| --- Log opened Wed Feb 13 00:00:59 2013 | ||
| @kanzure | "geneart does their synthesis on ordinary tecans. they dont have specialized "synthesizers" at all." | 00:12 |
|---|---|---|
| @kanzure | nmz787: let's run a mask through stanford's mems facility | 00:19 |
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| @kanzure | http://www.epiloglaser.com/laser_faqs.htm#qspot | 00:45 |
| @kanzure | nmz787: do you have a link to your laser cutter test results? | 00:47 |
| @kanzure | "Opera to switch to WebKit rendering engine" http://www.opera.com/press/releases/2013/02/13/ | 00:52 |
| @kanzure | whaat. | 00:52 |
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| archels | paperbot: http://www.nature.com/nphoton/journal/v7/n2/pdf/nphoton.2012.329.pdf | 01:18 |
| @paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/a29da6d6b1bab6a6545c1be705004e9e.pdf | 01:18 |
| -!- mode/##hplusroadmap [-o paperbot] by kanzure | 01:19 | |
| archels | Marker-free phase nanoscopy | 01:19 |
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| @kanzure | hmm they stopped supporting gtkmozembed in 2011, https://groups.google.com/forum/#!topic/mozilla.dev.embedding/c_NMcO-N8wo/discussion | 02:03 |
| @kanzure | haha lkcl is ranting in that thread, hilarious | 02:05 |
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| nmz787 | kanzure: laser cutter results? | 03:08 |
| @kanzure | i think you did a few cuts and then ran it through a .. um. a mass spec maybe?? | 03:09 |
| @kanzure | no.. it wasn't a microscope, but you ended up with microscopy images anyway. | 03:09 |
| @kanzure | and i can't find that link. | 03:09 |
| nmz787 | ahh | 03:10 |
| nmz787 | i don't think i have those pics up anywhere | 03:10 |
| @kanzure | then how did i see them | 03:10 |
| nmz787 | maybe they were on an old server that's not up anymore? | 03:11 |
| nmz787 | email? | 03:11 |
| @kanzure | :( | 03:13 |
| nmz787 | i saw them last week | 03:14 |
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| chris_99 | http://thepaperbay.com/ | 05:22 |
| superkuh | http://reddit.com/r/scholar is a bit more established. | 05:25 |
| chris_99 | ooh cool | 05:26 |
| chris_99 | i think we need a P2P program though :) | 05:26 |
| chris_99 | to do this automatically | 05:27 |
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| @kanzure | i like how incomplete this is, http://thepaperbay.com/others/ | 10:55 |
| @kanzure | "If you are operating another service along these lines of if you are aware of one please let me know through j@ww.com , and I'll update this page." | 10:55 |
| @kanzure | what's funny is that i have actually had extremely long email threads with him in the past, and he's well aware of the existence of other initiatives | 10:55 |
| @kanzure | http://www.jacquesmattheij.com/introducing-thepaperbay | 11:05 |
| @kanzure | ah, various news commentary http://news.ycombinator.com/item?id=5212186 | 11:15 |
| ParahSailin | there's boxes with data fields and a submit box, but what's on the other side? | 11:17 |
| ParahSailin | a hyperintelligent paperbot hooked into a university network? | 11:17 |
| ParahSailin | site owner manually completing requests? | 11:17 |
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| @kanzure | ParahSailin: not even that.. he's expecting other users to fulfill requests. | 11:22 |
| @kanzure | paperbot: http://eplex.cs.ucf.edu/papers/risi_alife12.pdf | 11:24 |
| @kanzure | "An Enhanced Hypercube-Based Encoding for Evolving the Placement, Density and Connectivity of Neurons " | 11:24 |
| @kanzure | http://eplex.cs.ucf.edu/publications/2012/risi-alife12 | 11:24 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/edfdd2ce0e54e4ad7e04faac7bf69674.pdf | 11:24 |
| ParahSailin | kanzure: i can't see outstanding requests there, how would i help fulfill them | 11:25 |
| @kanzure | maybe they have all been satisfied | 11:25 |
| ParahSailin | hm, probably | 11:26 |
| @kanzure | also, i'm posting pdfparanoia to HN if anyone wants to upvote https://github.com/kanzure/pdfparanoia | 11:26 |
| @kanzure | hmm http://wesleytansey.com/the-acm-is-violoating-the-can-spam-act/ | 11:29 |
| ParahSailin | cool good job on watermark removal | 11:29 |
| @kanzure | paperbot is using pdfparanoia at the moment | 11:30 |
| ParahSailin | oh god-- guy-who-left's code is awful and its my job to salvage | 11:48 |
| @kanzure | hire a lawyer, hit the gym, quit, etc. | 11:49 |
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| @kanzure | scholar.google.com seems to be broken | 12:57 |
| nmz787 | paperbot: http://www.physics.rutgers.edu/ugrad/387/388s06/film_deposition/Musgraves05.pdf | 12:59 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/5d621e5501b976c228062d92946b3cde.pdf | 12:59 |
| nmz787 | kanzure: this paper from 2004 is saying oligos were $0.11 per base... WHAT? http://arep.med.harvard.edu/pdf/Tian04.pdf | 13:09 |
| @kanzure | not surprised | 13:10 |
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| nmz787 | paperbot: http://arep.med.harvard.edu/pdf/Tian04.pdf | 13:12 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/d7780918d5a9afbc18cf1b255ef035ce.pdf | 13:12 |
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| nmz787 | ttyl | 13:20 |
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| @kanzure | http://computerhistory.org/atchm/adobe-photoshop-source-code/ | 14:09 |
| @kanzure | http://torrentfreak.com/anti-piracy-group-rips-off-pirate-bay-website-faces-lawsuit-130213/ | 14:09 |
| @kanzure | sciquest integration guide http://supplier.wpengine.netdna-cdn.com/wp-content/uploads/SuppliercXMLIntegrationSpecification_V3-1.pdf | 14:20 |
| @kanzure | transcriptic/max hodak stuff, pre-transcriptic http://boss.blogs.nytimes.com/2009/11/18/tune-in-start-up-drop-out/ | 14:20 |
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| @kanzure | wow, heroku crippled itself http://rapgenius.com/James-somers-herokus-ugly-secret-lyrics | 14:35 |
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| klafka_ | remember | 14:51 |
| Juul | hm, not sure my last messages got through | 14:51 |
| klafka_ | OWNED BY SALESFORCE | 14:51 |
| Juul | anyone know anything about this Jacques Mattheij? | 14:51 |
| Juul | if he is a dutch citizen living in somewhere that's not the U.S. then it's kinda foolish to use a .com domain | 14:51 |
| Juul | that makes extradition to the u.s. much more likely | 14:51 |
| klafka_ | why? | 14:51 |
| @kanzure | Juul: yeah i've talked with jacques often | 14:52 |
| @kanzure | Juul: he's very responsive by email, j@ww.com | 14:52 |
| Juul | ok | 14:53 |
| @kanzure | are you back in the US? | 14:54 |
| @kanzure | paperbot: http://www.cell.com/retrieve/pii/S0092867412015000 | 14:55 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/System-wide%20Rewiring%20Underlies%20Behavioral%20Differences%20in%20Predatory%20and%20Bacterial-Feeding%20Nematodes.pdf | 14:55 |
| Juul | kanzure, yep! | 14:55 |
| Juul | only questioned for half an hour at the border :-S | 14:55 |
| @kanzure | https://github.com/openworm/CElegansNeuroML | 14:55 |
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| @kanzure | https://optimal-neuron.readthedocs.org/en/latest/ | 14:56 |
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| @kanzure | paperbot: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0050276 | 14:57 |
| paperbot | error: HTTP 500 http://diyhpl.us/~bryan/papers2/paperbot/Robust%20Short-Term%20Memory%20without%20Synaptic%20Learning.pdf | 14:57 |
| chris_99 | re. pdf paranoia kanzure someone had a good idea on HN, you could grab the paper from multiple users and do a diff, and remove user specific id's | 14:58 |
| @kanzure | most users do not have access to multiple sources of the same paper | 14:58 |
| @kanzure | however, i have done that diffing process manually for nature and sciencedirect and found that the hashes are exactly the same. | 14:59 |
| @kanzure | obviously, this needs to be performed for all of the other publishers. but so far i don't think it's happening. | 14:59 |
| @kanzure | i mean, so far i don't think any publisher is watermarking images or including hidden tracking data. | 14:59 |
| chris_99 | aha | 14:59 |
| @kanzure | based on my testing. | 14:59 |
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| @kanzure | valve is dumping jeri ellsworth? that seems like a crazy thing to do. | 15:24 |
| streety | if anyone was you would assume it would be one of those two | 15:29 |
| streety | ^ in ref to the tracking of pdf files | 15:30 |
