The course syllabus is here. (Last updated 28 February 2020.)

Office hours are on:

• Tuesdays from 2:00-2:45
• Wednesdays from 3:30-4:15

Please e-mail me if you plan to attend office hours so that we can confirm the location!

Lecture Slides

Slides from Lecture 1: Introduction

Slides from Lecture 2: Writing as you go, efficiency, motivation

Slides from Lecture 3: Abstracts and figures

Slides from Lecture 4: Communicating with coauthors

Slides from Lecture 5: Choosing a journal

Slides from Lecture 7: Responding to reviewers

Slides from Lecture 8: More figure-making

Vicky Stein’s slides from Lecture 9: Guest lecture on science journalism

Reference management software: slides and video

Science journalism with Vicky Stein

Check out the writing of Sabrina Imbler at Atlas Obscura and on her personal webpage.

And consider adding your name to the “Request a Woman Scientist Directory” if you identify as a woman, and contributing to 500 Queer Scientists if you identify as queer. This will make it easier for science journalists to find you!

Here are the recommended readings:

• “This new ‘army’ of spiders is named after Star Wars stormtroopers”
• And please read at least two of the following articles:
  • New 3D maps of the Milky Way confirm our galaxy is warped
  • Butterflies are disappearing in Ohio. Here’s what that means for insects everywhere
  • Canada wants to ban single-use plastics. Would it make a difference?
  • This genetic test can predict your odds for obesity from the day you’re born
  • How to teach a honeybee to do math
  • Why these sea slugs look so much like David Bowie

Resources

In response to questions received in class, I want to let everyone know how to use two great resources.

First is Responsible Conduct of Research training. Any Stanford students, staff, technicians, etc. can take this training and I highly recommend it. Head to this website and then click the red “Launch Module on CITI” icon. This training covers ethics, authorship, and more!

Next is Publons, the website that allows you to get public credit for your peer reviews. If you are concerned that the titles of the articles you reviewed will be listed publicly, check out this page that explains how to manage your privacy settings. If you want information on how to add your previous reviews to your Publons profile, send me an e-mail and I’ll let you know.

Ethics

Please read the following articles in advance of our class discussion on ethics in publishing:

• Eye for Manipulation: A Profile of Elisabeth Bik
• Here’s What Happens When You Report Plagiarism To A Journal Editor
• Nobel Prize-winning scientist Frances Arnold retracts paper
• Top geneticist ‘should resign’ over his team’s laboratory fraud
• Text recycling guidelines
• He may have invented one of neuroscience’s biggest advances. But you’ve never heard of him
• The cascade of Pruitt retractions:
  • The original report on PubPeer
  • What to do when you don’t trust your data anymore
  • Authors questioning papers at nearly two dozen journals in wake of spider paper retraction
  • The Pruitt retraction storm Part 1: The current state
  • Statement regarding recent retractions
• Some thinkpieces on the cascade of Pruitt retractions:
  • Trust your collaborators?
  • Who can we trust?

There is also a whole entire book, freely available online, written by a researcher who fabricated data: Faking Science: A True Story of Academic Fraud.

And, on a happier/more optimistic note, here’s Stanford’s page on Responsible Conduct of Research training. I highly recommend this resource.

Preprints and Peer Review

Here are some readings with more information about preprints:

• Why choose preprints?
• Shoddy Coronavirus Studies Are Going Viral And Stoking Panic
• Are preprints the future of biology? A survival guide for scientists

And here are some articles about variants of peer review (CN: ableist language)

• Reviewer bias in single- versus double-blind peer review
• To Sign or Not to Sign: A Slice of Transparency in Peer Review
• Why I don’t sign (most of) my reviews

Abstracts & Figures

Be sure to check out Steve Easterbrook’s “How to write a scientific abstract in six easy steps.”

Here are some links for figure-making software:

• Update: In the original list I forgot OmniGraffle and Lucidchart, programs for making flowcharts and the like. A flowchart is often a great way to illustrate the ideas in your Introduction.
• You already know what Excel is, but perhaps you were not yet aware that it can be used to make shockingly gorgeous graphs these days.
• Tableau is a point-and-click program like Excel, but its default graphs look much prettier. This software is horrendously expensive, but you can use it for free while you are a student. Tableau is mainly used by corporate folks and professional data visualizers, but don’t let the lack of scientific examples fool you—this software can make great figures that will be appropriate for your manuscripts.
• Then there are lesser-known point-and-click programs that make gorgeous graphics and are completely free: Data Illustrator, RAWGraphs, and the public version of Flourish.
• Adobe Illustrator is expensive and has a ton of features you do not need. Affinity Designer is an affordable alternative that will let you do everything you’re used to doing in Illustrator. (Its sister software Affinity Photo also makes a great alternative to Adobe Photoshop.)
• InkScape is a completely free, open-source alternative to Adobe Illustrator and Affinity Designer, but has a steep learning curve whereas Affinity Designer is very easy to use if you already know Illustrator.