daemonk

22 ms·

211.
by daemonk 10y ago
I'd argue that it's not really meant for developing software. It's meant for data analysis. When I do my analysis, I am not really concerned with developing the script/algorithm. I am mainly concerned with manipulating o
212.
by daemonk 10y ago
My comment is not related to the topic at all. Don't you think that these terminology we call each other by (liberal/conservative..) is stifling constructive discussion? I am sure there is a popular or objective definition of thes
213.
by daemonk 10y ago
Is there a spot instance-like mechanism with google cloud? I regularly request high memory spot instances (r3.8xlarge) on AWS for 1-2 days processes (genomic analysis). With spot-pricing it can be pretty cheap.
214.
by daemonk 10y ago
A great short story Ted Chiang wrote that have some themes similar to Arrival (free will) is the one he wrote for Nature Futures: http://www.nature.com/nature/journal/v436/n7047/full/436150a...
215.
by daemonk 10y ago
I really miss gameplay driven games rather than presentation/story driven games. I think both are great, but I really enjoy the technical intricacies of street fighter or mega-man games.
216.
by daemonk 10y ago
Yeah, I kinda agree. But it really depends on use case though. I do data analysis and I have a beefy server that I log on to for heavy duty tasks, so I'll probably not use my macbook for anything that requires more than 16gb.
217.
by daemonk 10y ago
This all sounds great. I'll definitely look into it for myself. However, coming from academic biology (I am a bioinformatician) where most of my collaborators won't even know what git is, this is just not a realistic solution. If
218.
by daemonk 10y ago
I've used sharelatex and overleaf. I find them great. But what people in my field want are tracked changes features that you see in MS word. So deleted/added text highlighted by who changed it, comment boxes, etc.
219.
by daemonk 10y ago
I personally really like using latex. But the main problem for me is that latex is not really designed for collaborative editing, especially with people who don't know latex. are there any track changes feature plugin/app that&#x2
220.
by daemonk 10y ago
Playing devil's advocate here. Is the outrage towards this kind of system essentially a criticism of the technology? Specifically, can we guarantee that the system would be secure and can we guarantee that the system is accurate (objec
221.
by daemonk 10y ago
The main reason is because no one wants to publish technical or "methods" type papers where they assess the technology. There is usually one or two initial big papers introducing the technology that makes a big splash. No one subs
222.
by daemonk 10y ago
With single cell data, gene expression data from each cell is considered a dimension. So you end up with something in the range of 20-30k genes and possibly thousands of cells (~25k x thousands matrix). I don't think the technology is
223.
by daemonk 10y ago
The seurat R package ( http://satijalab.org/seurat/ ) tries to give you more information on how to choose your PCs. But as with anything in biology, it becomes subjective at some point.
224.
by daemonk 10y ago
I work mostly remotely by ssh-ing into the work ubuntu server from my macbook, so I don't really use the local terminal all that much. I've noticed in the past that the local osx terminal can be somewhat different from a standard
225.
by daemonk 10y ago
Most people aren't very diligent with naming their tags and organizing their data. I am definitely guilty of this. Are there any data management services out there that can use some kind of semantic understanding to let you search thro
226.
by daemonk 10y ago
What's vastly different between software instructions in dwarf fortress vs DNA is what actually computes the code. There is a negligible amount of complexity in made-made computers vs what goes on in a cell. There are layers upon layer
227.
by daemonk 10y ago
That's a bit harsh. The analogy made is not an uncommon one, but that doesn't mean there isn't some merit to the idea. I appreciate that people are at least trying to learn new things and form their own ideas.
228.
by daemonk 10y ago
I never said to not read the book or learn the maths. They are obviously important. I apologize if I sounded dismissive. But I've met people in my field that are great at the maths (which should be a given), but can't execute the
229.
by daemonk 10y ago
My issue with these sanitizing pipelines is that they only really work for fields where the data generation is relatively stable. Meaning, whatever instrument/method used in generating the data doesn't change dramatically every ye
230.
by daemonk 10y ago
The high theory stuff is great, but a significant portion of the job is being a data janitor. Being experienced and fast at manipulating data structures, recognizing patterns in text datasets, understanding common formats used in the field
231.
by daemonk 10y ago
I am not trying to inject my opinion. I am looking for genuine discussion. The idea of privacy has always been kind of vague to me. Where do we draw the line of acceptable information sharing and not? If a company is collecting data on our
232.
by daemonk 10y ago
Yeah definitely. I actually work in academia (I guess I wasn't very qualified to speak about SV). But it's the same shtick everywhere. Passion has become an euphemism for soft corporate brain-washing. I am reminded of this blog ar
233.
by daemonk 10y ago
I am getting to old geek status myself. From a more cynical perspective, I am not sure if we can compete with early twenty-somethings who are unjaded and buy into the silicon valley mystique. They are willing to work 12 hour days and still
234.
by daemonk 10y ago
This seems very standard to me. The only thing that can't be reproduced immediately is the CNV algorithm?
235.
by daemonk 10y ago
I am not sure there is really a large enough corpus of data out there that covers multiple facets of this system to really give us a strong predictive value. Just variant calls is probably not enough. There might be, if we can somehow conso
236.
by daemonk 10y ago
Evolution doesn't foresee the catastrophic event that may happen in ten thousand generations. If there is no selective pressure, this gene is free to build up mutations and diverge away.
237.
by daemonk 10y ago
From a data analysis perspective (which seems like some of her rules are related to), my number one rule that I always try to follow is to: work with the data, not with the tools. It can be really easy to go down the rabbit hole of messing
238.
by daemonk 10y ago
I can see the value in the organization of these activities. But without some kind of manual curation into "layman" categories or translations of what these activities are, it's still difficult for me to interpret.
239.
by daemonk 10y ago
I am a bioinformatician. 130tb of raw reads or processed data? Are you trying to build a general purpose platform for all *-seq or focusing on something specific (genotyping)?
240.
by daemonk 10y ago
I often see packages or solutions to problems related to browsers/servers on hackernews. Why don't people who make browsers or servers implement these things as a standard? IE. There seems to be so many people using jquery/re

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