| @kanzure | hmm well, nature seems to not include visible watermarks either. i assume they put some thought into this and they chose not to. | 15:31 |
| streety | cool, I have something of a love/hate relationship with nature - I love that they send me free print editions of nature methods but hate I, at least personally, don't have electronic access. Seems strange | 15:33 |
| @kanzure | how do you get print editions of nature methods for free? | 15:34 |
| Juul | yeah how? | 15:34 |
| Juul | i'm like a third author or some such on a couple of articles in the next edition | 15:34 |
| Juul | would be fun to have a print | 15:34 |
| streety | Seems to be a thing they do, nothing special about me. I just fill out a 5 min survey maybe once a year | 15:35 |
| @kanzure | s/third author/third wheel/ (the guy who wrote most of it, probably) | 15:35 |
| @kanzure | can you give us a link to that survey..? | 15:35 |
| Juul | haha, actually the first author did most of the work | 15:35 |
| @kanzure | ah good | 15:35 |
| streety | I'll try and find it | 15:35 |
| streety | Juul: what are the articles on? | 15:35 |
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| streety | I can't find the link I initially used to subscribe, only the renewal links but they ask for an account number | 15:44 |
| @kanzure | can you show the renewal link, possibly with a modified id? | 15:45 |
| streety | http://www.sunbeltfs.com/forms/nh/lookup.asp?eid=R99999 | 15:47 |
| @kanzure | fbi replied to my foia, i have a request id <3 | 15:48 |
| streety | what did you request? | 15:48 |
| @kanzure | anything related to me. | 15:48 |
| streety | would they release anything interesting/currently active? | 15:50 |
| @kanzure | unfortunately their letter is just telling me the request id number | 15:51 |
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| @kanzure | paperbot: http://www.sciencedirect.com/science/article/pii/S0306987710002045 | 16:10 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/The%20unreasonable%20effectiveness%20of%20my%20self-experimentation.pdf | 16:11 |
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| streety | what is paperbot? | 16:16 |
| Juul | streety, predictable composable promoters and ribosome binding sites | 16:16 |
| streety | I shall look out for it | 16:17 |
| @kanzure | paperbot is just a bot that downloads papers given links to academic publishers | 16:19 |
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| streety | cool, what does the bit about the translator mean? | 16:24 |
| @kanzure | paperbot uses zotero to download papers and metadata, but sometimes that doesn't work and i wrote a backup. | 16:25 |
| @kanzure | https://github.com/kanzure/paperbot#readme | 16:25 |
| @kanzure | https://github.com/kanzure/translation-server | 16:26 |
| @kanzure | https://github.com/kanzure/translators | 16:26 |
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| nmz787_ | Sup | 16:35 |
| @kanzure | trying to score a copy of nature methods for everyone, so far no luck | 16:38 |
| nmz787_ | I've downloaded their paparrs | 16:39 |
| nmz787_ | Via if | 16:39 |
| streety | kanzure, I think last time I renewed they gave an option to forward the offer to interested colleagues | 16:39 |
| nmz787_ | Via UC berkeley | 16:39 |
| nmz787_ | I think | 16:39 |
| mutagen | if i went to berkly | 16:40 |
| mutagen | i wouldnt tell anyone | 16:40 |
| mutagen | id be afraid theyd think i was some communist hippie drug addict | 16:40 |
| nmz787_ | I don't go there, so I guess I'm OK | 16:41 |
| nmz787_ | BUT I'VE | 16:41 |
| nmz787_ | considered it | 16:41 |
| nmz787_ | Android touchtyping sucks compared to apple | 16:42 |
| nmz787_ | I was so much better on my old flip phone | 16:42 |
| nmz787_ | With T9 | 16:42 |
| nmz787_ | Kanzure you mentioned running a mask at Stanford... Just to have a relative comparison? | 16:43 |
| nmz787_ | That paper I found earlier simply reversed the last projectorle | 16:44 |
| nmz787_ | Lens before mounting it in front of the microscope ocular | 16:44 |
| nmz787_ | So I'm pretty close to doing a DLP mask exposure | 16:44 |
| nmz787_ | The lab even has some old Su-8 | 16:45 |
| nmz787_ | Really old though, so its a toss up if it works | 16:45 |
| @kanzure | no i mentioned running the mask and chip production just to have a working chip | 16:45 |
| @kanzure | for android typing i suggest https://play.google.com/store/apps/details?id=com.volosyukivan | 16:46 |
| streety | kanzure - I'm just going through the renewal process now (so will probably be getting two copies again next month) and have the option to supply names for three colleagues who would like to receive copies | 16:46 |
| @kanzure | streety: when that happens, can you show me the renewal form so i can see if it is vulnerable to an exploit? i definitely know >3 people who want this.. | 16:47 |
| @kanzure | oh wait | 16:47 |
| nmz787_ | Man | 16:47 |
| @kanzure | you gave the link earlier | 16:47 |
| nmz787_ | Kanzurr | 16:47 |
| nmz787_ | Kanzure that link doesn't improve phone input | 16:48 |
| @kanzure | it does if you have a laptop | 16:48 |
| nmz787_ | I am on my phone though | 16:48 |
| nmz787_ | No laptop | 16:48 |
| -!- Viper168 [~Viper@unaffiliated/viper168] has joined ##hplusroadmap | 16:50 | |
| -!- Urchin[Emacs] [~user@unaffiliated/urchin] has joined ##hplusroadmap | 16:51 | |
| streety | kanzure it may be possible to just add additional fields to the form but I think the simplest approach will be to daisy chain requests - I invite 3 people who, because you don't seem to need to wait until the end of your subscription, immediately invite 3 others, etc | 16:52 |
| -!- Juul [~Juul@50-0-146-110.dsl.dynamic.sonic.net] has left ##hplusroadmap ["Leaving"] | 16:53 | |
| @kanzure | streety: could you try this for me? | 16:54 |
| @kanzure | streety: http://www.sunbeltfs.com/forms/nh/lookup.asp?eid=R99999%22%3E%3Cscript%20type=%22text/javascript%22%3Ealert('hi');%3C/script%3E%3C%22 | 16:54 |
| @kanzure | chrome seems to block it because it sees the javascript in the request url. damn. | 16:55 |
| streety | :/ that actually works for me | 16:55 |
| @kanzure | ha ha ha | 16:55 |
| @kanzure | so you get the alert? | 16:55 |
| streety | yeah | 16:55 |
| @kanzure | fantastic.. now we can start our evil scheme to read science and learn things. :( | 16:55 |
| -!- safitan [~safitan@75-105-12-23.cust.wildblue.net] has joined ##hplusroadmap | 16:58 | |
| -!- mutagen [~safitan@75-105-12-23.cust.wildblue.net] has quit [Ping timeout: 252 seconds] | 17:00 | |
| nmz787_ | Kanzure what 3 ppls should I list? | 17:01 |
| nmz787_ | Anyone? | 17:01 |
| @kanzure | i don't get it. anyone can list themselves? then why is there a for-pay version at all? | 17:01 |
| nmz787_ | Thank you for applying for a free subscription to Nature Methods. | 17:05 |
| nmz787_ | Thank you for applying for a free subscription to Nature Methods. We will inform you shortly if your application has been successful. | 17:05 |
| nmz787_ | Well then, ok! | 17:06 |
| streety | excellent, what did you need to do? | 17:06 |
| nmz787_ | Just name address and survey | 17:06 |
| nmz787_ | I clicked that link that said somethin about 'if youbdont have an account' | 17:07 |
| -!- augur_ [~augur@208.58.5.87] has joined ##hplusroadmap | 17:07 | |
| nmz787_ | Using the 'hi( | 17:07 |
| nmz787_ | 'Hi' popup link | 17:07 |
| nmz787_ | You will be notified by way of e-mail as to the status of your application. | 17:08 |
| streety | it says that every time I renew | 17:09 |
| nmz787_ | You will be notified by way of e-mail as to the status of your application. A limited number of subscriptions to Nature Methods are available to qualifying life scientists and chemists in North America and Europe. Due to the limited availability, not all applicants will qualify. We ask for your patience in this process as we receive a large number of applicants. | 17:09 |
| @kanzure | "limited availability"... of digital content -_-. | 17:09 |
| nmz787_ | What is sunbeltfs? | 17:09 |
| nmz787_ | Is it digital or paper | 17:09 |
| @kanzure | "Authentification, (which can include username and password) allowing subscriber access to publishers web site or denying access. Sending messages to subscribers on their current subscription status." | 17:10 |
| @kanzure | "Allowing subscribers to renew, make a payment, change address or reverify their subscription online real time and sending an instant email acknowledging." | 17:10 |
| @kanzure | maybe this is how nature manages subscriptions.. | 17:10 |
