Scientific Communication
Scientific Computing Seminar
Summer 2015

http://people.sc.fsu.edu/~jburkardt/classes/sc_2015/sc_2015.html

SC_2015 is the home page for the class "Scientific Communication" a 2 credit pass/fail seminar course offered at Florida State University, Summer Session 2015, May 11 - August 7th.

This course includes two goals:

The topic of the document is up to you. You will be expected to describe the document you intend to write, and then over the course of the semester to submit three draft versions of it. The second draft will be submitted to an anonymous panel, who are expected to return comments, criticisms and suggestions, somewhat in the way that articles submitted for journal publication are referreed. On the last class, each student will make a short oral presentation of the work described in their document.

The other focus of the course involves a discussion of scientific communication. Issues that may be considered include:

The official course number is ISC5939, with the generic name "Advanced Graduate Seminar in Scientific Computing". Because of late registration, these semester's version of the class had the subtitle "Numerical Models of Partial Differential Equations".

Despite the title, you don't have to be working on PDEs to take this seminar...you just have to have a computational project in mind, and the desire to write it up.

As part of the course work, each student is expected to write a report in the style of a publishable research paper. At the 8th week, these papers will be reviewed by an anonymous panel, and the students will have a chance to improve their papers before final submission.

Each student will:

Schedule

  1. 11 May 2015 (Introduction) (1 hour class):

    syllabus/syllabus.pdf, the class syllabus.

    Credits; workload; exercises, homework, projects.

    Discussion: Scientific communication.

    Lecture: Examples of scientific communication.

    Classwork: Write a short document that explains to a high-school student what a differential equation is.

    Homework #1: Describe a scientific communication challenge that you face. Explain how this course could help you with this challenge. if you are planning to write or improve a paper, then you can simply discuss what you have written so far, and what you think remains to be done.

  2. 13 May 2015 (Abstracts) (1 hour class):

    Discussion: Your scientific communication challenge (Homework #1)

    Turn in: Homework #1.

    Lecture: The structure of a scientific paper;

    Classwork: Write a short document that explains to a friend why (your favorite language: Basic / C / C++ / Fortran / Java / Lisp / Maple / Mathematica / Matlab / Pascal / Python ) is better than (some other programming language). For instance, why should a Matlab user consider learning Python?

    Lecture: The importance of abstracts:

    http://people.sc.fsu.edu/~jburkardt/classes/sc_2015/abstracts/abstracts.txt , examples of 50 abstracts from papers in computational science.

    Homework #2: Go to the web page "nature/top100", which is an article about the 100 most cited papers in Nature. There is a box in this article, labeled "The top 100 papers" which allows you to choose a rank from 1 to 100, and then see the corresponding paper (or at least its abstract). Choose an abstract that you like or hate, print it out, bring it to the next class, and be prepared to discuss its merits and flaws. Does the abstract capture your interest? Is it full of jargon, unclear, full of abbreviations, or too long? We'll give awards for WORST and BEST.

    Homework #3: I will hand you a sample paper #3 whose title, author, and abstract are missing. Write an abstract for this paper. You will read your abstract out loud next week.

    Your paper: Set up a Latex file for your paper. Pick a title. Based on our discussion today, and on how you hope your paper will turn out, try to put together the abstract for your paper.

  3. 20 May 2015 (Outline of Articles):

    Discussion: What are you working on? How is your document doing? What do you need to learn?

    Discussion: Homework #2 asked you to pick an abstract from the Nature top 100 papers. Read out your candidate and comment on it. My choice was paper #24.

    Lecture: Last time we talked about abstracts a lot. You've had a chance to look over some abstracts in Homework #2. I will present the abstract for a paper I am working on.

    Discussion: Homework #3 asked you to create an abstract for a paper. Be prepared to read your abstract out loud. I will present my guess for the abstract. Then we'll look at the actual abstract and see how we did.

    Turn in Homework #3.

    Discussion of outlines: I will go through the process of describing the ideas that I want to put into a paper, and then lay out an outline that will help me to organize my work.

    Lecture: "Physics Writing Guide" by James McLean Although this guide is for physics articles, it has many useful comments for us as well.

    Lecture: Sample paper #4 is by Strang (visiting us this fall) and Persson. Let's look over this paper together. Notice the difference between the abstract and introduction. Remember that the abstract must be short, and functions as an advertisement or eye-catcher, while the introduction assumes that the reader is interested and wants to get an overview of the paper.

    Homework #4 (not turned in): Read sample paper #5, by Akhtar, Wang, Borggaard and Iliescu. You don't need to understand the equations, but try to follow the argument well enough to be able to summarize it in a discussion at the next class.

