If I were teaching this class, I would break the same papers into sections and move on to a new paper after one, rather than using a new study for each section of the research. Also, the grading for this lesson is a little different than my other writing lessons, where it is more based on right or wrong opinion. I may change the grading a little bit.
  • I may focus more on how to present and how to write. I know that is difficult to do given its very subjective, but some more guidance on that front, given that it is the majority of the grade comes from those two things, would be helpful.
  • The class is too long. If the goal is to teach us how to read and write about scientific literature, it could be done better with a shorter class period where we read something at home and talk about it in class. I have a hard time reading during class because there are too many distractions, so this approach would have been better for me.
  • Alex’s grading standards were tougher than those in other writing–intensive courses. Therefore, preparing for my presentation and writing my paper was more stressful than expected. In addition, I believe this course should primarily focus on evaluating students’ understanding of their papers and observing their progress throughout the term.
  • If you asked me what I learned from this class I could barely give you a list. I didn’t understand the purpose of the class I wish that this was an elective rather than required because I think that students who want to go into academia should take this course, but others like myself who would want more of an industry focus where you could be working on actual projects or something that could give them experience in the field would’ve been better.
  • Nothing much
  • nothing

Are there any specific areas or topics in which you feel I excelled as an instructor or any areas where I could have been more effective?
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  • You gave great feedback whether it was for assignments in class or for our questions regarding post–graduation plans (grad school or work). Especially being so close in age to us I think is something you should use to your advantage and can make your future semesters great. It just makes it easier to talk to you as a person and professor since you were in our shoes not too long ago.
  • I think the general inclusivity and mindfulness of all students was excellent. I feel like for such a small class, we may have benefited from required individual meetings at some point. I have had professors cancel a class and replace the class time with some one on one meetings around the midpoint in the semester.
  • I believe you excelled at helping us understand the research papers better and how to effectively read scientific literature. I believe the only area that could have been more effective is explaining the purpose and how exactly to write the final paper, as I wasn’t entirely sure what I was supposed to write until the second draft (I was also writing similarly to the unofficial microbiology papers).
  • you were very good at engaging with the class. it made speaking in front of everyone easier.
  • I think you did a very good job of giving feedback and being available for students
  • The beginning of the class work.
  • I really enjoyed how honest you were as an instructor and the relaxed environment you were able to provide. Going to class can be stressful but I did not feel that with this class because I felt comfortable participating.
  • Communication!
  • I think the small in class activities we would do were effective.
  • N/A
  • no
  • No
  • NA
  • No

Is there anything else you’d like to share regarding my teaching style or my role as your instructor in this course?
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  • Keep your style of teaching. You were very approachable and kind which made it much easier to engage with you and participate in class and with my classmates.
  • I really enjoyed how you incorporated your other interests into the class content. The graphic design stuff was cool to see. I though you were very approachable and a great knowledge base for students trying to figure out their post–undergrad plans.
  • I liked how comfortable the environment was. It felt more interpersonal which facilitated more learning.
  • You looked out for the students’ best interests by extending deadlines and providing thoughtful feedback, this was a very nice thing to do for us.
  • I really enjoyed your class
  • I really liked your teaching style and the way you ran the class
  • no I liked the teaching style
  • The website was great and very helpful
  • Thank you
  • You were very amiable which made the class environment a lot more comfortable! Thanks for a great semester Alex!
  • N/A
  • N/A
  • Nope
  • :)

Midterm
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The following passages are unmodified student responses (13 out of 21) to a Midterm Course Survey administered by OMET.

Results

I am comfortable speaking in this class
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Strongly disagree: 0

Disagree: 0

Neutral: 4

Agree: 3

Strongly agree: 4

This class stimulates my interest in the subject
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Strongly disagree: 0

Disagree: 2

Neutral: 2

Agree: 5

Strongly agree: 2

The instructor treats students with respect
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Strongly disagree: 0

Disagree: 0

Neutral: 0

Agree: 0

Strongly agree: 11

What is helping you to learn in this class?
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  • The different activities.
  • I think working with certain articles in portions is definitely beneficial for this class.
  • I really like and appreciate the organization of the class with Alex’s use of his website. I think it’s been really helpful to see what we’re doing each week ahead of time.
  • Alex is very good at explaining things in a way that actually makes sense.
  • The discussion style and lots of group work make the class enjoyable to learn.
  • I enjoy hearing the perspective of a recent PhD student and hearing about actual research.
  • I think the group activities that we do every class are very helpful.
  • I like the activities. It’s a long class so for normal lecture–style things its hard not to zone out.
  • Class activities! Also, the presentations are extremely informative and we are given a bunch of helpful resources!
  • I think that focusing on discussing a part of the research paper in each class helped my understanding and learning. As well as being able to hear different perspectives from other classmates helped me to think more.
  • The teacher’s willingness to meet with me and have personal discussions about the class materials and activities
  • The lectures are helping a lot. I like that we are doing activities in order to better understand scientific literature.