| nmz787_ | That's what sunbelt does? Auth? | 17:11 |
| @kanzure | yes that is from sunbeltfs.com | 17:11 |
| @kanzure | this has a list of related pages: https://www.google.com/search?q=sunbeltfs+nature | 17:11 |
| @kanzure | nature climate change: https://www.sunbeltfs.com/forms/nq/subscribe.asp | 17:12 |
| streety | my understanding is this is only paper subscriptions | 17:12 |
| @kanzure | nature biotechnology: http://www.sunbeltfs.com/forms/bi/lookup.asp?eid=z61099 | 17:12 |
| @kanzure | old nature methods link (their page looks broken) https://www.sunbeltfs.com/forms/nh/subscribe.asp?eid=E710XZ | 17:12 |
| -!- yashgaroth [~ffffff@cpe-66-27-118-94.san.res.rr.com] has joined ##hplusroadmap | 17:13 | |
| @kanzure | yashgaroth: free print subscription to nature methods, http://www.sunbeltfs.com/forms/nh/lookup.asp?eid=R99999%22%3E%3Cscript%20type=%22text/javascript%22%3Ealert('hi');%3C/script%3E%3C%22 | 17:13 |
| -!- safitan is now known as mutagen | 17:14 | |
| yashgaroth | looks a little sketch | 17:14 |
| @kanzure | the whole science publishing industry is sketch skeet. | 17:15 |
| yashgaroth | well whatever I can just have it sent to the carlsbad lab | 17:16 |
| yashgaroth | does the one for nature biotechnology work too? | 17:17 |
| @kanzure | "Publisher reserves the right to limit complimentary subscriptions to qualified individuals." | 17:18 |
| @kanzure | it looks the same | 17:18 |
| yashgaroth | hmm what's a good title and company to make up | 17:18 |
| @kanzure | Blackhat Molecular | 17:19 |
| yashgaroth | let me know how your foia pull looks when you get it | 17:20 |
| @kanzure | sure | 17:20 |
| mutagen | lol | 17:21 |
| jrayhawk | Requests for your FBI file go into your FBI file | 17:21 |
| mutagen | im white hat | 17:21 |
| mutagen | i work for the nsa | 17:21 |
| @kanzure | mutagen: stop lying dude. i'm tired of your crap. | 17:21 |
| mutagen | lol | 17:21 |
| * mutagen punches kanzure | 17:22 | |
| @kanzure | /kick mutagen | 17:22 |
| * mutagen punches kanzure in the cocksucker | 17:22 | |
| mutagen | lol | 17:22 |
| yashgaroth | preeeetty sure he's that dixiebassline schizo | 17:22 |
| -!- mode/##hplusroadmap [+q mutagen!*@*] by kanzure | 17:22 | |
| @kanzure | yes, it's all in the logs. | 17:22 |
| streety | the company name an address don't need to make sense - I've listed an residential address 200 miles from the company name/institution | 17:22 |
| streety | *and | 17:23 |
| -!- mutagen [~safitan@75-105-12-23.cust.wildblue.net] has left ##hplusroadmap [] | 17:23 | |
| -!- mode/##hplusroadmap [-q mutagen!*@*] by kanzure | 17:23 | |
| -!- dixiebassline [~safitan@75-105-12-23.cust.wildblue.net] has joined ##hplusroadmap | 17:24 | |
| @kanzure | aha | 17:25 |
| @kanzure | https://www.sunbeltfs.com/forms/na/digital.asp | 17:25 |
| @kanzure | " | 17:25 |
| @kanzure | "Complimentary subscriptions to Nature Digital Edition are available to qualified applicants. Nature Digital Edition is a weekly digital reproduction of the print edition plus all the benefits of electronic navigation for your convenience." | 17:26 |
| -!- nmz787_ [~androirc@static-50-43-81-14.bvtn.or.frontiernet.net] has quit [Ping timeout: 260 seconds] | 17:27 | |
| * dixiebassline fucks yashgaroth with a chainsaw | 17:30 | |
| dixiebassline | mind your own business | 17:30 |
| yashgaroth | uh huh | 17:30 |
| dixiebassline | <kanzure> Blackhat Molecular | 17:31 |
| dixiebassline | <yashgaroth> let me know how your foia pull looks when you get it | 17:31 |
| dixiebassline | blackhat and whitehat are just subjective | 17:31 |
| dixiebassline | im afk | 17:32 |
| yashgaroth | that's nice, dear | 17:32 |
| @kanzure | paperbot: http://www.nature.com/protocolexchange/protocols/153 | 17:33 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/ed47ec5170f7d965b71ed031089e8442.txt | 17:33 |
| @kanzure | paperbot: http://www.nature.com/nprot/journal/v7/n12/abs/nprot.2012.115.html | 17:34 |
| paperbot | HTTP 401 unauthorized http://www.nature.com/nprot/journal/v7/n12/pdf/nprot.2012.115.pdf | 17:34 |
| @kanzure | it's supposed to be "Generation of human induced pluripotent stem cells from urine samples" | 17:34 |
| @kanzure | google still sucks at pdf->html, geeze http://scholar.googleusercontent.com/scholar?q=cache:e7xWwRhdVhUJ:scholar.google.com/&hl=en&as_sdt=0,44 | 17:35 |
| @kanzure | paperbot: http://jasn.asnjournals.org/content/22/7/1221.short | 17:35 |
| paperbot | error: HTTP 300 http://diyhpl.us/~bryan/papers2/paperbot/Generation%20of%20Induced%20Pluripotent%20Stem%20Cells%20from%20Urine.pdf | 17:35 |
| @kanzure | there we go | 17:35 |
| @kanzure | "The human kidney contains an extensive network of tubules whose total surface is bigger than the skin. As part of normal physiology approximately 2000 to 7000 cells from this tubular system and downstream parts of the urinary tract (ureters, bladder, and urethra) detach and are excreted in urine daily." | 17:39 |
| @kanzure | oh hm. retroviruses. | 17:41 |
| yashgaroth | yup | 17:41 |
| dixiebassline | www.reddit.com/user/yashgaroth/ | 17:46 |
| -!- mode/##hplusroadmap [+q dixiebassline!*@*] by kanzure | 17:47 | |
| yashgaroth | my terrible secret revealed | 17:47 |
| ThomasEgi | a terrible secret ?.. so... how much would you pay me for not clicking this link? :p | 17:50 |
| yashgaroth | I don't know how his elite haxxing skills uncovered that I have a reddit account, but I will pay you all the bitcoins you require | 17:51 |
| yashgaroth | now he's PMing me about shit | 17:51 |
| @kanzure | http://www.youtube.com/watch?v=veTxerywR9c | 17:52 |
| @kanzure | .title | 17:52 |
| yoleaux | A cleared spinal cord tissue of a GFP-M mouse imaged with 2-photon microscopy. - YouTube | 17:52 |
| ThomasEgi | bitcoins sound fun. too bad i'm not an asshole squeezing out money of people. so i'll not click it for free | 17:52 |
| yashgaroth | now he's just repeatedly posting that link in PMs | 17:52 |
| @kanzure | yeah now he's harrassing me in another channel | 17:53 |
| yashgaroth | he seems to be mad that I dislike reddit, what a fucking surprise | 17:53 |
| @kanzure | for someone who dislikes reddit, you sure do use it a lot | 17:53 |
| ThomasEgi | yashgaroth, mental image of "fucking surprise" ... caused me a giggle | 17:53 |
| @kanzure | paperbot: http://www.nature.com/nprot/journal/v7/n12/abs/nprot.2012.140.html | 17:54 |
| paperbot | http://diyhpl.us/~bryan/papers2/paperbot/Monitoring%20local%20synaptic%20activity%20with%20astrocytic%20patch%20pipettes.pdf | 17:54 |
| yashgaroth | you consider that 'a lot'? | 17:54 |
| jrayhawk | 2012-06-12 20:32 < atum> tomorrow is my last day of highschool, and i dont have any real direction. currently im looking into becoming a rapper | 17:54 |
| -!- ElixirVitae [~Shehrazad@unaffiliated/shehrazad] has quit [Quit: Quit] | 17:55 | |
| @kanzure | jrayhawk: ? | 17:58 |
| yashgaroth | same guy | 17:58 |
| ThomasEgi | a rapper?.. that Is a real direction.. | 17:59 |
| ThomasEgi | really straight down | 17:59 |
| @kanzure | jrayhawk: yes, this is gl00m/safitan/ArmilusDajjal/TheBeast666/dixiebassline | 18:00 |
| -!- SphericalMouse [62cfd610@gateway/web/freenode/ip.98.207.214.16] has joined ##hplusroadmap | 18:02 | |
| @kanzure | SphericalMouse: hello | 18:03 |
| SphericalMouse | Yo Kanzure | 18:03 |
| SphericalMouse | You asked me to drop by? | 18:03 |
| @kanzure | which one are you? | 18:03 |
| SphericalMouse | indeed, who? | 18:03 |
| SphericalMouse | bioautomation at biocurious | 18:03 |
| @kanzure | you are either the biocurious person or the desktop person or the-- ah okay. | 18:03 |
| @kanzure | SphericalMouse: i was hoping you could talk about your project a bit | 18:04 |
| SphericalMouse | well, to be fair, the kickoff meeting is on sunday, so project is a bit generous | 18:04 |
| @kanzure | have you built any lab equipment before? | 18:05 |
| SphericalMouse | of sorts. I've done lots of microfluiducs and lab automation in labview. cell culture, image capture, experimental system design, fabrication, and control of PDMS microfluidics system, blah blah. | 18:07 |
| SphericalMouse | made a reprap too, if that counts | 18:07 |
| @kanzure | yes that definitely counts | 18:07 |
| @kanzure | we were working on a laser cutter to improve the prototyping times for microfluidic devices, | 18:07 |
| @kanzure | http://diyhpl.us/laser_etcher/laser_etcher | 18:08 |
| SphericalMouse | yeah, I saw | 18:08 |
| @kanzure | http://diyhpl.us/~bryan/nucleic/fbi-diybio-dna-v1.pdf | 18:08 |
