User talk:Nicholas A. Rohacz

Week 12 Journal Feedback

 * I see that you had a little trouble with interpreting your GO terms for this assignment, but hopefully it helped when we went over it in office hours.
 * Also, you should look up the individual transcription factors that you added to the model at SGD to see if there is any further connection with these transcription factors and cold stress.

&mdash; Kam D. Dahlquist 00:13, 28 April 2011 (EDT)

Announcement Concerning Matlab
The computers (24 iMacs) on the first floor of Hannon Library have matlab installed. You should be able to access them most of the weekend (hannon hours). Ben G. Fitzpatrick 20:47, 4 February 2011 (EST)

On your notes to my talk page
(1) It's hard to pick out one favorite aspect, because I enjoy lots of different things. Maybe the variety of math... but that sounds like a cop-out. I'd have to say doing something that seems very abstract but then becomes applicable (especially if the same kind of tool can be applied in several different contexts).

(2) Let me reiterate what I said during class. You're welcome during my office hours (1330-1430 TR, 1400-1500 MW) or by appointment. I'd be happy to help with matlab (or anything else for that matter).

Ben G. Fitzpatrick 00:25, 17 February 2011 (EST)

Week 5 Journal Feedback
Ben G. Fitzpatrick 20:04, 16 February 2011 (EST)
 * Parameters are not quite the same as independent variables. We tend to think of independent variables (like time) as changing in some range as a key part of the process.  While we change parameter values to investigate their effects on a system, we think of them as constant values for a given system.  The constants a and K are missing from your list, while M = a*n is not really a parameter, as it depends on one of the state variables.
 * The state variables are indeed n and y, but the formulas you provide are not valid when the two vary simultaneously (which is why we need matlab).
 * The labeling on the figures is quite confusing. I am not at all sure what I am looking at.
 * You did not address question 5.
 * I would welcome you to revisit this set of tasks. Please come to see me if you have questions.

Week 4 Journal Feedback
Ben G. Fitzpatrick 20:04, 16 February 2011 (EST)
 * Sorry about the long delay in providing feedback.
 * Terminology this week was a bit fuzzy. Michaelis Menten uses mass action, plus the additional assumption that complex and enzyme are constant, in order to produce a simplified dynamic model of nezyme kinetics.  The Lineweaver Burk experiment requires a certain type of measurement (what?) in order to be able to use linear regression to get the parameters.  You may want to revisit the Assignment 5 notes to get a more detailed idea of the chemostat.  Exponential growth models a situation in which the rate of change in a variable is proportional to that variable's value.
 * Your graphs need some sort of labeling (and preferably a line or two of description).
 * Your Lineweaver Burk computations are correct.
 * Thanks for the input on matlab. I hope that as we continue you'll start to feel more comfortable.  Computer simulation is a key ingredient of many modeling efforts.

Week 3 Journal Feedback
Ben G. Fitzpatrick 20:04, 16 February 2011 (EST)
 * Sorry about the long delay in providing feedback.
 * Terminology is good.
 * Equations are very close. First and second set are right on.  Third one is missing a factor of (1/2) in the C equation.  Fourth one should have factors of (1/2) and (1/3) instead of powers of (1/2) and (1/3).  Please see this for more discussion.
 * Matlab plot looks good.
 * Homeostasis is more about the organism's regulation of processes to maintain certain conditions. The conditions could be thought of as equilibrium.

Week 2 Journal Feedback

 * As we discussed, please make sure that you submit next week's assignment on time. It is due midnight Monday, meaning the cusp between Sunday night and Monday morning.  For this week, the shared assignment was posted on time, but the edits to your User page and the Week 2 definitions/outline were late.

Week 1 Redux

 * There are still some changes that you need to make to your User page:
 * OpenWetWare auto-generated some content for you. Where it says "I learned about OpenWetWare...", you should fix the sentence so it is a complete sentence.
 * Please let us know if you have any worries or concerns or if there is anything else you would like us to know. Even if the answer to these questions is "no", please let use know that.
 * Your image is not displaying correctly on the page because you have an extra "Image:" in the syntax you used. When you save your page, you should look to see if the change you thought you made showed up.  This is a good way to catch errors.  Please fix this so that the image actually appears.
 * You also need to practice uploading and linking to a file. You can look at your classmates' user pages to get some ideas of what to do there.
 * Thanks for adding the Category to your User page. You should add it to your template page so that each time you use your template, it automatically creates the category for you.
 * You still have not posted a question to Dr. Fitzpatrick on his User talk pages (be sure to sign it with your wiki signature,  ~ ).
 * Finally, please make sure to write a short descriptive phrase tha summarizes the changes you made in the "Summary" field at the bottom of the page before you save your edits each time.

