Math Bio Introduction Helpful Tips

Expectations (lunch)

Food should arrive a few minutes early (~11:45)

Make sure you have vegetarian friendly options (I aim for 50%)

Plates, utensils, cups, drinks we keep a store of them around, but don’t plan on those being available

Stay to help clean up, or arrange for someone to do it for you (if you have class)

Average price should be between $100 and $150

Keep receipt, sign in sheet, sample abstract for reimbursement

You are responsible for the sign in sheet (paper, pen)

Purpose of the seminar

To learn some mathematical biology

To get practice/feedback:• speaking publicly in a low stakes setting• reading/understanding in depth a topic on a short timescale• explaining/contextualizing information for experts and non-experts• asking questions/providing answers about complex material

Reasonable Person Principle

• Everyone will be reasonable. • Everyone expects everyone else to be reasonable. • No one is special. • Do not be offended if someone suggests you are not being reasonable.

Reasonable people think about their needs

and the needs of others

and adjust their behavior to meet the goals of a common good for the community

but accepting and accommodating the needs of others.

Paraphrased from CMU Computer Science Department

to spend time efficiently

to understand your talk

start your presentation early read the paper

respect the time and effort of others

Expectations (presentation)

• To read the paper in enough time to understand it and explain it

this includes leaving time to ask questions (of another grad student or a professor) if there are parts that you are confused about

• To give a clear, coherent presentation of the material in the paperthis may mean leaving some details out, or giving a practice talk beforehand

• To be on time for your presentation, and to end before 12:50there is almost always a class in this room after us, so we have to start and end on time

• It is better to run short than to run long

• To be prepared to engage critically with the material, and ask questions

Preparation/FeedbackIn our time here there has been no formal method of providing feedback to students about presentations

On Monday of each week, Jay and Jeff will be available to go over whatever part of your presentation you have ready, even if it’s just an outline

You don’t have to meet with us, but it will be one regular chance to get feedback before your presentation

After your presentation, we will set a time to sit down with you and provide some constructive feedback

The feedback portion is not optional — it gives us all a chance to think critically about the material presented, and it gives us all a chance to improve our presentation skills

Information PresentationTry to avoid a giant information dump

Information PresentationTry to avoid a giant information dump

TOO MUCH

Information PresentationTry to avoid a giant information dump

TOO MUCH

Information Presentation

Assume infinite intelligence but zero knowledge

Aim for clarity and comprehensiveness

Try to avoid a giant information dump

But at the same time don’t go so slowly that the audience gets frustrated

Notes on figures

https://imgs.xkcd.com/comics/convincing.png

Notes on figures (plotting)

Time x

yx

An example of two coupled brusselators

0.5

1

1.5

2

2.5

3

3.5

0 5 10 15 20 25 30 35 40 45 50

1

1.5

2

2.5

3

3.5

4

4.5

0.5 1 1.5 2 2.5 3 3.5

Time x

yx

An example of two coupled brusselators

Notes on figures (plotting)

An example of two coupled brusselators

Notes on figures (plotting)Two Coupled Brusselators

0 10 20 30 40 50Time (s)

0

1

2

3

4

xposition

Time Course

0 1 2 3 4x position

1

2

3

4

5

yposition

Phase Plot

B1B2

Notes on figures (screencaps)

Turner, S., and Sherratt, J. "Intercellular adhesion and cancer invasion: a discrete simulation using the extended Potts model." Journal of Theoretical Biology 216.1 (2002): 85-100.

TOO SMALL

Notes on figures (screencaps)

Turner, S., and Sherratt, J. "Intercellular adhesion and cancer invasion: a discrete simulation using the extended Potts model." Journal of Theoretical Biology 216.1 (2002): 85-100.

TOO G

RAINY

Notes on figures (screencaps)

Turner, S., and Sherratt, J. "Intercellular adhesion and cancer invasion: a discrete simulation using the extended Potts model." Journal of Theoretical Biology 216.1 (2002): 85-100.

Notes on figures (screencaps)

Turner, S., and Sherratt, J. "Intercellular adhesion and cancer invasion: a discrete simulation using the extended Potts model." Journal of Theoretical Biology 216.1 (2002): 85-100.

Jc≠c

d ma

x

Notes on figures (screencaps)

• High resolution or vectorized screenshots

• Go to journal website to get high resolution copies of figures

• Worst case scenario — replot the figure yourself

Helpful Resources

Image Manipulation

• GIMP (Bard) • Inkscape (Jay, Ben) • Artweaver • a ton of others

• Illustrator (Jeff) • Photoshop

Plotting• MATLAB • Matplotlib • Plotly • PyPlot • GNUplot • Desmos (website)

Presentation• Beamer (Jeff, Jay) • Keynote (Jeff) • Powerpoint • Latexit (or non-Mac alternatives)

Free

Limited Access for students