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Introduction: Grant Roy

Hi,

I'm a software engineer in the Pierce Lab at Caltech, where I work on NUPACK as part of the molecular programming project. I'm interested in algorithms and applications geared toward understanding and designing bio-molecular functionality. I'm also really interested in quantum computing, and in particular the design of novel quantum algorithms/circuits that could be useful in the biological sciences. I have a more general interest in the idea of open scientific collaboration and learning, and consequently I am very excited about this course!

Comments

  • 1.

    Hi! Did we meet when I gave the General Biology Seminar at Caltech last November? I'm bad at remembering names. Anyway, category theory has made an impact on quantum computing, especially topological quantum computing where "modular tensor categories" are important... but it could be useful far more widely, and I hope everyone in this course helps figure out a lot of new applications!

    What's "NUPACK"?

    Comment Source:Hi! Did we meet when I gave the [General Biology Seminar](http://math.ucr.edu/home/baez/bio_asu/) at Caltech last November? I'm bad at remembering names. Anyway, category theory has made an impact on quantum computing, especially topological quantum computing where "modular tensor categories" are important... but it could be useful far more widely, and I hope everyone in this course helps figure out a lot of new applications! What's "NUPACK"?
  • 2.

    Hi John! No, I saw your talk and unfortunately my group had a meeting at the same time and I was really bummed I couldn't make it....I was like 'ah come on, are you serious group meeting?' :)

    If you scroll down a little bit here: http://molecular-programming.org/ you can see a description of NUPACK and some of the other projects within the umbrella of mpp. NUPACK stands for NUcleic acid PACKage, and is a suite of stand-alone executables and a web application for designing and analyzing nucleic acid systems. Basically, if you're working with DNA or RNA nanotechnology for a lot of applications you will need to design the equilibrium base pairing interactions for 1 to N number of stands to do cool stuff.

    Comment Source:Hi John! No, I saw your talk and unfortunately my group had a meeting at the same time and I was really bummed I couldn't make it....I was like 'ah come on, are you serious group meeting?' :) If you scroll down a little bit here: http://molecular-programming.org/ you can see a description of NUPACK and some of the other projects within the umbrella of mpp. NUPACK stands for NUcleic acid PACKage, and is a suite of stand-alone executables and a web application for designing and analyzing nucleic acid systems. Basically, if you're working with DNA or RNA nanotechnology for a lot of applications you will need to design the equilibrium base pairing interactions for 1 to N number of stands to do cool stuff.
  • 3.

    Grant wrote:

    In the Caltech study group, we were talking about having a Github repo for coding up some exercises, in Jupyter Notebook format. I wanted to ask, is there an Azimuth Github? Or is this something we could add to a repo associated with the course? Also, I don't want to copy exercises from the book and put them somewhere publicly without permission. Do you think this would be OK or should I email Brendan or David and ask?

    Comment Source:Grant wrote: > In the Caltech study group, we were talking about having a Github repo for coding up some exercises, in Jupyter Notebook format. I wanted to ask, is there an Azimuth Github? Or is this something we could add to a repo associated with the course? Also, I don't want to copy exercises from the book and put them somewhere publicly without permission. Do you think this would be OK or should I email Brendan or David and ask?
  • 4.
    edited June 2018

    My reply:

    I wanted to ask, is there an Azimuth Github?

    Yes, see this page on the Wiki for information on that:

    You might also be interested in this:

    If you do interesting stuff that people should know about, please update the relevant wiki pages and notify us all on the forum - see "Azimuth Forum - Latest Changes" at left. If you do something wrong, I can help you fix it iff I know about it!

    Also, I don't want to copy exercises from the book and put them somewhere publicly without permission. Do you think this would be OK or should I email Brendan or David and ask?

    Brendan and David have already given us permission to do stuff like this:

    and I encourage you to continue doing more of this - click the links to see what this stuff is.

    Comment Source:My reply: > I wanted to ask, is there an Azimuth Github? Yes, see this page on the Wiki for information on that: * [[Azimuth code repository]]. You might also be interested in this: * [[Azimuth Code Project]]. If you do interesting stuff that people should know about, please update the relevant wiki pages and notify us all on the forum - see "Azimuth Forum - Latest Changes" at left. If you do something wrong, I can help you fix it iff I know about it! > Also, I don't want to copy exercises from the book and put them somewhere publicly without permission. Do you think this would be OK or should I email Brendan or David and ask? Brendan and David have already given us permission to do stuff like this: * [[Applied Category Theory - Chapter 1 - Exercises]] * [[Applied Category Theory - Chapter 2 - Exercises]] * [[Applied Category Theory - Chapter 3 - Exercises]] and I encourage you to continue doing more of this - click the links to see what this stuff is.
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