User talk:James C. Clements

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 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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Hello, James C. Clements! 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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