I am a bioinformatician
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wrote on 23 May 2020, 15:03 last edited by
I recently moved from the software development group into the bioinformatics group. Since I was doing bioinformatics for this company since before they had a bioinformatics department, and since I had no interest in writing UI code for the rest of my career, I requested and was granted this transfer. Now all my peers are math/bioinformatics PhDs and my boss is a math/physics PhD from Harvard. Recently my company has been trying to release a covid virus assay for use with our ddPcr instrument and I was chosen to lead the effort to develop the algorithms and tools to process the data and call results. Mayo will be our first customer, who plan on running 3000 samples/day through this analysis tool. We're also working with Johns Hopkins apparently. It will hopefully be released within a couple weeks, but now we're running into issues with the assay which will be show stoppers if not fixed.
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wrote on 23 May 2020, 15:13 last edited by
What a great development for you, and for us.
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wrote on 23 May 2020, 15:44 last edited by
Thank you for your work, Horace! If you make a visit to Mayo, let me know.
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wrote on 23 May 2020, 15:45 last edited by
I’ll never accuse Horace of not understanding how science works!
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wrote on 23 May 2020, 15:47 last edited by
That’s cool.
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wrote on 23 May 2020, 15:53 last edited by
Looking forward to updates!
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wrote on 23 May 2020, 15:56 last edited by
@Loki said in I am a bioinformatician:
I’ll never accuse Horace of not understanding how science works!
I know exactly how quick and dirty science works.
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wrote on 23 May 2020, 16:06 last edited by
@brenda said in I am a bioinformatician:
Thank you for your work, Horace! If you make a visit to Mayo, let me know.
The way it works is, I create the tool, explain to the marketing folk what the tool does, and then they present it to our users. I never so much as see them on a video call, so I don't anticipate any travel. However I have been interacting with company higher-ups through this project so that's been a rare treat.
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wrote on 23 May 2020, 16:17 last edited by
Yeah okay. And now I'm a mathematologist.
Seriously though, sounds cool.
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wrote on 23 May 2020, 16:19 last edited by
Good for you!
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wrote on 23 May 2020, 17:19 last edited by
Cool update, interesting work!
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wrote on 23 May 2020, 17:59 last edited by
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wrote on 23 May 2020, 21:01 last edited by
Sounds cool! What, more specifically, is your job? Do you write the algorithms yourself? What kinds of algorithms are these?
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wrote on 23 May 2020, 21:22 last edited by
In this case the algorithms we needed were a clustering algorithm and an algorithm to detect messy data so we don't provide a false positive or false negative. I write them myself, though the reason they had me do it was because they needed to be written very quickly and I've been going around my whole career telling people I can write algorithms. I have in fact been given that opportunity on occasion, and now that I'm in bioinformatics it won't be politically difficult to be more involved in that stuff.
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wrote on 23 May 2020, 22:07 last edited by
Aren't libraries containing these kinds of algorithms readily available? Why do you bother to write them yourself?
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@brenda said in I am a bioinformatician:
Thank you for your work, Horace! If you make a visit to Mayo, let me know.
The way it works is, I create the tool, explain to the marketing folk what the tool does, and then they present it to our users. I never so much as see them on a video call, so I don't anticipate any travel. However I have been interacting with company higher-ups through this project so that's been a rare treat.
wrote on 23 May 2020, 22:44 last edited by@Horace said in I am a bioinformatician:
@brenda said in I am a bioinformatician:
Thank you for your work, Horace! If you make a visit to Mayo, let me know.
The way it works is, I create the tool, explain to the marketing folk what the tool does, and then they present it to our users. I never so much as see them on a video call, so I don't anticipate any travel. However I have been interacting with company higher-ups through this project so that's been a rare treat.
Well, if they're not Minnesooota nice to you, let me know. I'll get them in line to behave again.
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Aren't libraries containing these kinds of algorithms readily available? Why do you bother to write them yourself?
wrote on 23 May 2020, 22:55 last edited by@Klaus said in I am a bioinformatician:
Aren't libraries containing these kinds of algorithms readily available? Why do you bother to write them yourself?
I would be happy to place any bet on my custom written algorithm to solve these particular problems on this particular data against any standard out of the box algorithm. We do have someone in the bioinformatics group working on a machine learning approach to clustering this sort of data, she has been working on that for many months now, but when it came to this need for this algorithm to be delivered to a customer in very short time, they asked me to do it.
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wrote on 23 May 2020, 23:03 last edited by
I did end up independently inventing Mahalanobis_distance in the couple days I spent thinking about and implementing this algorithm. I described what I was doing to my boss and he told me it had a name.
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wrote on 24 May 2020, 00:39 last edited by
Interesting work that makes a difference.
Can't ask for much more than that...