McNair Symposium/SACNAS 2015 Conference

[trixr4kdz]

The McNair Symposium is actually going to be held on October 3rd instead of what @trixr4kdz originally thought as the week before the SACNAS Conference. The SACNAS Conference will be held on Oct 29-31 in Washington, DC. @trixr4kdz will be doing a poster presentation about the GRNmap research over the summer. She will need to make a poster and upload it to the "Documents" folder.

[trixr4kdz]

I've uploaded a draft of my research poster titled Roque - McNair/SACNAS 2015 Poster in the documents folder in master. I've taken some information from the LMU symposium that @juansc and I made. Can you have a quick look and see if I am on the right track?

[kdahlquist]

@trixr4kdz , I've had a chance to review your poster. Here is my feedback:

• remove the abstract
• move the activity diagram to either the middle or bottom of the poster
• you need to introduce GRNmap and what it does more graphically. You should include the equations, a network diagram, and the flow chart that you used to put it in context from your final McNair presentation for the summer.
• The flow chart that Trixie made that shows all 16 ways to run the program would also be helpful
• Just like in an oral presentation, each section heading of your poster should be a longer phrase or sentence that gives that message of that section, not just the topic.
• We may not have room for the list of worksheets, but if we do, we have better documentation of what the sheets contain on our wiki, please use the information from there.
• You should include as bullet points what you accomplished in the summer, like the slide you had for the McNair summer presentation.
• in terms of Future work, we should be a little more specific as to the tasks we are actually working on now. Some of the things you list are in the too-far-away future. Our shorter term goals are:
  • complete the testing framework for all current functionality of the code, fixing bugs and refactoring code as needed
  • clean up the variable names, and how the program discovers which strains are present and which genes are deleted
  • move the documentation for how to use GRNmap from the wiki to the documentation page of the web site
  • add functionality so that GRNmap computes the within- and between-strain ANOVA values
• you talk about making a Mac version, but that is not one of our priorities right now, we may never get to that (we don't even have it as an issue yet)
• you talk about adding radio buttons and check boxes in Excel, and again that is a very low priority right now (we don't have an issue for that either).
• For the sigmoidal model at least, you can reference a paper that is in press:

Dahlquist, K.D., Fitzpatrick, B.G., Camacho, E.T., Entzminger, S.D., and Wanner, N.C. (2015) Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, in press.

We will talk more at the meeting today. Since you are presenting a week from Saturday, we want to print it out by a week from Thursday, so we will need to iterate some new versions before then.

[trixr4kdz]

We will need to shoot for Monday for a new version of the poster so that we can revise as needed and so we can print the final version by Thursday.

[trixr4kdz]

I've uploaded the newest revision of the poster in the master branch in both .pdf and .pptx format

[kdahlquist]

I just downloaded your latest version and will try to get some comments back to you by tomorrow.

I just realized that you were uploading these files to the master branch. In terms of process, we should never be committing new changes to the master branch--it should always remain pristine--all new work, even posters and documentation that don't really affect the code, should be pushed to a branch instead.

So, in the interim before we do some merges, will you take these down from master and post them to the beta branch? Thanks.

[trixr4kdz]

Ok, I just moved them.

[kdahlquist]

I'm going to write up the feedback to your poster here. So that I don't lose my changes, I am going to save the comment quite frequently and then go back and edit the same comment so that all of the changes are in the same comment. I don't think that it will generate a new e-mail every time I edit the comment, so you will need to view it on GitHub in order to see it all.