    Homework #5 (to be turned in next class): Prepare an abstract for your document. It should be created using Latex, and printed as a PDF file. If you have trouble using Latex, please let me know!

    Your paper: You should have a title section (title, author, affiliation) done. You should have the abstract done. You should be thinking about an introduction. You should have at least an outline of the entire paper.

  4. 27 May 2015 (Writing a Paper):

    Discussion: How is your document coming along?

    Discussion: Homework #4 asked you to read the paper by Akhtar, Wang, Borggaard and Iliescu. Let's talk about the structure of the paper, and the logic of the argument. What is their argument? What things do they have to explain? What evidence do they present?

    Lecture: I suggested that people writing articles ought to find a suitable journal, download their style file and advice to authors, and try it out. I will tell you my adventures with the ACM Transactions on Mathematical Software!

    Discussion: Homework #5 asked you to prepare an abstract for your document. Let's hear some of them. I will read out mine. Was it difficult to "talk" this way?

    Turn in: Homework #5 (paper or email).

    Lecture: I promised I would start writing a paper. I will discuss the mess I have made so far.

    Lecture: "Whiteside's Group: Writing a Paper". We will discuss a short text by George Whiteside, of the Harvard Chemistry Department, laying out the rules for what he wanted his students to write before he collaborated with them on a research paper.

    Lecture: Sample paper #6 is by Brian Hayes, "The Best Bits". This is an informal article from "American Scientist", introducing the topic of compressive sensing. A scientific document is an effort at communication. Let's consider how well Brian Hayes does his job. What does he decide NOT to try to explain? What techniques does he use for the ideas he does try to communicate?

    Homework #6 (not turned in): Read sample paper #7, by Purcell, "Life at Low Reynolds Number". This is the transcript of a talk. The talk is good enough that it could be a journal article, but it's missing some of the things we would expect. Try to come up with an abstract. Try to come up with sections, that is, a division of the talk into 5 or 6 pieces with subtitles.

    Homework #7 (to be turned in next class): Your first draft!

    Your paper: Your first draft could have holes in it, that's OK, but it better have a skeleton or outline, so we can see what your plans are. And I hope that some sections have been filled in, either with fine, finished writing, or with a good first try. If you get discouraged, take a look at my paper for a good laugh.

  5. 03 June 2015 (Plagiarism):

    Discussion: What can we say about our first drafts?

    Discussion: Homework #6 involved a paper by Purcell on viscosity. Since this was actually simply a recorded talk, I asked you to try to divide the paper up into sections with section headings. This will give us practice in organization.

    Turn in: Homework #7: Your first draft (PDF please).

    Lecture: Typical plagiarism policies:

    Lecture: Article from Scientific American: "'Your Name Here' in a Prestigious Science Journal"

    Lecture: Web document by Zilberberg: "How does it feel to have your scientific paper plagiarized?"

    Lecture: Web document by Tommaso Dorigo: "Fighting Plagiarism in Scientific Papers"

    Lecture: Clifton Phua, "Resilient Identity Crime Detection". Note that this paper follows an article style that is common in biology, medicine, sociology, psychology. I will present the ideas in the paper, compare its form with those we are more familiar with, and then explain why this paper will be useful to us.

    Homework #8 (not turned in): Clifton Phua provided a list of publications which he felt had plagiarized his work. Get a copy of one of these papers, and see what you think. Was there cut-and-paste copying? Was there copying of ideas?

    Homework #9 (to be turned in next class): You are the editor of a top journal, and have received three papers to be reviewed, by Albinaa, Alhazaleh, and Shabir, respectively. You suspect that plagiarism has occurred. Write a statement explaining your decision.

    Your paper: Since I will be reviewing your first draft and giving you some suggested changes to what you have written, you might want to focus this week on sections you haven't actually written yet.

  6. 10 June 2015 (Publishing):

    Guest presentation by Max Gunzburger on scientific journal articles: writing and revising, submitting, refereeing, and plagiarizing.

    http://people.sc.fsu.edu/~jburkardt/classes/sc_2015/publishing/publishing_questions.txt , questions for Max Gunzburger about publishing.

    Your paper: I have made some comments and suggestions on each paper. You may take the suggestions or not. Fill in the missing sections of your paper, even if you can't express your thoughts exactly the way you want.

  7. 17 June 2015 (Job Search):

    Discussion: What is the status of your paper?

    Discussion: Homework #8 asked you to look over Clifton Phua's paper, and compare it to one of the papers he says plagiarized him. What did you find? How serious was the offense, if any?

    Turn in: Homework #9 asked you to compare three papers and make a judgment about whether plagiarism was involved. Let's talk about this, but then please turn in your written judgement.

