User talk:James C. Clements

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Week 12 Journal Feedback

  • Thank you for turning this assignment in on time.
  • Your interpretation of the GO terms is essentially correct. Ribosomes are stabilized by cold temperatures, but they need to be able to undergo conformational changes to function. Thus, ribosomes could become "stuck" in non-useful conformations. So, the cell upregulates ribosome biogenesis to make new ribosomes to replace the damaged ones.
  • 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.

— Kam D. Dahlquist 00:45, 28 April 2011 (EDT)

Week 11 Feedback

  • I've had a chance to further review your submission for Week 11. Upon closer inspection, the updated spreadsheet that you submitted has some differences with the calculations I performed myself in Excel. This is most likely due to missing data that led to errors in the calculations. If you look at your spreadsheet, it has a lot of "NaN's" in it. For this reason, the number of genes changed with the various filters is slightly different in my sheet than yours. To be sure that your model is running properly, you should verify that the "NaN's" don't appear in any of the genes that you are including in your model (it is likely that you would have noticed this already anyway.)
  • When you determined how many genes met the filter of p < 0.05 and were either increased or decreased, I meant that you should find this out for the regular p values, not the Bonferroni corrected p values. It would be best if you found this out for inclusion in the table in your final report.
  • For your interpretation of the down-regulation of the PHA2 gene, I would rephrase it a little. After two hours of cold, the cell has slowed its growth rate so it does not need a lot of additional proteins to grow larger and divide, so it would not need the amino acids that go into making proteins.
  • The Materials and Methods of the Schade paper are a little murky, but they do state what they used for a significant gene expression change: "To ensure significant data quality, we selected genes with at least twofold variation and a Student’s t test p value of < 0.03."
  • Let me know if you need any further assistance with interpreting this portion of the project.

— Kam D. Dahlquist 22:19, 25 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)

Week 5 Journal Feedback

  • Very nice job and thorough job on the graphs and parameter studies.
  • The nonlinearity of the equations make applying the Laplace (or Fourier) transform a bit tricky. There are techniques of analysis in nonlinear systems that can be applied. For example, if the system has an equilibrium, one can determine whether or not it's stable by linearizing the equations around that equilibrium. The eigenvalues of the resulting matrix (that defines the linear system) determine the stability (or lack thereof).

Ben G. Fitzpatrick 14:19, 16 February 2011 (EST)

Week 4 Journal Feedback

  • Sorry (again!) I'm so slow to provide feedback here.
  • Terminology looks good.
  • You did a nice and thorough job on the graphs.
  • Your Lineweaver-Burk computation is correct.
  • Relative to your shared journal entry, I would like to challenge you to use the matlab function 'lsqnonlin' to fit the parameters with nonlinear regression. I introduced Lineweaver-Burk because it is the oldest and best known technique. We will certainly encounter nonlinear regression after the break. I was concerned about too much matlab complexity all at once to bring the nonlinear regression in along with the differential equation solving.

Ben G. Fitzpatrick 14:19, 16 February 2011 (EST)

Week 3 Journal Feedback

  • Sorry I'm so slow to provide feedback here.
  • Definitions and refs are fine. We were looking for an additional personal interpretation, too.
  • You did very well on the rate equations. Thanks for the nice presentation of them in your pdf. The only errors were in the higher order reactions. Those square roots should be factors of (1/2), not powers of (1/2). Likewise, the third root should be a factor of (1/3). Please see this for detail.
  • The matlab work is very nicely (and correctly) done.

Ben G. Fitzpatrick 14:19, 16 February 2011 (EST)

Week 2 Journal Feedback

  • Thank you for submitting your assignment on time.
  • Your definitions and outline are complete.
  • You could have had a little more detail in your description of the figures (what are the X and Y axes?), especially for the one that you presented in class.
  • Be careful, in the abstract portion of your outline, you refer to NADH or NADPH activity. It is actually the activity of the glutamate dehydrogenase that you are referring to, the GDH1 and GDH2 just have different preferences for NADH or NADPH as a cofactor.
  • To clarify, an oligonucleotide is any short DNA or RNA sequence. PUT4 was also detected with a 32P labeled oligonucleotide. The authors gave the actual sequence for it, while they referenced another article for the sequences of the other oligonucleotides. GDH2 was detected with a much larger piece of DNA, 2,500 nucleotides long, whereas the oligonucleotides were around 20 nucleotides long.
  • I noticed that you made several notes about the article that were commented out (one of them is visible due to a mistake in the syntax for a comment). You don't have to hide these--one of the goals of having journal club is to critically evaluate the papers we read and comments are welcome!

— Kam D. Dahlquist 17:22, 26 January 2011 (EST)

Week 1 Journal Feedback

  • Thank you for submitting your assignment on time.
  • Your assignment is complete with a couple of minor omissions/suggestions:
    • Please let us know if you have any worries or concerns about the course or if there is anything else you want us to know. If the answers to these questions are "no", then please let us know that as well.
    • You have completed all of the wiki skills, I have a couple of suggestions for improving your page:
      • You could add the table of links to the assignment pages to your template so that anytime you use your template on subsequent journal assignments, it will make your life easier. You could also add your Categories to your template so that it will automatically be added each time you use your template.
    • Please be in the habit of adding a meaningful summary before you save the page. You did it a couple of times for the changes you made to your user page, but ideally, you should do it every time you save a page.
  • You can delete the auto-generated content from OpenWetWare at the bottom of the page if you want.

— Kam D. Dahlquist 19:43, 17 January 2011 (EST)

Reponses to Instructor Questions

You asked Hello Dr. Fitzpatrick. What do you think future has in store for biomathematicians? Thanks, James C. Clements 00:34, 17 January 2011 (EST)

I answered *Ben G. Fitzpatrick 02:05, 17 January 2011 (EST) Wowsers, that's a tough one. Folks at the interface of computer science, applied math, and molecular biology have a lot of work cut out for them. Sorting through all the genomics and proteomics data being collected, figuring out the interoperability of genes and proteins, that's going to keep people busy for awhile. Another area that is going to be very interesting is the brain. There are a lot of math/ee/bio people trying to understand how the brain works. I'll think about this matter and add more later... old people like me start to poop out at 11pm. Ben G. Fitzpatrick 11:40, 17 January 2011 (EST) A few more thoughts this a.m. For people who with impaired hearing or sight, for people with missing limbs, integrated approaches to connecting devices to the brain will require not only good engineering, but good science as well. The successful teams will have biologists, mathematicians, physicists, chemists, and engineers that are very capable of collaborating.

You asked "Hello Dr. Dahlquist. Perhaps a simple question for you: What do you think is the role of engineering in the field of bio research? James C. Clements 00:30, 17 January 2011 (EST)"

I answered: Biology is becoming increasingly interdisciplinary and is pulling theories and methods from the mathematics, physical sciences, and engineering in order to understand the very large datasets we are not generating in biology. For example, genomics needs to make sense of the huge amount of information generated when a genome is sequenced, as well as other high-throughput methods that are regularly being used. Other fields in biology are also generating large data sets such as studies in biodiversity. The fields of mathematical biology and bioinformatics are explicitly pulling from mathematics and computer science and are the ones with which I am most familiar, so I can be more specific about those. We are going to be learing about gene regulatory networks later in the course; scientists are thinking of them as biological circuits and are applying principles from electrical engineering to understand them and also create them in the lab. The field of synthetic biology is actively trying to engineer biological circuits. A lot of the people in this field have pages on this wiki. Conversely, I think that increasingly, engineers are getting interested in biology as a rich domain of problems to solve. — Kam D. Dahlquist 19:59, 17 January 2011 (EST)


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