| @kanzure | ah okay, cool | 18:08 |
| SphericalMouse | that can make channels, but I'm not sur if it would work for valved PDMS devices | 18:08 |
| @kanzure | quake valves? | 18:08 |
| SphericalMouse | yes | 18:08 |
| @kanzure | how many iterations before a microfluidic chip would start working for you? | 18:09 |
| SphericalMouse | depends on what features you're adding. a simple chip you can make the first time. you need cleanroom access though | 18:09 |
| SphericalMouse | those systems are very sensitive to microscale features | 18:10 |
| yashgaroth | how clean of a cleanroom? | 18:10 |
| @kanzure | well, i was estimating 100 iterations to knock out bugs from a potential design, but someone yesterday was telling me i was off by a factor of 10. | 18:10 |
| @kanzure | (he was saying only 10 prototypes) | 18:11 |
| SphericalMouse | it really depends on how agressive your features are | 18:11 |
| @kanzure | basic channels, valves, a few world-to-chip ports. | 18:11 |
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| SphericalMouse | for example, usually the channels are something lke 15 microns tall, but I spent a few months trying to make 0.5 micron channels work | 18:11 |
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| SphericalMouse | ports are easy, valves take a few practice runs to learn the alignment technique, but then you're trained, basica channel are easy, if you make the molds right | 18:12 |
| nmz787 | hi | 18:13 |
| @kanzure | how long per chip did it take to bake? | 18:13 |
| SphericalMouse | the cleanroom doesn't really have to be clean, there are magic tricks for pulling off dust | 18:13 |
| nmz787 | like plasma etch? | 18:13 |
| SphericalMouse | about hours total | 18:13 |
| SphericalMouse | no, scotch tape | 18:13 |
| SphericalMouse | 8 hours | 18:13 |
| yashgaroth | I mean, a tissue culture hood makes a pretty good cleanroom | 18:14 |
| @kanzure | holy hell i would cry if it took 8 hours to test a new version of my software | 18:14 |
| SphericalMouse | you can finish a chip in a day if you start early and do it like a machine. you need to make the mold previously | 18:15 |
| nmz787 | SphericalMouse: doesn't spin-coating get the thickness right? | 18:15 |
| SphericalMouse | for what? | 18:15 |
| nmz787 | are you saying you played with spin-coater settings to get from 15 to 0.5? | 18:15 |
| nmz787 | 18:11 < SphericalMouse> for example, usually the channels are something lke 15 | 18:16 |
| nmz787 | microns tall, but I spent a few months trying to make | 18:16 |
| SphericalMouse | the mold determines the channel height | 18:16 |
| nmz787 | 0.5 micron channels work | 18:16 |
| SphericalMouse | you just use a thinner photoresist | 18:16 |
| @kanzure | we've been thinking of just skipping the mold step and using laz0rs or dlp | 18:16 |
| nmz787 | what | 18:16 |
| nmz787 | ? | 18:16 |
| nmz787 | you didn't make your own molds SphericalMouse ? | 18:16 |
| SphericalMouse | of course I did | 18:17 |
| nmz787 | so why did it take you months to figure out the thickness? | 18:17 |
| SphericalMouse | but you may have a different idea of processing than I use | 18:17 |
| SphericalMouse | because the channels would collapse | 18:17 |
| nmz787 | seems like you just do 10 runs, develop a curve of thickness vs RPM or time | 18:17 |
| nmz787 | you mean aspect ratio? | 18:18 |
| nmz787 | of height to width? | 18:18 |
| SphericalMouse | the mold is easy to make, you can vary the spin speed, as you said, and measure it on a profilometer | 18:18 |
| nmz787 | of the channel? | 18:18 |
| SphericalMouse | partially, yes. | 18:18 |
| nmz787 | kanzure: link to that test pattern? | 18:18 |
| SphericalMouse | also, the mask quality made a big difference | 18:18 |
| @kanzure | huh? that was your test pattern, shouldn't you have the link? | 18:18 |
| * kanzure digs | 18:18 | |
| nmz787 | yeah but you mirrored it | 18:18 |
| SphericalMouse | usually we would use transparancy masks, but those have low quality at small feature sizes | 18:19 |
| @kanzure | http://diyhpl.us/~bryan/papers2/diybio/mccorkle_tomkins-tinch_microchannels.svg | 18:19 |
| nmz787 | SphericalMouse: that's what I would start with on any system | 18:19 |
| nmz787 | then you can test all the different aspect ratios at once | 18:20 |
| nmz787 | to see which dont work | 18:20 |
| nmz787 | cool | 18:20 |
| nmz787 | so what are you going to start working with for mold production? | 18:21 |
| SphericalMouse | I just don't now if laser cutting PDMS would create the channels you need | 18:21 |
| nmz787 | i just got DLP projector ripped apart the other day, and got it focused to about 1 cm so i can feed it into my microscope | 18:21 |
| nmz787 | SphericalMouse: yeah it can, but I've abandonded it due to the positioning system being PITA | 18:22 |
| SphericalMouse | I mean, have you actually gotten valves to work using it? | 18:22 |
| -!- aristarchus [~aristarch@unaffiliated/aristarchus] has quit [Quit: Leaving] | 18:22 | |
| nmz787 | I can oversample position information optically with a camera and re-position by oversampling pixels on the projector to correct for alignment issues | 18:22 |
| nmz787 | SphericalMouse: nope, but valves are easy according to their prevalence in the literature | 18:23 |
| nmz787 | I've actually just learned about a microfluidic device for touchscreens that might work as a valve controller | 18:24 |
| nmz787 | SphericalMouse: what was your trouble with valves? | 18:24 |
| nmz787 | SphericalMouse: it sounds like you had to figure out aspect ratio to prevent channel collapse, what else? | 18:24 |
| SphericalMouse | the fluid channel needs a pretty recise cross-sectional geometry to get good sealing | 18:24 |
| nmz787 | SphericalMouse: were you not replicating a previously published protocol? | 18:24 |
| nmz787 | i have some 3D scans of some laser cut microchannels in PDMS | 18:25 |
| @kanzure | ah that's the thing i wanted earlier | 18:25 |
| SphericalMouse | ok, toss em up | 18:25 |
| nmz787 | it was on silicon so cut-through didn't occur, and the channel bottoms were swiis-cheese-like | 18:26 |
| nmz787 | lemme fire up this external drive | 18:26 |
| klafka_ | http://life.nationalpost.com/2013/02/12/totally-drug-resistant-tuberculosis-spreading-in-south-africa-as-researchers-warn-outbreak-of-bacteria-would-be-untreatable/ | 18:27 |
| klafka_ | eep | 18:27 |
| nmz787 | SphericalMouse: http://nathanmccorkle.com/pdf/jmm9_3_037002.pdf | 18:28 |
| @kanzure | paperbot: http://nathanmccorkle.com/pdf/jmm9_3_037002.pdf | 18:28 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/65ebbce757594db82c8d27cc43c72fd1.pdf | 18:28 |
| nmz787 | SphericalMouse: so the main thing with laser cutting is you want CW laser, not pulsed, and you'd ideally use servos not steppers to smooth it all out | 18:30 |
| nmz787 | SphericalMouse kanzure here are the veeco interferometer pics of PDMS cut with a Universal Laser Systems desktop laser | 18:31 |
| SphericalMouse | I don't think valves would work with those channels as shown | 18:31 |
| nmz787 | https://picasaweb.google.com/109403794341975968814/DIY02?authuser=0&authkey=Gv1sRgCMvrhpPZ9MWIAg&feat=directlink | 18:31 |
| nmz787 | SphericalMouse: why not? | 18:32 |
| SphericalMouse | they would probably form a poor seal, you need your fluid chamber to have curved edges or you get leaks | 18:33 |
| SphericalMouse | depends how critical that is | 18:33 |
| nmz787 | huh? why wouldn't bonding the layers seal it? | 18:33 |
| SphericalMouse | no, leaks around the valves | 18:33 |
| nmz787 | add more PSI? | 18:34 |
| nmz787 | I've always seen people in MEMS going for as straight as possible | 18:34 |
| nmz787 | it's easier to model, for instance | 18:34 |
| SphericalMouse | it depends on the device | 18:34 |
| nmz787 | mmm | 18:35 |
| nmz787 | yeah but anyway I've abandoned that because of the aforementioned reasons | 18:35 |
| nmz787 | the laser cutting part | 18:35 |
| SphericalMouse | the quake valve style channels have a parabolic cross-section, something like a 100 um across and ~15 high in the center, with very little roughness | 18:36 |
| @kanzure | fenn: what was that absurdly cheap, really awesome, 32-channel oscilloscope? | 18:36 |
| SphericalMouse | the channels you linked are fine for a flow through device | 18:36 |
| nmz787 | SphericalMouse: have you seen other valve styles? | 18:39 |
| SphericalMouse | there is the stuff out of rich mathies lab | 18:39 |
| SphericalMouse | they have a suck up rather than push down style | 18:40 |