    Lecture: Andrew Fazekas, "How to Get a Job in Academia"

    Lecture: Rebecca Schuman, "Why Your Cousin with a PhD is a Basket Case" or, "Understanding the Byzantine hiring process that drives academics up the wall"

    Lecture: Hans-Werner van Wyk, "How I Got My Job in Academia"

    http://people.sc.fsu.edu/~jburkardt/classes/sc_2015/job_search/academic_job_questions.txt , questions for Hans-Werner van Wyk about the academic job search.

    Lecture: Google Scholar

    Homework #10 (not to be turned in) Go to Google Scholar, determine the C, H, and I10 indices for the following people and send me your results:

    Homework #11 (to be turned in next class): You should already have a "curriculum vitae", better known as a "CV". Print or email me a copy of your CV.

    Your paper: you should be working hard this week to fill in all the sketchy parts of your document. Read it over from beginning to end and see if it is organized well, and has a logical structure.

  8. 24 June 2015 (CVs):

    Discussion: What is the status of your paper?

    Homework #10 asked you to get the C, H, and I10 indices for various people. Let's tabulate them, and discuss what they mean.

    Homework #11 asked you for a CV. Please turn it in.

    Wikipedia: "The h-index"

    Ivars Peterson, "Rating Researchers"

    University of Illinois, "Curriculum Vitae Tips and Samples:

    University of Minnesota, "Graduate Resume/Curriculum Vitae Guide"

    "Dr Karen's Rules of the Academic CV"

    Sample CV's

    Using HUNSPELL to spell check a Latex file.

    Demo: using HUNSPELL to spell check a sample file called "naver.tex":

    Homework #12 (not to be turned in) Get a copy of the file "bogus.tex" Use HUNSPELL to search for spelling errors and correct them. There are other mistakes in this file, by the way.

    Homework #13 (to be turned in next class): Your paper to be refereed!

    Your paper: Be finished WRITING your paper, and take some time for READING it.

  9. 01 July 2015 (Jobs):

    How well did you do on preparing your second draft?

    Homework #12 asked you to try a spellchecker on "bogus.tex". Did you find lots of errors? Were your errors automatically corrected? Did anyone try to find more errors, or use a grammar checking facility?

    Homework #13 is your second draft. You should have mailed me a PDF of this by today. This is going to the anonymous reviewers.

    A shocking announcement

    Academic/Lab/Industry, Job Locations, Job Skills, Job Postings

    Engineering Day

    The importance of keywords

    Sample Jobs:

  10. 08 July 2015 (Interviews)

    Presentation by Amanda Sargent of the FSU Career Center.

  11. 15 July 2015 (Resumes):

    FSU Career Center: "Writing a Resume"

    University of Texas at Austin: "Resumes and CV's"

    CV + JOB = Resume Example

    Brent Miller, "Why I Tossed Your Resume"

    Isaiah Hankel, "10 Things Smart PhDs Do NOT Put on Their Industry Resumes"

    Matt Might, "How to get a great letter of recommendation"

    Daniel Greenfield, "Github is my resume"

    Homework #14: (not required) Take your current resume or CV to the FSU Career Center. Have it reviewed. If your score is below 18 points, try to improve it.

    Homework #15 (to be turned in next class): Determine a job you'd like to apply for. It would really be best to have a specific job posting in mind, but if you can't find one, you can be generic: "Game Designer", "Postdoctoral appointment in scientific computing", "Neural Network Simulator". Turn in your job description AND resume!

  12. 22 July 2015 (Grant proposals):

    Presentation by Max Gunzburger

    "Writing an NSF Grant Proposal: A First-Timer's Perspective", Philip Guo

    "Grant Proposals, or 'Give me the money'", UNC Writing Center

    "Writing a good grant proposal", Simon Peyton Jones and Alan Bundy

    "Advice on Writing grant proposals" (NSF or DOE), Dennis Lindle
    AND "Grant Proposals for NIH", Martin Schiller

    "Opportunities", FSU Office of Graduate Fellowships and Awards

    Homepage for grants.gov:

    Homepage for NSF Fastlane:

    Turn in a copy of your resume and job posting.

  13. 29 July 2015 (Mock Interviews):

    Bring your resume and job posting to your interview! 

      Gordon Erlebacher, Room 416
  ---------------------------
  3:00-3:20 Mike Schneier
  3:20-3:40 Chad Sockwell
  3:40-4:00 Zlatko Sokolikj

  Priya Pai, Room 468
  ---------------------------
  3:00-3:20  Dan Smith
  3:20-3:40  Evan Cresswell-Clay
  3:40-4:00  Dave Witman
  14. 05 August 2015 (Student Presentations):

    10 minute oral presentations:

    Turn in final document version.

You can return to the CLASSES web page.

Last revised on 30 July 2015.