• I like the overall layout and organization better now. However, there are still a few tweaks that need to be made to the layout.
• Reference should be on the far right, Acknowledgments in the middle, and Future Work on the left.
• I think your fonts are too large for the headings and body text and your title is too small. The overall poster title should be the largest font on the page. The section headers should be about 36 point font and the body text should be about 24 point font. You will need to increase your title font. Also, don't leave one word of your title hanging by itself on the second line. There is a natural break at the comma in your title to break to the second line. Your title area will get bigger with these changes, but your other sections will get smaller, so it should compensate.
• Now that you have the paper listed in your references section, you need to actually cite it somewhere else on your poster. The place to do that is near where you talk about the sigmoidal equation and you do it by putting (Dahlquist et al., in press) next to the bullet point.
• Since you are citing that paper, you no longer need to acknowledge Nathan Wanner, Stephanie Kuelbs, or Erika Camacho in the acknowledgments since they are authors on the cited paper. But you left out Katrina. Thus, your acknowledgments should be: "We would like to acknowledge Juan S. Carrillo, Nicholas A. Rohacz, Katrina Sherbina, and Alondra J. Vega for previous work on the GRNmap program."
• Then as for the funding sources, you only cite the sources for the current authors of the poster and the current work. So that part should read: "This project was supported by the Summer Undergraduate Research Program at Loyola Marymount University (T.A.R.), a Kadner-Pitts Research Grant (K.D.D.), and the Clarence Wallen, S.J. Chair in Mathematics (B.G.F.)."
• Figure 4 has an error. The bottom arrow should be pointing from left to right. Once you have a test and are passing it, you can refactor the code with more confidence because you can run the test and make sure that the changes you made don't break the program. Also, if you want to color-code your bubbles, the top one should be red, the bottom left green, and the right one blue.
• The rest of my comments have more to do with the "meat" of the content of the poster. Generally, someone should be able to read your poster without hearing your explanation and be able to understand your project. Right now, I think your poster could be understood by someone from our team who is already familiar with GRNmap, but not by someone who is not already familiar with the program. You need to provide more extensive background on how GRNmap works and also elaborate each bullet point further. I'll try to take this section by section (not necessarily in order).
• For the Future work section, please make all of the bullet points complete sentences and say "why" you want to do each of those things. The first bullet is OK, but needs to be a complete sentence. For the second bullet, something like: "We plan to revise the variable names and worksheet formats so that they follow a consistent style and make intuitive sense to the user. In the future, GRNmap will automatically detect when data are present for different strains, based on the worksheets present." The latter sentence only makes sense if you have previously introduced that GRNmap works with gene deletion strains in your introduction. For the third bullet point, say that with the above changes, the documentation will be ready to be moved from the wiki (which is mainly for the developers) to the production web site (which is for the users). The last bullet point should read: "Add new functionality so that GRNmap computes (note you have a type there right now) the within- and between-strain ANOVA p values for the expression data, not just the standard deviations. This will allow the user to judge the quality of the expression data upon which the model parameters are based."
• Move the description of test driven development from the GRNmap functionality changes section to the right-hand section, where you are showing the figures for test-driven development. Don't quote this exactly, but you need to explain that GRNmap has been in development for over 7 years and has only recently in its history been refactored and moved to the version control system at GitHub. It is a complex program upon which we are trying to impose test-driven development post-hoc. The first step was to develop some manual tests (as shown in the flow chart) for all the ways that the program can be run with the different options available (in your introduction, you need to say a little more about the different options). Then you started to automate the tests; then you are switching over to writing the tests first. So I would rearrange the order of your figures to 5 first, then 6, then 4.

[trixr4kdz]

I've updated the poster in the beta branch

[kdahlquist]

I can look at it later tonight.

Kam D. Dahlquist, Ph.D. Associate Professor of Biology Loyola Marymount University http://myweb.lmu.edu/kdahlqui

-------- Original message -------- From: Trixie Roque notifications@github.com Date:09/30/2015 3:44 PM (GMT-08:00) To: kdahlquist/GRNmap GRNmap@noreply.github.com Cc: Kam Dahlquist kdahlquist@lmu.edu Subject: Re: [GRNmap] McNair Symposium/SACNAS 2015 Conference (#122)

I've updated the poster in the beta branch

— Reply to this email directly or view it on GitHub.

[kdahlquist]

Its looking good. I have a couple minor comments after which it will be ready to print:

• The title for the top left section should read: "GRNmap uses ODEs to Model Gene Regulatory Networks"
• The title for the top middle section should read: "GRNmap Uses Data Provided by Our Interdisciplinary Research Group"
• You should go through one more time and make sure that all sentences have periods and everything is spell- and grammar-checked. Getting someone else from the group to proofread it would be good, if that's possible. Unfortunately, I won't have time myself because I've got a crazy day tomorrow.

[trixr4kdz]

McNair Symposium went well! Question I have for later though, since I already have a printed poster, should I just use that for the SACNAS conference at the end of the month, or would you like to look at it some more and see it there is anything you would like to change?

[kdahlquist]

Let's see how things go. If I have time to look at it again and give you feedback in enough time before you leave, maybe we'll change some things. However, the way things are looking, I may not get to it, so we'll just go with the one you have. Remind me again at out meeting next week and I'll be able to give you a firmer answer.

[kdahlquist]

@trixr4kdz is back from the conference!