| SphericalMouse | there you would have un patterned pdms, and then you could cut out channels from some substrate | 18:40 |
| nmz787 | SphericalMouse: i've seen this style, and others like it http://ars.els-cdn.com/content/image/1-s2.0-S0925400511008537-gr1.jpg | 18:40 |
| SphericalMouse | thats something like what i'm talking about | 18:41 |
| nmz787 | luckily there's so much research on aspect ratio in photoresist, getting channels to be more parabolic probably means using a cheaper photoresist | 18:42 |
| SphericalMouse | you just put down an appropriate PR, pattern it, then melt it | 18:42 |
| nmz787 | SphericalMouse: ahh here's what you're describing as the problem http://ars.els-cdn.com/content/image/1-s2.0-S0924424706000914-gr3.gif | 18:43 |
| nmz787 | SphericalMouse: before you develop it? | 18:43 |
| SphericalMouse | no, afterwards | 18:43 |
| nmz787 | i thought the developer just washed away unpolymerized reagent | 18:43 |
| SphericalMouse | yah, that link is basically the problem | 18:44 |
| nmz787 | paperbot: http://www.sciencedirect.com/science/article/pii/S0924424706000914 | 18:44 |
| paperbot | no translator available, raw dump: http://diyhpl.us/~bryan/papers2/paperbot/Buckled-type%20valves%20integrated%20by%20parylene%20micro-tubes%20.pdf | 18:44 |
| SphericalMouse | different scale, same problem | 18:45 |
| SphericalMouse | you can have rectangular channels for the valve lines (and you usually do), but the fluid lines need structure if the thing is monolithic pdms | 18:46 |
| SphericalMouse | or pushdown vlaves | 18:46 |
| nmz787 | so do you work with microfluidics a lot? | 18:47 |
| SphericalMouse | not as much, now its more instrument design | 18:48 |
| nmz787 | SphericalMouse: why not do everything on-chip | 18:49 |
| SphericalMouse | it depends | 18:49 |
| nmz787 | on? | 18:50 |
| SphericalMouse | integrated chips are expensive, fluidigm sells theirs for a couple of hundred each. if you add stuff to the chip, you toss that away each experiment | 18:50 |
| nmz787 | i mean why not make your own | 18:50 |
| nmz787 | with everything integrated | 18:50 |
| nmz787 | then add the I/O instrument (data, fluids) | 18:51 |
| SphericalMouse | same reason, integrating things takes work. if you can have a bunch of reusable things off chip, then you save having to re-add them to each new one | 18:51 |
| nmz787 | if the chips aren't glass, they're pretty cheap in production | 18:51 |
| nmz787 | so are you hoping to make some of the micro versions with biocurious? so people in the future can reuse those modules? | 18:52 |
| @kanzure | nmz787: show him your spectrometer | 18:52 |
| nmz787 | SphericalMouse: openspectrometer.com | 18:52 |
| SphericalMouse | probably not. making those things is a black art, and most people wouldn't have access to the equipment | 18:53 |
| nmz787 | i guess i'm heading to that hackathon next weekend in SF | 18:53 |
| nmz787 | SphericalMouse: what do you mean? there are a few DIY mems and photoresist printing projects | 18:53 |
| SphericalMouse | making the molds is the easy part | 18:53 |
| SphericalMouse | mostly | 18:54 |
| SphericalMouse | it would be nice tyo have an automatic mold maker, for sure | 18:54 |
| nmz787 | so what's the black art part? | 18:54 |
| SphericalMouse | the timing of the bake, mixtures of the layers, the alignment of the layers, setting the damn things up, getting them running properly | 18:55 |
| nmz787 | definitely there's no @home microfluidics cookbook, but from my research it seems totally achievable at home, or in a community lab | 18:55 |
| SphericalMouse | it is | 18:55 |
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| SphericalMouse | but its not trivial to expect someone to make a quality microfluidics device straight off | 18:56 |
| SphericalMouse | my term is "artisan microfluidics" | 18:57 |
| nmz787 | right buy why even waste any time on macro equipment anymore? | 18:58 |
| nmz787 | there's plenty of room down at the bottom | 18:58 |
| nmz787 | i guess it's just preference | 18:58 |
| SphericalMouse | because the equipment required to access the bottom is often more then the equipment required to access the middle | 18:58 |
| @kanzure | how is it a waste? | 18:59 |
| SphericalMouse | the old joke in the microfluidics community is that people will show around a chip, and neglect to mention the gian machine that surrounds it | 18:59 |
| @kanzure | the giant syringe pump? | 19:00 |
| nmz787 | this is pretty cool, heating the solution causes it to become ultra viscous http://www.google.com/patents?hl=en&lr=&vid=USPAT6382254 | 19:00 |
| SphericalMouse | the pump, the automated microscope, the 60 control lines, the fluid input ports | 19:00 |
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| SphericalMouse | it would often take a couple of hours to set up and load a device. mind you, i probably made the most absurd system of all time | 19:01 |
| nmz787 | lol | 19:02 |
| nmz787 | i'm specifically interested in DNA synthesis, so keeping reagent cost low got me interested in microfluidics in the first place | 19:02 |
| nmz787 | but now i have access to nanoscale milling, so I'm looking at nanofluidics too | 19:03 |
| SphericalMouse | i saw, thats definitely an application where you can't have leakage | 19:03 |
| nmz787 | and the error correction wouldn't work well at all in macro scale | 19:03 |
| SphericalMouse | ? | 19:03 |
| nmz787 | too much loss and reduced signal to noise | 19:04 |
| nmz787 | product loss* | 19:04 |
| nmz787 | i've been thinking more about electrowetting recently | 19:05 |
| nmz787 | i'm not sure if that cuases electrolysis though | 19:05 |
| SphericalMouse | it doesn't | 19:05 |
| nmz787 | because no current flow? | 19:05 |
| nmz787 | or what? | 19:05 |
| nmz787 | i guess current might flow in the moment that a droplet is between electrodes | 19:06 |
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| SphericalMouse | and because you have dielectric materials between the electrode and liquid | 19:06 |
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| nmz787 | ah | 19:06 |
| nmz787 | so the electrode is coated in a few nm or microns? | 19:06 |
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| SphericalMouse | probably sub micron, but that isn't my field | 19:07 |
| nmz787 | hmm, kanzure if electrowetting doesn't cause electrolysis, maybe we should look into that instead of quake--like vavles | 19:07 |
| @kanzure | jonathan cline did an electrowetting prototype | 19:07 |
| nmz787 | there's a few DIY electrowetting videos on youtube | 19:07 |
| nmz787 | just using a razon on copper clad | 19:07 |
| SphericalMouse | look into thermocapillary movement | 19:08 |
| @kanzure | http://88proof.com/synthetic_biology/blog/archives/tag/microfluidics | 19:08 |
| nmz787 | kanzure: i'm sure there's a nice grid to parallel wire breakout for sale commodity | 19:08 |
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| nmz787 | kanzure: if not it would probably be within my reach to fab one, for testing | 19:08 |
| @kanzure | what's wrong with macro-machine dna synthesis? | 19:09 |
| nmz787 | reagent cost, i thought | 19:09 |
| SphericalMouse | i know some of quakes ex students of have tried it | 19:09 |
| nmz787 | i was planning on testing some nano crevice chemistry hiding ideas | 19:10 |
| @kanzure | nmz787: reagent costs are important, but that will go down eventually anyway. the machines still cost a fuckton and they shouldn't. | 19:10 |
| nmz787 | kanzure: were you in virginia in 2011? | 19:10 |
| @kanzure | i can't remember. | 19:10 |
| nmz787 | i think it was after the NYC meeting | 19:10 |
| @kanzure | maybe not. | 19:10 |
| SphericalMouse | kanzure, did you read the spew I put int he biocurious posting? | 19:11 |
| @kanzure | SphericalMouse: i read your google docs document, and added some things. | 19:11 |
| nmz787 | kanzure: i would have to look at the reagent costs | 19:11 |
| nmz787 | SphericalMouse: you wrote the whole email? | 19:11 |
| nmz787 | the original ? | 19:11 |
| SphericalMouse | patrik wrote a section in the middle | 19:12 |
| nmz787 | are you dietrich? | 19:12 |
| SphericalMouse | yes | 19:12 |
| nmz787 | ahh nice to 'meet' | 19:12 |
| @kanzure | i think nmz787 used to work for patrik | 19:12 |
| nmz787 | i did | 19:12 |
| SphericalMouse | where? | 19:12 |
| nmz787 | jbei | 19:12 |
| @kanzure | institute of asskicking | 19:12 |
| @kanzure | oh | 19:13 |
| SphericalMouse | ah indeed. I worked around him a couple of years | 19:13 |
| nmz787 | cool | 19:13 |
