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| rkneue1 | hi everybody | 06:17 |
|---|---|---|
| rkneue1 | I don't mean to waste your time, but I've a (simple? ) question for any genomics-related field researchers in here... | 06:18 |
| rkneue1 | me and my group are planning to develop a new bioinformatics toolkit… main aim of our project is to allow integration of most available genomics data online (e.g. ngs data such as chip-seqs and so on) and a complexive and non-redundant genes annotation and the actually missing cross-referencing between different genes aliases in different annotations (e.g. ensembl, ncbi, vega, etc.). according to your experiences and needs… what would it | 06:18 |
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| ParahSailin | make a free version of geneious | 06:41 |
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| rkneue1 | geneious cannot do these things... | 07:20 |
| rkneue1 | geneious is a clcbio-like toolkit… and according to my opinion it's kinda heavy... | 07:21 |
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| ParahSailin | i know geneious is something different | 08:43 |
| ParahSailin | you should make that instead | 08:43 |
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| ParahSailin | btw, eureka genomics is hiring bioinformaticists again | 09:06 |
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| kanzure | ParahSailin: worst salesman ever... isn't this the company that gave you mountains of php to maintain? | 09:29 |
| ParahSailin | lol, well thankfully i dont have to touch any php, and the person theyre hiring wont have to either | 09:30 |
| kanzure | pinky promise? | 09:31 |
| gradstudentbot | I remember the paper, I just don't remember the details. | 09:31 |
| ParahSailin | spit shake | 09:32 |
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| chris_99 | i was just thinking something like a cell counter would be pretty easy to make once you've got a microscope and camera wouldn't it | 10:11 |
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| FourFire | chris_99, what do you mean by that? | 11:14 |
| chris_99 | i just thought it'd be something that could be easily made, using simple image recognition | 11:15 |
| ParahSailin | yeah fundamentally a flow cytometer is pretty simple | 11:15 |
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| kanzure | gradstudentbot .add yeah fundamentally a flow cytometer is pretty simple | 11:18 |
| gradstudentbot | That's the control group, right? | 11:18 |
| FourFire | I really need a soundgif to this: http://boourns.dynu.net/pics/rDGrP.gif | 11:18 |
| chris_99 | i was actually thinking of a static slide, with cells on, that have been dyed, along with the lines denoting the separation, but if you could do it for flow cytrometry too.. | 11:19 |
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| kanzure | https://github.com/mayosmith/openbitcoinatm | 11:20 |
| FourFire | the best I can do is an imaginary marble on wood sound, like the booming, works like the booming sound with the gif of the high voltage cable tower skipping-rope | 11:20 |
| kanzure | start yer hax0ring | 11:20 |
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| juri_ | I'm continuing to specialize in image recognition, so if someone wants to get me some video / stills of cells, i can tell you how likely current simple image recognition technology is going to solve your problem, FYI. | 13:24 |
| chris_99 | cool, what kind of image recognition do you do | 13:26 |
| chris_99 | do you do stuff similar to SIFT for example | 13:27 |
| juri_ | i'm the maintainer of GNU GIFT, but i've recently been creating a new web interface, with other imaging technologies integrated. | 13:27 |
| juri_ | nope. what i use is very fixed scale, and abuses that fact. ;) | 13:27 |
| chris_99 | aha | 13:28 |
| juri_ | SIFT makes more sense in the real world. most of what i'm doing is really working against 2d objects scanned at a consistent size (sheets of paper, one way or the other.) | 13:28 |
| gradstudentbot | Argh, what do you mean you don't accept LaTeX submissions?? | 13:28 |
| chris_99 | aha gotcha | 13:28 |
| chris_99 | what algs do you use for that? | 13:31 |
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| juri_ | chris_99: i'm using gabor transforms, hough transforms, and am looking at MSER. | 13:47 |
| chris_99 | ah cool, i had a play with hough transforms to find lines, then ported some LSD code to java | 13:48 |
| wallmani | LSD code? | 13:49 |
| chris_99 | http://www.ipol.im/pub/art/2012/gjmr-lsd/ | 13:50 |
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| delinquentme | paperbot, http://stm.sciencemag.org/content/5/214/214ra170.full | 14:55 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1126%2Fscitranslmed.3006870 | 14:55 |