What is making learning difficult? (structure of class)
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  • Sometimes having to present in class for activities.
  • I think the massive presentation and writing assignments are daunting, but I know that’s just how the structure of the class is required to be.
  • I think just the disconnect between each week because there’s so much time in between classes. It feels like I sometimes put this class on the back burner just because I have so many other assignments.
  • Some of the papers have just been difficult to understand, especially if we don’t have a lot of time to understand it and ask questions.
  • It is too long. 2.5 hours is too long to stay focused and making meaningful connections.
  • Sometimes the activities feel a bit redundant. I feel as though at some times too much time is given for discussions but at others too little.
  • I’m not sure what to do with assignments or even the activities. I don’t know what you are looking for. Also I have no idea how you find all these papers so easily.
  • The timing of the class is really long unfortunate, it’s a very long class structure and sometimes it becomes difficult to stay focused.
  • I think that although reading research papers is great, I didn’t make it my hobby because of my previous classes or my free time. So at the beginning of the semester, reading and understanding a different research paper each week was something I found difficult
  • The structure if the class works fine for my learning style.
  • Nothing in particular is making learning difficult in class.

What changes could be made to help you learn?
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  • No changes needed.
  • I like the class format that we have.
  • Honestly not sure.
  • It could be fun to have a story time where you read a paper with us and walk through what you look for and how you go about it.
  • I don’t take much away from the in-class presentations, they are a bit stressful without much benefit
  • Examples would be nice.
  • Perhaps taking 2 breaks (a 5min one and a 10min one) instead of just one
  • I think using Perusall is very useful and allows me to see some helpful explanations very quickly
  • Maybe incorporating some journal club discussions instead of always doing the in class activities. I take really long to digest scientific literature so sometimes the activities are a little fast paced for me.
  • N/A
  • Possibly looking at papers that are reviewing or critiquing another paper so we can get a better understanding of how to write our final paper and what to include in it.

What do you still find confusing or unclear? (content of material)
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  • Nothing.
  • N/A
  • I’m still not 100% how our paper review presentations are going to go.
  • N/A
  • Unsure.
  • Reading these papers feels like I have never learned anything ever, but that’s just how that goes with these.
  • Creating GOOD presentations! I feel like it’s so important, but I’m still not fully able to do it.
  • At the moment I don’t have any confusion about the whole course, but may have doubts about the review paper later on
  • Nothing in particular.
  • Some of the procedures that are used in the papers are hard to follow along with, but it’s easy to research these unclear points outside of class.

What steps could you take to improve your own learning in this course?
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  • Be more proactive about reading papers before class.
  • N/A
  • Putting in more time outside of class to prepare.
  • Read more thoroughly.
  • I could take more time for reading the articles. However, I struggle with finding a good in between for reading completely in-depth vs skimming.
  • I need to do more of the readings beforehand.
  • I could take more initiative and go back and explore the website, I think that it has been created with so much care and we have so many resources available.
  • I think I will plan my time well to read the research paper I choose and then understand it. As well, I will use school’s writing center as a resource to help me in structuring my review paper.
  • Spending more time outside of class reading the papers discussed in class.
  • I think reading more papers outside of class would be beneficial to better understand comp bio jargon and the methods that researchers use.

Which class activities, assignments, and/or resources are working well for you in this class?
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  • Group activities where we break down different papers and studies.
  • I think the smaller assignments leading up to the larger one is helpful.
  • Group activities.
  • The mini presentations are helpful in building my presenting skills.
  • Presenting in front of the class is enough of a push to make me try and do a good job.
  • The class activities using LLMs are interesting.
  • The activities are nice, but does everything have to be in groups?
  • I like engaging with the material in class because that allows for direction in real time.
  • I think they all work well.
  • I like the in class activities where we breakdown sections of the paper.
  • All the activities that involve analyzing research papers have been working well.

Is there anything else you would like the instructor to know?
#

  • No.
  • I really like the more informal discussions that we have in this class; it really creates a low stress environment where students are comfortable sharing.
  • Nope :).
  • Thank you for taking the time to incorporate our suggestions.
  • I like the ducks.
  • I think that Alex is doing a great job, and all the efforts are so greatly appreciated. This class is not the easiest to teach, but it is going SO well. Thank you so much for all your hard–work and dedication to making this class a valuable learning experience.
  • You are great.
  • Alex is a great professor, he creates a good classroom environment conducive to learning.
  • This class has been very interesting so far and I really like the way it is being taught!