| nmz787 | i was his summer intern | 19:13 |
| SphericalMouse | are you in the sf area? | 19:13 |
| nmz787 | portland or now | 19:13 |
| SphericalMouse | ? | 19:13 |
| nmz787 | but i'm coming down next weekend to some hardware hackathon | 19:14 |
| nmz787 | portland Oregon* | 19:14 |
| SphericalMouse | doing what? | 19:14 |
| nmz787 | developing a means to DNA synthesis, currently aiming for micro/nanoscale | 19:14 |
| nmz787 | i also seem to just got a job building a combined 3d scanner/printer | 19:15 |
| nmz787 | i generally like programming, light, nano/micro stuff, DNA, and metabolic engineering | 19:15 |
| nmz787 | but the whole metabolic engineering has been but on hold due to not having a rapid gene compiler | 19:16 |
| SphericalMouse | the biocrious guys are excited about goldenbraid recently | 19:17 |
| nmz787 | wazzat? | 19:18 |
| nmz787 | (looking now) | 19:18 |
| SphericalMouse | kanzure, what is your take on the lab robot? | 19:18 |
| SphericalMouse | do you have any experience in building lab equipment? | 19:19 |
| SphericalMouse | I think patrik has a point that we should have a need in mind as its made | 19:20 |
| nmz787 | how does goldenbraid prevent reverse directional inserts? | 19:20 |
| SphericalMouse | i haven't looked into it | 19:20 |
| gnusha | https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=b176f978 Bryan Bishop: las vegas diybio group | 19:21 |
| @kanzure | SphericalMouse: i think we need more open source hardware | 19:21 |
| @kanzure | SphericalMouse: i think it's a shame that reprap is the only major open source hardware project that has a version control system | 19:21 |
| @kanzure | instructables is not how you solicit updates to a project.. | 19:22 |
| SphericalMouse | does it? reprap looks split all over. | 19:22 |
| @kanzure | yes it's very split; they have an upstream svn repo. we were converting them over to git almost, but it exploded in 2010. | 19:22 |
| @kanzure | http://diyhpl.us/cgit/reprap | 19:23 |
| SphericalMouse | whats the opinion on makerslide? | 19:24 |
| @kanzure | is that makerbeam? | 19:24 |
| SphericalMouse | aluminum extrusion with rails for sliding platform | 19:24 |
| @kanzure | ah no, this is the makerbeam knock-off | 19:24 |
| @kanzure | i like extruded construction sets in general | 19:24 |
| @kanzure | have you seen cubespawn? | 19:25 |
| @kanzure | http://cubespawn.com/ | 19:25 |
| @kanzure | i think it was all 80/20 | 19:25 |
| SphericalMouse | makerslide isn't just an extrusion though, but i've never used it | 19:26 |
| @kanzure | me either | 19:27 |
| SphericalMouse | something akin to the cube is what i'm thinking of as the general frame | 19:27 |
| @kanzure | james wanted to make cubespawn so that he could have stackable, repeatable-reliable frames for moving things around and to build off of. | 19:28 |
| SphericalMouse | the raw extrusions might be easier to work with | 19:29 |
| nmz787 | what is cubespawn exactly? | 19:29 |
| nmz787 | nothing purchasable | 19:30 |
| @kanzure | nmz787: i think it is supposed to be a set of standards, but there also seems to be some software or something.. | 19:30 |
| @kanzure | he had a campaign on kickstarter at one point, but i don't remember why. | 19:30 |
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| SphericalMouse | what is your take on Bioc? | 19:30 |
| nmz787 | SphericalMouse: i liked the place a lot | 19:33 |
| SphericalMouse | any issues I should be aware of? | 19:34 |
| @kanzure | yes, it's run by a cabal | 19:35 |
| nmz787 | i think ray may have got rid of some equipment a while ago against the wishes of others | 19:35 |
| nmz787 | cabal? | 19:35 |
| @kanzure | a secret group of backstabbers that all secretly hate each other | 19:35 |
| nmz787 | ahh | 19:35 |
| nmz787 | seems fair | 19:35 |
| SphericalMouse | ? | 19:35 |
| nmz787 | i dunno really tho | 19:35 |
| nmz787 | just people being weird i think is the general picture | 19:36 |
| nmz787 | but it seems to work | 19:36 |
| @kanzure | if you ignore that aspect, otherwise, biocurious seems pretty good... i've been a little disappointed with a few web choices though | 19:36 |
| @kanzure | for instance, publishing the bioprinter to instructables.. yuck. | 19:36 |
| @kanzure | and using pbwiki? who chooses pbwiki these days, geeze. | 19:36 |
| SphericalMouse | whats wrong with instructables? (i haven't really looked at it) | 19:37 |
| @kanzure | instructables is fine for show-and-tell | 19:37 |
| @kanzure | but it's not a version control system for open source projects.. | 19:37 |
| nmz787 | patrik is a good guy though, and I know he seems to really enjoy helping out there | 19:37 |
| SphericalMouse | all flash, no depth? | 19:37 |
| SphericalMouse | i see | 19:37 |
| @kanzure | like if i want to update some source code, i can't do that because instructables is for a totally different purpose. | 19:38 |
| @kanzure | if i want to revise some of the cad parts, can't do that either through instructables. | 19:38 |
| curtiss | instructables makes me think of about.com | 19:38 |
| @kanzure | "owned by AOL" ? | 19:38 |
| nmz787 | curtiss: how do you mean? | 19:38 |
| @kanzure | about.com has lasted an amazingly long time considering how crappy their pages are. they figured out the longtail stuff pretty fast. | 19:39 |
| nmz787 | SphericalMouse: so did you do any of the microfluidics for work? | 19:39 |
| nmz787 | SphericalMouse: or was it all hobby? | 19:39 |
| nmz787 | kanzure: longtail? | 19:39 |
| SphericalMouse | yechnically, I am a microfluidics engineer, but I haven't done much recently | 19:39 |
| curtiss | nmz787: mostly spammy looking site. possibly some useful stuff in there but who would know due to horrible design | 19:40 |
| SphericalMouse | the microfluidics was during my postdoc | 19:40 |
| docl | I've been considering use of the chick eye model for cryonics research. Chicks are inexpensive, and they have large eyes per unit bodyweight. | 19:40 |
| @kanzure | nmz787: longtail content is the idea of using obscure niche keywords on the web to attract eyeballs. so you might have 1,000 articles about niche topics, but they each get 2-10 views over their lifetime, rather than trying to hit for 1-10 articles that get 20 million views. | 19:40 |
| nmz787 | SphericalMouse: so what advice would you give me if i am to continuing pursuing micro/nano DNA synthesis? | 19:40 |
| SphericalMouse | depends on the mode you're operating in. if you are just going to reuse the same parts over and over, you may want to just make a library and then pcr up the parts | 19:41 |
| @kanzure | nmz787: it's called longtail for a number of reasons, but the most obvious reason is because if you look at the distribution of incoming referrals to any website, the vast majority of users tend to come in from one or two search terms, whereas all the other traffic trickles in. of course, in certain markets/niche, the traffic might be more haphazard. | 19:42 |
| nmz787 | SphericalMouse: no, denovo is my goal | 19:42 |
| SphericalMouse | beware of materials incompatibilities. sometimes pdms (or other materials) have the tendency to absorb and release solutions that flow through | 19:43 |
| nmz787 | SphericalMouse: what about using SU-8, seems pretty compatible | 19:43 |
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| SphericalMouse | I ostensibly work in a company that does a form of DNA synthesis, and the incomplete chemistry is what gets you at each cycle | 19:44 |
| nmz787 | cool, that's where i was targeting to tackle | 19:44 |
| SphericalMouse | you basically have zero tolerance for incomplete washing or mixed reagents | 19:44 |
| nmz787 | SphericalMouse: ever seen free solution DNA synthesis? | 19:45 |
| SphericalMouse | or low quality reagents | 19:45 |
| SphericalMouse | isn't free solution still done with bead support? | 19:45 |
| nmz787 | well i'd consider that solid support | 19:46 |
| SphericalMouse | all synthesis I know of uses solid support or template DNA, but i'm not an expert | 19:46 |
| nmz787 | hmm | 19:47 |
| nmz787 | do you know how to do CFD? | 19:47 |
| SphericalMouse | yeah, you open up comsol and hit go | 19:47 |
| nmz787 | can you tell me what to do to learn? i.e. books, papers, tutorials | 19:48 |
| nmz787 | what software should i learn, what should i avoid? | 19:48 |
| @kanzure | comsol haha | 19:48 |
| SphericalMouse | i like comsol | 19:48 |
| @kanzure | yeah comsol is pretty plug and play | 19:48 |
| @kanzure | costs a bunch, grab a copy on thepiratebay | 19:48 |
