daemonk

19 ms·

151.
by daemonk 9y ago
Yeah, agreed. The number of times I hear tech bros giving me buzz words to "solve" my analysis...
152.
by daemonk 9y ago
Might be cool to implement a weighted relationship based on reciprocal linking or number of links.
153.
by daemonk 9y ago
That's like saying: given a flowchart where A->B->C, A leads to C, not B.
154.
by daemonk 9y ago
Yeah agreed. I don't think most people actually understand the level of complexity involved in biology. A cell is literally a bag of molecules where everything inside is just bouncing around. And somehow, things self organize and stuff
155.
by daemonk 9y ago
I've never heard of the Andy Grove fallacy, but it is extremely relevant. As a bioinformatician actively working in the field, I get the same statements from people in the tech industry. Often it comes down to: "why don't you
156.
by daemonk 9y ago
Sure. It was shitty when US did it and it is also shitty now when China does it.
157.
by daemonk 9y ago
I wonder if academic papers are usually dense and non-accessible because they are not opened up to the public. Perhaps more effort should be made on the part of the academic to make their findings more accessible without compromising on the
158.
by daemonk 9y ago
Who are your customers? Normal consumers? Academia? I am actually looking to get my genome sequenced. I am looking to do ~30X and I just want the fastqs. I am a bioinformatician and can do my own analysis. Is that a service you provide?
159.
by daemonk 9y ago
I can add to this with my anecdotal evidence. In my experience (looked at ~15gb of basecalled data total), there is a large amount of indel errors. The mismatch rate is much lower. But it's hard to calculate exactly the mismatch rate w
160.
by daemonk 9y ago
If you want to do absolutely everything yourself from DNA extraction to sequencing and data analysis, then yes, this is probably the cheapest way. But you also need to consider how you prepare your DNA to go into the Nanopore. It's a l
161.
by daemonk 9y ago
There is a group in UK (Matt Loose's group) that I think is working a lot on read-until. I haven't really kept up with it. I think the key for read-until to work is ultimately probably going to be better hardware as you need to be
162.
by daemonk 9y ago
It's fine for bacteria where even with 10-20% error, you can do consensus calling with very high (200-500X) coverage.
163.
by daemonk 9y ago
I am using it professionally for a lab. The best bang for the buck right now is to buy their starter pack which includes library prep kit and 2 flow cells. This is limited to one per person. I got two members of the lab to buy two starter k
164.
by daemonk 9y ago
The flowcell is a consumable. You can run it for ~2 days on average. You can wash it out and run other samples during the 2 days if you want, but it will stop working after ~2 days of running. And in my experience, the washing buffer doesn&
165.
by daemonk 9y ago
I just ran a couple of flowcells last week. I've ran 8 total so far now. My impression is that it can be very inconsistent depending on the quality of the flowcell that they send you and your DNA prep. Great for smallish genomes (bacte
166.
by daemonk 9y ago
The number of data points is a bit misleading. Unless I am interpreting it wrongly, it looks like less than 100 rats were actually used to look at the hazard rate? Most of the ~3000 rats were censored because they moved/euthanized for
167.
by daemonk 9y ago
Yeah seriously. Are people really that insecure with their job titles that they need to invent bullshit to make UX seem more scientific?
168.
by daemonk 9y ago
Has governmental tax laws changed in response to corporation taking advantage of loopholes? If that is the case, then is it actually to ones disadvantage to not use loopholes, which has become the new norm?
169.
by daemonk 9y ago
There needs to be more of a narrowing of the gap between biology and tech. I feel like right now the giants in both fields are still very much experts of their own biology or technology domains. The perspective one takes on the biological s
170.
by daemonk 9y ago
Isn't this the software that turns alignments into images to run through an image analysis pipeline? They just jerryrigged alignment data onto an image analysis system? Does it offer speed/memory advantages over traditional varian
171.
by daemonk 9y ago
Cool. Looking at this closer, I realized this doesn't create a maze with multiple branching paths. It creates just linear paths.
172.
by daemonk 9y ago
What I meant by "values" is some kind of moral superiority that seems to be espoused by a lot of people I've met in academia. That somehow not pursuing academic research is "selling out". This idea is implicitly ing
173.
by daemonk 9y ago
I agree about their communication and support. It does seem like they put all their support behind the few big labs in the UK that are actively using nanopore (free R&D for them I guess). I get a sense of "if you can't get thi
174.
by daemonk 9y ago
Are you working on cell lines or bacteria? Genomic dna? I find most people that tell me they get good data yield are working on samples where dna extraction is relatively straightforward and dna yield is abundant. I used the flowcell versio
175.
by daemonk 9y ago
Because not all work in academia is interesting. I don't know about your field but academic research is more about doing what your funding bodies want you to do or following the latest trend to get funding. Publishing can be a politica
176.
by daemonk 9y ago
I've personally prep libraries and used nanopore. While there is a lot of promise to the technology, I found it to be too inconsistent. Nanopore claims they can get 10gigs of data, while power users claim they get 2-5gig on average. I
177.
by daemonk 9y ago
Isn't that just really standard employment? Or maybe similar to an academic tenure position? I think UBI is meant to be "universal", with no prerequisites.
178.
by daemonk 9y ago
I really want to get into these types of apps as I think it will greatly improve my work speed. But I am always afraid of becoming over-dependent on these tools. I commonly change environments in my work, so I often have to adapt to new sys
179.
by daemonk 9y ago
"Good enough" is often very subjective.
180.
by daemonk 9y ago
Yeah I can even imagine a thriving "marketplace" for specialty code that top players would keep secret. And it doesn't have to just be for micro. For people who are bad at macro, maybe code can be written to consistently main

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