| delinquentme | so I kinda want one of these? http://www.flickr.com/photos/garry_rocks/11729002556/in/photostream/ | 15:00 |
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| delinquentme | http://www.flickr.com/photos/garry_rocks/11330550364/in/photostream/ | 15:01 |
| gradstudentbot | Well, I can't really talk about it because I'm trying to get it published in Science or Nature. | 15:01 |
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| delinquentme | paperbot, http://stm.sciencemag.org/content/5/214/214ra170 | 15:04 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1126%2Fscitranslmed.3006870 | 15:04 |
| delinquentme | paperboot these links do not work ! | 15:05 |
| kanzure | then fix it | 15:06 |
| kanzure | https://github.com/kanzure/paperbot | 15:06 |
| gradstudentbot | Wow, I'm definitely not including this data in the paper. | 15:07 |
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| delinquentme | paperbot, http://stm.sciencemag.org/content/5/214/214ra170 | 15:19 |
| paperbot | http://libgen.org/scimag/get.php?doi=10.1126%2Fscitranslmed.3006870 | 15:19 |
| delinquentme | kanzure, where is paperbot running? and are there instructions to make a live push and update? | 15:19 |
| chris_99 | haha that lego thing is cute delinquentme | 15:20 |
| delinquentme | I kinda want a small collection of them now! | 15:20 |
| chris_99 | heh | 15:20 |
| delinquentme | has anyone thought about running data munging / standardization / wrangling as a service? | 15:25 |
| delinquentme | I thought I had some wild insight by paying multiple cheap labor individuals in a far off land to run the cleaning | 15:26 |
| delinquentme | then run a diff on the finalized data as a quality check. | 15:26 |
| kanzure | delinquentme: if you make a pull request, i'll push the changes to the right place | 15:31 |
| delinquentme | is there anyway that I could get my own paperbot up and running? | 15:36 |
| delinquentme | are there details on that ? | 15:36 |
| kanzure | the README explains the dependencies | 15:36 |
| kanzure | there is an environment variable that it will ask you for, but you can just set it to an empty string | 15:36 |
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| chris_99 | http://www.youtube.com/watch?v=HUW7dQ92yDU | 16:22 |
| chris_99 | .title | 16:22 |
| chris_99 | " | 16:22 |
| chris_99 | Transcranial Magnetic Stimulation project - part 1" | 16:22 |
| gradstudentbot | Hood life: https://www.facebook.com/photo.php?fbid=296519020495014 | 16:26 |
| chris_99 | http://www.youtube.com/watch?v=B_olmdAQx5s | 16:28 |
| chris_99 | that is amazing | 16:28 |
| gradstudentbot | I don't remember the paper, but someone definitely did that. | 16:29 |
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| nmz787 | juri_: ever do any android dev? you say you have a webserver with some image proc? maybe android dev isn't needed, maybe users (bio ppl with cell images) could just upload to your site... things like counting cells on a petri dish is an easy goal... then distinguishing their color is another | 17:07 |
| juri_ | No. | 17:07 |
| juri_ | and yes, my site is designed for users to just sign up, and use all these image processing tools. | 17:08 |
| juri_ | wanna take a peek at the 'new hotness'? i've got a new version i'm trying to get out the door next week. | 17:08 |
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| kanzure | you should just use normal image processing tools, and then the web server can be just an api to those tools | 17:35 |
| kanzure | there's no reason to couple software that much :( | 17:35 |
| juri_ | gift doesn't work like 'normal image processing tools'. | 17:36 |
| kanzure | i don't care, i strongly odubt it requires a website to function | 17:37 |
| kanzure | *doubt | 17:37 |
| juri_ | no, but it requires a web site to be useful. | 17:37 |
| kanzure | i doubt it. if the algorithm doesn't work without http then your algorithm is fundamentally flawed.. | 17:37 |
| kanzure | you said it was image processing related? | 17:37 |
| * juri_ rolls her eyes into the next continent. | 17:37 | |
| juri_ | did you not READ WHAT I SAID? | 17:38 |
| juri_ | now, i'll take helpful input from anywhere, but just saying "i doubt that" to everything i say is not fucking helpful. | 17:38 |
| kanzure | you're telling me that gift requires a website to be useful | 17:38 |
| juri_ | gift was an accademic application. and that makes it VERY broken. | 17:38 |
| juri_ | 'useful'. | 17:38 |
| juri_ | yes, i am. i've put together a site, where people i know can accomplish tasks in their day to day lives, that use gift for image processing. | 17:39 |
| kanzure | all i see on the site is "query by example"... so ./thing --examples=path | 17:39 |