Definitions and Outline

 * Your definitions and outline are now complete.
 * The link you provided for the "oligonucleotide" definition goes to an "error" page. Make sure that after you save your page, you check that the links work and the page appears as you expect.
 * ACT1 and H2A-H2B are not actually biosynthetic genes (they do not code for enzymes that carry out biosynthesis reactions). Instead, ACT1 codes for actin which is a component of the cytoskeleton (literally cell's skeleton, providing structure support).  H2A-H2B are histone proteins, which the DNA winds around in the nucleus to keep it compact and organized.  These are controls for which the gene expression should remain constant in the experiment.  If they had shown the blots, we should have been able to see that.
 * For future reference, you can include the answers to the specific questions within the outline itself.
 * You could have had a little more detail on the figures you presented in class.

&mdash; Kam D. Dahlquist 11:57, 27 January 2011 (EST)

Week 1 Journal Feedback

 * Here is some feedback on your user page.
 * OpenWetWare auto-generated some content for you. Where it says "I learned about OpenWetWare...", you should fix the sentence so it is a complete sentence.
 * In your Education section, you could say the words "Major", "Expected graduation year", and "upper division courses taken" so that other readers know what your answers mean.
 * Please let us know if you have any worries or concerns or if there is anything else you would like us to know. Even if the answer to these questions is "no", please let use know that.
 * Be careful about creating too many new pages. The Image and BIOL398-01/S11:Assignments pages are superfluous.  Your individual journal pages fulfill the "create new wiki page" part of the assignment.
 * For your numbered list, it is best to use numbering when the list has more than one item in it.
 * Even if you don't have an image of yourself yet that you'd like to use (we can take a picture of you with the department camera if you want), you should practice uploading and displaying an image on the page. It could be a picture of something else.
 * You also need to practice uploading and linking to a file. You can look at your classmates' user pages to get some ideas of what to do there.
 * Please add   to your page.
 * Please create your template and use it on your user page. Your table of assignments could go into your template.  So that way, you can use your template to create navigation links from all of your pages without having to re-type your table.
 * Also, please post a question for me and  Dr. Fitzpatrick on our User talk pages and be sure to sign it with your wiki signature,  ~ .
 * Finally, please make sure to write a short descriptive phrase tha summarizes the changes you made in the "Summary" field at the bottom of the page before you save your edits each time.
 * Please come by my office if you would like assistance with any of this.

&mdash; Kam D. Dahlquist 17:01, 18 January 2011 (EST)

Week 1 Feedback Redux
I answered your question on my talk page, here it is as well.

You asked:Hi Dr. Dahlquist, I was wondering, after reading the Stewart and Janovy reading, whether or not you have ever thought about switching the specimens you currently do research on, for a completely different animal? Nicholas A. Rohacz 20:11, 23 January 2011 (EST)

I answered: When I was an undergraduate, I worked on an single-celled algae species named Chlorella pyrenoidosa. For two of my rotation projects in graduate school, I worked on the plants Ginkgp biloba and Arabidopsis thaliana. For my thesis, I studied E. coli. During my postdoctoral research, the lab was studying mice, but I was not directly involved with working with the mice myself, although I did take the training when I first started. I've also worked with the fruit fly, Drosophila melanogaster, for a genetics lab I taught at another school. It's only when I started my first faculty position that I decided to work on yeast. Now that you have asked and I've thought about it, if I were to switch organisms, I would probably pick another single-celled one. I'm most interested at what goes on at the cellular level and it seems simplest to me to work on that with an actual single-celled organism. They are simpler than cells from multicellular organisms. They are definitely easier to work with and the work is more straightforward because there is less complexity in these cells in general. In my Biological Databases class that I teach with Dr. Dionisio in the Fall, the students create gene databases for different microorganisms, so if I was really going to switch organisms, I might pick a bacteria that we worked on for Biological Databases. In that class we've worked on Vibrio cholerae, Plasmodium falciparum, Mycobacterium tuberculosis, Mycobacterium smegmatis, Helicobacter pylori, Salmonella typhimurium, and, of course, yeast. &mdash; Kam D. Dahlquist 13:24, 24 January 2011 (EST)

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