| nmz787 | is it as easy as making the 3d CAD model and literally hitting go? | 19:48 |
| @kanzure | yes if you're using solidworks | 19:48 |
| @kanzure | if you want an open source solution, go pick up a copy of openfoam | 19:48 |
| SphericalMouse | setting boundary conditions | 19:49 |
| @kanzure | it's nothing like comsol but it works | 19:49 |
| @kanzure | comsol is vastly easier to use | 19:49 |
| SphericalMouse | the comsol internal cad is ok | 19:49 |
| @kanzure | or ansys' stuff.. i forget what ansys calls their thing. | 19:49 |
| nmz787 | does it have a lib of viscosities n params for common fluids or industrially available chmes? | 19:49 |
| nmz787 | chems? | 19:49 |
| SphericalMouse | you can easily paramatrize the geometries | 19:49 |
| SphericalMouse | some | 19:49 |
| nmz787 | see that's where my understanding stops | 19:50 |
| SphericalMouse | you should also have a few dozen gigs of ram | 19:50 |
| nmz787 | i can think of geometry, surface chemistry, liquid composition (solutes, suspended solids) | 19:50 |
| @kanzure | nmz787: http://www.youtube.com/watch?v=mkmtC0iManM#t=30 | 19:50 |
| @kanzure | .title | 19:50 |
| yoleaux | COMSOL Tutorial: Simulating a Closing Gate Valve Part 1 - YouTube | 19:50 |
| nmz787 | SphericalMouse: i am a student so there are research computers with those | 19:51 |
| SphericalMouse | you will probably want to avoid putting pirated software on research machines | 19:52 |
| nmz787 | no they probably already have it | 19:52 |
| SphericalMouse | but dont worry, a base license of comsol is a mere 12k | 19:52 |
| SphericalMouse | might as well learn it | 19:53 |
| nmz787 | kanzure: this vid is pretty good | 19:53 |
| SphericalMouse | you probably dont want the cfd module, the microfluidics is what you're looking for | 19:54 |
| SphericalMouse | and diffusion | 19:55 |
| nmz787 | they have a microfluidics module? | 19:55 |
| SphericalMouse | many many modules | 19:56 |
| @kanzure | i get spam from comsol in my inbox :( | 19:57 |
| @kanzure | "Reminder: COMSOL Multiphysics Version 4 Workshop in Austin Tomorrow" | 19:57 |
| @kanzure | shit like that | 19:57 |
| @kanzure | SphericalMouse: have you ever used git? | 19:57 |
| SphericalMouse | no, but johann sundqvist is your best friend | 19:58 |
| nmz787 | just pinged the director of Research Computing re COMSOL | 19:58 |
| @kanzure | if you have comsol, then you probably have it through citrix or some other shitty file storage system assigned to you | 19:58 |
| @kanzure | actually, jules will know | 19:59 |
| SphericalMouse | i have not ussed git | 19:59 |
| nmz787 | SphericalMouse: what about him? | 19:59 |
| @kanzure | 19:59 <@jblake> dunno | 19:59 |
| SphericalMouse | he is the king of comsol spam | 19:59 |
| @kanzure | so much for that | 19:59 |
| @kanzure | ah really? | 20:00 |
| SphericalMouse | never really needed something like that | 20:00 |
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| @kanzure | lord_hackr: welcome | 20:01 |
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| @kanzure | lord_hackr: what brings you here? | 20:03 |
| SphericalMouse | so kanzure, i don't really want to reinvent the wheel here, am I retreading over well tread ground with this stuff? fluid robots seem really obvious so I was suprised not to see one available | 20:03 |
| @kanzure | SphericalMouse: carl crott was working on a design for one, but i think he gave up for some reason. he had a working prototype and a rails server for some reason. | 20:04 |
| @kanzure | https://github.com/delinquentme/lh001 | 20:04 |
| SphericalMouse | rails server? | 20:05 |
| @kanzure | rails is a framework for the ruby programming language to respond to http requests | 20:05 |
| @kanzure | so he was aiming to control it over http | 20:05 |
| @kanzure | http://www.youtube.com/watch?v=ZY5IY5CZ1es | 20:05 |
| @kanzure | .title | 20:05 |
| yoleaux | LH001 - YouTube | 20:05 |
| @kanzure | well that's a dumb title.. carl should fix that. | 20:05 |
| nmz787 | i pinged him about it | 20:06 |
| @kanzure | SphericalMouse: i think there's a lot more work to do to get everytihng to a usable stage, the concept is important and needs to happen.. it's not incredibly difficult, which is a good thing. | 20:07 |
| @kanzure | *everything | 20:07 |
| SphericalMouse | yeah, thats my thinking. its only really going to be useful if there is a way to add lots of modules. move fluid around 1 96 well plate will be a bit underwhelming | 20:08 |
| @kanzure | did you ever see POGO? | 20:09 |
| @kanzure | it was this $20k open source arrayer | 20:09 |
| @kanzure | http://bioinformatics.org/pogo/ | 20:09 |
| @kanzure | the big downside was how much they spent on it (wtf) and the gas environment | 20:09 |
| nmz787 | SphericalMouse: my take on it is, if there's so much to be done, why not invest it in a machine that can do that all, but on the micro level | 20:10 |
| @kanzure | because micro is much more work | 20:10 |
| SphericalMouse | indeed | 20:10 |
| nmz787 | SphericalMouse: the point of curved channels is a good and important one, one I hadn't completely thought about | 20:10 |
| nmz787 | but micro is ultimately cheaper and more powerful | 20:11 |
| SphericalMouse | the bonding techniques is important too | 20:11 |
| nmz787 | more parallelizable | 20:11 |
| SphericalMouse | thats an assertion, its not clearly true. | 20:11 |
| SphericalMouse | you have to look at the total system | 20:11 |
| @kanzure | nmz787: max hodak was telling me hte other day that geneart doesn't even use dna synthesizers for their dna production.. they just use a fleet of tecans. | 20:12 |
| @kanzure | SphericalMouse: btw, jonathan cline also put out a perl/CPAN module for controlling tecan liquid handlers. | 20:12 |
| nmz787 | SphericalMouse: have you seen these videos http://www.youtube.com/watch?v=N-R0_nXpc7I&list=UUGCzKZ2WM4eyrPCnLO9UnFw&index=7 | 20:12 |
| @kanzure | http://cpansearch.perl.org/src/JCLINE/Robotics-0.23/lib/Robotics/Tecan/Genesis.pm | 20:12 |
| @kanzure | http://search.cpan.org/~jcline/Robotics-0.23/lib/Robotics/Tecan.pm | 20:13 |
| SphericalMouse | o2 plasma bond sucks, its really flaky and sensitive to process conditions | 20:13 |
| SphericalMouse | pdms to pdms bond is way stronger | 20:14 |
| abetusk | evening | 20:14 |
| nmz787 | most of the engineering reports show plasma to be pretty strong | 20:14 |
| nmz787 | at least that's how i remember it | 20:14 |
| nmz787 | kanzure: what was the pdf manager you told me could take a dir of pdfs and organize it? | 20:15 |
| @kanzure | zotero | 20:15 |
| nmz787 | SphericalMouse: what about su-8? | 20:15 |
| SphericalMouse | what about it? | 20:15 |
| @kanzure | http://zotero.org/ | 20:16 |
| nmz787 | SphericalMouse: you keep mentioning pdms | 20:16 |
| nmz787 | SphericalMouse: i was just reading that su-8 is more resistant to wider range of solvents than PDMS | 20:17 |
| nmz787 | have you ever used it directly | 20:17 |
| SphericalMouse | su-8 isn't going to allow you make valves | 20:17 |
| SphericalMouse | i've used it to make molds for PDMS | 20:17 |
| nmz787 | if you're using electrowetting | 20:18 |
| nmz787 | ? | 20:19 |
| SphericalMouse | needs to be hydrophobic for electrowetting | 20:19 |
| SphericalMouse | but just because it has a wide range to solvents, doesn't mean it has a wide range to your solvents | 20:20 |
| nmz787 | so what are your plans for biocurious? | 20:23 |
| nmz787 | is there anything you specifically have in mind? | 20:23 |
| nmz787 | macro/micro etc | 20:23 |
| SphericalMouse | theoretically, build a liquid handling robot with a series of modules allowing for different functions, more macro | 20:24 |
| SphericalMouse | make it so other people can build it and share protocols | 20:24 |
| SphericalMouse | we'll see how it goes. realistically it will be a lot of work, and I'll see what resources we have | 20:24 |
| @kanzure | SphericalMouse: do you know about transcriptic.com? | 20:25 |
| SphericalMouse | there is a good reason these things go for 100k+ | 20:25 |
| @kanzure | their goal is to let customers write small scripts that they upload to their machines, and through a common programming language control each piece of equipment. | 20:25 |
| @kanzure | it would be really great if there is an open source alternative to that which happens to be compatible.. like "you could run it on transcriptic's machines.. or this open source machine." | 20:26 |
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| @kanzure | i guess that's sort of a "down the road" issue :) | 20:27 |
