User talk:William A. C. Gendron

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Week 11 Feedback Part 2

  • I have some observations about your Week 11 assignment as you prepare your final paper and presentation.
    • Remember that t60 is still a cold shock timepoint. The cells are moved back to 30 degrees C after the harvesting for that timepoint.
    • GO Terms 1, 2, 3, 4, 7, 8, and 10 are all related. It seems that the cell is responding by degrading the mRNA, or it could simply be referring to the fact that in order to process the 3' end of the mRNA, it actually has to be cleaved before the polyA tail is added. We would have to look at the specific genes to see in more detail what is going on here.
    • GO Terms 5 and 9 are nearly identical and again, we would need to look at the specific genes to see which compounds this is referring to. Since the ribose sugar is a ring, it could even be related to the above terms.
    • GO Term 6 refers to the cell wall. It is known that during cold shock, yeast up-regulate genes required for the cell wall. So, this is a known response.

Kam D. Dahlquist 14:58, 5 May 2015 (EDT)

Week 13 Feedback

  • Thank you for submitting your work on time.
  • I have confirmed that you made the requested change to the "optimization_parameters" sheet.
    • Now that I've read your electronic notebook, the GRNsight error could have been generated because you used LibreOffice. When you fix your "network" sheet, make sure you do it in actual Microsoft Excel.
  • Your electronic notebook is good, but could be improved by the following:
    • Link to your own individual assignment pages throughout the protocol when it refers to data coming from previous assignments.
    • You need to state which transcription factors did not have degradation rates in the file provided and which you had to substitute the specified value.
    • Some of the sheet names you refer to are incorrect. While I know what you are talking about, you should really use the exact name from the spreadsheet.
  • You are missing the links from your individual journal page to the assignment page and to your user page. You are missing the category. Don't forget, this is part of every assignment.

Kam D. Dahlquist 19:00, 21 April 2015 (EDT)

Week 11 Feedback Part 1

  • I checked your spreadsheet and your equations are all correct. However, don't forget to put a column header on column S.

Kam D. Dahlquist 01:25, 26 March 2015 (EDT)

Week 7 Feedback

  • Your Week 7 individual journal assignment was late by 51 minutes and your shared journal reflection was late by 55 minutes.
  • Your individual journal page does not link back to your user page or to the assignment page. It is missing the category.
  • Your electronic notebook is minimal. The intent of an electronic notebook is to record what you did so that you or somebody else could reproduce what you did based on the information there. In addition to the MATLAB files, you need a description of what values you used for each run of the model and why you chose them, and the the resulting plots and your interpretation of what they mean. You only commented on how you worked with your partner, not what you actually did for the analysis.
  • You needed to perform an analysis of the steady state.

Kam D. Dahlquist 12:55, 17 March 2015 (EDT)

Week 1 Redux

  • I have reviewed your changes to the Week 1 assignment; again, be careful that you give yourself enough time so that you are not submitting changes after the deadline.
  • I noted that your usage of the summary field has improved; you have written comments in the summary field for 42% of the last 50 contributions you made. Remember, we are aiming for 100%.
  • Some of the requested changes were not completed, including third level sub-headings, and fixes to the formatting of bulleted lists. You did not add the category "BIOL398-04/S15" to your template. You should do so, so that this is an automatic thing that happens when you invoke your template.

Kam D. Dahlquist 19:54, 10 February 2015 (EST)

Week 1 Feedback

Here is the feedback to your Week 1 journal assignment.

  • Please be sure to submit your assignment on time. Your individual journal page was mostly there by the deadline, but subtantial editing ocurred after. Your shared journal was a few minutes late as well. You obviously put some care into making an online CV out of your page, but it probably also cost you by making you miss the deadline. Be cognizant of this in the future and make sure that you budget enough time to make the deadline.
  • The grade for this assignment is posted on the MyLMUConnect Grade Center for this course. You will be able to earn back the points you missed on this assignment by completing the requested revisions below by the Week 3 journal assignment deadline of midnight on Tuesday, February 3 (Monday night/Tuesday morning).
    • Every time you make a change to a wiki page, please type something in the summary field (found above the "Save page" button). It appears that you did not do this at all for this assignment.
    • Please provide your LMU mail box number as part of your snail mail address.
    • For your research experience, are there any links you can provide to online abstracts or presentations?
    • For your publications, be in the habit of using a complete citation style (like the APA recommended for this class) that includes all co-authors, year, title, journal, volume, and page numbers. For papers that are not yet published, you can substitute the word submitted for the volume and page numbers.
    • Please make a link to an external web site.
    • The image that you uploaded to your wiki page was quite late after the assignment deadline.
    • Please upload a non-image file and link to it on your user page. Other students have uploaded resume's or scientific presentations they have done, for example.
    • You created a template, but did not actually invoke it on your user page using the following syntax {{William A. C. Gendron}}. This would then take everything that was on your template page and add it automatically to your user page. You could then remove the list of links that you put there manually. Every time you update the template, it will be automatically updated on every page in which the template is used.
    • You did not use and "third" level subheadings (three equals signs or more). Be sure to utilize this feature to organize content on your journal pages.
    • "Comment out" your wiki code--there were no comments other than what was already put there by OpenWetWare.
    • The formatting of your bulleted lists is a little off, stray bullet points appearing. Keep in mind that when creating a bulleted list, you cannot use empty lines in between a bullet point and it's sub-bullet or else it will make stray (extra) bullet points that look out of place. In general, check the formatting of your completed page to see if it looks right when you are done.
    • You can also remove the OpenWetWare automated text from the bottom of this talk page.

Kam D. Dahlquist 17:13, 29 January 2015 (EST)

I've answered your question on my User talk page. Kam D. Dahlquist 21:27, 29 January 2015 (EST)

Answer from Dr. Fitzpatrick

You asked What exciting things do you expect to come out of biomathematics in the coming decade?

I'm hoping we'll come up with math models of humans that will aid in all sorts of medical diagnostics, multi-scale models that go up from gene regulation to metabolism to organs to larger-scale physiological, models that can take into account all sorts of data to provide an accurate picture of health. I expect we'll continue to see molecular biology, computation, statistics, and mathematics converge: I'd love to see a complete model of yeast in terms of all 6000+ genes, signalling, metabolism, etc. I expect to see improved understanding of the processes of evolution. Ben G. Fitzpatrick 01:38, 21 January 2015 (EST)

Hello, William A. C. Gendron! This is a welcome message from OpenWetWare. By the way, we've announced you on the home page! You can leave messages to any OWW member by editing their User_talk pages like this one. And don't forget to personalize your User Page so that we can get to know you better! We've included some tips below to get you started.

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