| juri_ | sure, if you want, you can run it from a command line, manually import collections, start and restart and restart the daemon as you add images... | 17:39 |
| kanzure | yeah, so that doesn't require a web server. a web server is just a completely separate stack of software that shouldn't infect the gift source code. | 17:39 |
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| juri_ | but if you want to get stuff done, you use the web UI. | 17:40 |
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| kanzure | but also, now that you mention it, i am also skeptical of the daemon ;) | 17:40 |
| juri_ | its not 'infecting' the code. they're seperate projects, and seperate tools. | 17:40 |
| kanzure | what? that's not what you described earlier | 17:40 |
| juri_ | i HATE the daemon. | 17:40 |
| juri_ | well then, blame my ability to describe. | 17:40 |
| juri_ | i do. ;) | 17:40 |
| kanzure | easily done.... | 17:40 |
| juri_ | gift is fundamentally flawed and broken. i'm wrapping it, to make it not as flawed and broken. the wrapper has become its own monstrosity, which is now having new algorithms added to it.. | 17:41 |
| kanzure | digging a deeper hole to get out of the first hole? | 17:42 |
| juri_ | yep. | 17:42 |
| kanzure | can i sell you a shovel | 17:42 |
| juri_ | you can pay me to dig, you can dig, or you can get down in the hole, and look at what i'm digging through. i take no direction from people standing on the level earth. ;) | 17:43 |
| gradstudentbot | I am completely satisfied with the size of my bench space. | 17:43 |
| juri_ | there are several ways you're correct, and my approach is not quite sane. i'm trying to find the shortest route from accademic tool discarded a decade ago, to useful day to day tool for non programmers. sanity is left behind when you start talking to non-engineers. | 17:45 |
| kanzure | just because it's for non-engineers doesn't mean writing mangled software is worthwhile | 18:02 |
| kanzure | engineers aren't the only people that can make use out of stable, sane software | 18:02 |
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| pasky | kanzure: gee, you are such a perfectionist ;-) | 19:00 |
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| juri_ | he keeps us lesser beings on our toes. ;) | 19:28 |
| kanzure | never called anyone lesser | 19:41 |
| kanzure | pasky: more disappointed than perfectionist.. | 19:42 |
| juri_ | if you're going to be disapointed each time someone you know doesn't have the resources to do a job the way you both think it should be done, you're going to spend a lot of time disapointed. | 19:54 |
| kanzure | what do you mean you don't have hte resources | 19:54 |
| kanzure | i thought you said you just miswrote | 19:55 |
| juri_ | I'd much rather b espending the effort killing off the daemon. i find myself feeling like i'm re-inventing SQL in a gui. | 19:57 |
| juri_ | its just that re-inventing sql in the gui just a little bit better each time someone bugs me about it, or drops a few weeks paychecks on the table, is much easier than doing the right and proper work. | 19:57 |
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| kanzure | "High-end CNC machines can't be moved without manufacturers' permission" http://boingboing.net/2014/01/06/high-end-cnc-machines-cant-b.html | 20:42 |
| kanzure | "On Practical Machinst, there's a fascinating thread about the manufacturer's lockdown on a high-priced, high-end Mori Seiki NV5000 A/40 CNC mill. The person who started the thread owns the machine outright, but has discovered that if he moves it at all, a GPS and gyro sensor package in the machine automatically shuts it down and will not allow it to restart until they receive a manufacturer's unlock code." | 20:42 |
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| kanzure | seems to probably be just a gyroscope | 21:04 |
| kanzure | because there's no way that gps works inside of those metal buildings | 21:04 |
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| dantespeaks | It'll be moved out of the building then activates because of the gyroscope? To cover that distance of travel GPS will catch a signal somewhere... | 22:27 |
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| dantespeaks | It's amazing. I guess that CNC machine is a great value to manufacturing companies, they put such measures of security on it. But everything these days are... | 22:28 |
| dantespeaks | oh man i need to sleep. vertigo keeps coming back. can't grammatically make a structured sentence im not making sense...ugh | 22:42 |
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| --- Log closed Tue Jan 07 00:00:16 2014 | ||
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