| SphericalMouse | sure. at some level we'd just make a machine that accepts move and action commands. if it works, then we can work on a nice control system | 20:27 |
| SphericalMouse | yeah, I don't want to claim we're going to have some mega system tomorrow. | 20:28 |
| @kanzure | for whatever reason, carl spent >$3k on his prototype. iirc. | 20:29 |
| @kanzure | i think it should be cheaper than that to get some steppers to move liquids around though. | 20:30 |
| SphericalMouse | probably, depends on tooling costs and false starts | 20:30 |
| @kanzure | what, biocurious doesn't have a machine shop yet? | 20:31 |
| @kanzure | i guess it didn't the last time i visited | 20:31 |
| SphericalMouse | we have a meeting on sunday, i'm a bit worried that I might toss this idea out and shut down other directions | 20:31 |
| SphericalMouse | biocurious is a bit sparse | 20:31 |
| @kanzure | were you a part of the bioprinter group? | 20:31 |
| SphericalMouse | no | 20:31 |
| @kanzure | from what i recall, the bioprinter group was really hard to get going | 20:31 |
| @kanzure | you should go ask someone about how that happened | 20:31 |
| @kanzure | i'm just an outside observer; i wasn't able to be involved because they hate the internet (or they hate me, but that's impossible right) | 20:31 |
| nmz787 | SphericalMouse: well it sounds like you've got the expertise :) | 20:32 |
| nmz787 | SphericalMouse: i wonder if space will be a constraint at bioc | 20:32 |
| @kanzure | what, no 19 foot microarrayer?? | 20:32 |
| @kanzure | so disappointing | 20:32 |
| SphericalMouse | makeslide extrusions are only 1.8 meters max anyways | 20:33 |
| @kanzure | how much stock do they have? | 20:33 |
| @kanzure | makerbeam sorta died out once the kickstarter-funded stock vanished | 20:33 |
| @kanzure | guess it doesn't matter, people who care can just make more. | 20:34 |
| SphericalMouse | inventables has it perpetually in stock | 20:34 |
| nmz787 | SphericalMouse: i saw the same V profile on a machine at harbor freight yesterday | 20:34 |
| @kanzure | it was probably t-slot or 80/20 or something | 20:35 |
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| nmz787 | hah, curtiss was on a seedbox | 20:36 |
| @kanzure | SphericalMouse: btw i hope you will consider idling in here regularly. many of us just leave this open throughout the day. | 20:36 |
| nmz787 | so makerslide doesn't have stuff to buy? | 20:36 |
| @kanzure | and we complain at each other when things break | 20:36 |
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| SphericalMouse | no, its sold through inventables | 20:36 |
| SphericalMouse | possibly, i can drop by in the evening, but unlikely at work | 20:37 |
| nmz787 | what is inventables? | 20:37 |
| SphericalMouse | https://www.inventables.com/technologies/makerslide | 20:37 |
| nmz787 | ofund it | 20:37 |
| nmz787 | i mean, can anyone negotiate them adding their stuff to their manufacturing line? | 20:37 |
| nmz787 | or do they just fulfill orders like amazon | 20:37 |
| SphericalMouse | i think they have a stock and will make more stuff as it gets low | 20:38 |
| @kanzure | sounds like they might operate like shapeways | 20:38 |
| @kanzure | oh | 20:38 |
| @kanzure | then no not like shapeways | 20:38 |
| SphericalMouse | as I understand you have to make extrusion in large batches to keep costs down | 20:38 |
| SphericalMouse | if you needed to buy a kilometer of extrusion, I'm sure you could arrange something | 20:39 |
| SphericalMouse | do you think you have time or expertise to contribute to the robot? | 20:40 |
| @kanzure | i'm reasonably good at software, so yes. | 20:42 |
| nmz787 | fenn do you think the laser cutter could be fabbed with the makerslide stuff? | 20:42 |
| SphericalMouse | at some point I guess we'll need to come up with a framework to control separate pieces of equipment and keep track of commands | 20:43 |
| nmz787 | if so then we've already got some parts listed as far as motors and such | 20:43 |
| SphericalMouse | especially if we do cell culture we'd need a way to pause and extract samples without restarting | 20:44 |
| nmz787 | we could definitely help figure out a good protocol to use/settle on | 20:44 |
| nmz787 | by pause do you mean give up control to other experiments? | 20:44 |
| nmz787 | like processes running on one machine | 20:44 |
| SphericalMouse | yes | 20:45 |
| SphericalMouse | something like that | 20:45 |
| nmz787 | you might take advantage of celery | 20:46 |
| nmz787 | i dunno though | 20:46 |
| SphericalMouse | but lets not get ahead of ourselves. just think of what you'd like to see happen, or have it do. | 20:47 |
| nmz787 | well i need to look at DNA synth reagent costs for macro synthesis | 20:48 |
| nmz787 | but i guess that's exotic chem-wise | 20:48 |
| nmz787 | so maybe not biocurious approved | 20:48 |
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| SphericalMouse | you may want to see if there are alternate paths rather than straight up fresh synthesis | 20:49 |
| @kanzure | sure, libraries | 20:49 |
| nmz787 | there are some pdms friendly recipes | 20:49 |
| @kanzure | but it's sorta hard to store 8000 tubes | 20:50 |
| SphericalMouse | there is no point in going cheap if it increases error beyond what you can tolerate | 20:50 |
| nmz787 | but they still need dry ingredients and environment | 20:50 |
| SphericalMouse | anyways, time for bed, gotta go | 20:50 |
| nmz787 | SphericalMouse: ask patrik about why error but cheap synhtesis could be good | 20:50 |
| nmz787 | basically it is the entropy for metabolic engineering | 20:50 |
| nmz787 | *could be* | 20:50 |
| SphericalMouse | you can always add in error | 20:51 |
| nmz787 | as long as you have a rapid/in-vitro protein expression and functional analysis as well | 20:51 |
| nmz787 | SphericalMouse: right but you were complaining about the error, instead of taking advantage of it | 20:51 |
| SphericalMouse | anyways, later guys | 20:52 |
| @kanzure | SphericalMouse: thanks for dropping in, give us an update about the meeting too... | 20:54 |
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| @kanzure | a traffic jam is eliminated by lowering the speed limit? | 21:17 |
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| @kanzure | https://github.com/kliment/Splotbot | 21:32 |
| @kanzure | https://www.youtube.com/watch?v=crzPESP-tyA | 21:32 |
| @kanzure | .title | 21:32 |
| yoleaux | Splotbot - YouTube | 21:32 |
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| abetusk | gotta say, the level of discussion has really improved the last couple of months | 21:52 |
| archbox_ | thanks | 21:55 |
| archbox_ | that's when i joined | 21:55 |
| @kanzure | when did this happen? | 21:58 |
| @kanzure | http://techcrunch.com/2013/01/17/elsevier-mendeley-education/ | 21:58 |
| @kanzure | elsevier is buying mendeley? | 21:58 |
| archbox_ | rip | 21:58 |
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| abetusk | hey, kanzure, are you working on the pdfparanoia to continue where swartz left off? | 22:00 |
| @kanzure | pdfparanoia didn't exist until late january 2013, so it was impossible for aaronsw to have ever worked on it. | 22:01 |
| abetusk | I didn't say he did | 22:02 |
| @kanzure | then no.. i'm doing it for myself. | 22:03 |
| @kanzure | abetusk: you might find these things useful, https://groups.google.com/group/science-liberation-front | 22:04 |
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| abetusk | the whole thing makes me sick | 22:24 |
| @kanzure | fine, don't read papers then.. | 22:25 |
| abetusk | what? | 22:26 |
| @kanzure | "the whole thing makes me sick" i assume this was in reply to my message about science liberation front.. | 22:26 |
| abetusk | of course now. It was how Aaron Swartz was treated | 22:26 |
| abetusk | *not | 22:26 |
| @kanzure | ah. | 22:27 |
| @kanzure | yes that was wrong. | 22:27 |
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| nmz787 | what opensource 3d printer projects exist? | 23:32 |
| bkero | Many | 23:33 |
| nmz787 | do you know about what's good out there? | 23:34 |
| nmz787 | i've only used a makerbot | 23:35 |
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| @kanzure | nmz787: reprap. | 23:43 |
| @kanzure | by far, reprap has the most documentation. | 23:44 |
| @kanzure | also there's #reprap | 23:44 |
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| --- Log closed Thu Feb 14 00:00:00 2013 | ||
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