| --- Log opened Tue May 22 00:00:17 2012 | ||
| LionClan | Patient DL 589.2 has an exon 51-55 deletion | 00:00 |
|---|---|---|
| yashgaroth | oh it's exons 51-55, not codons | 00:01 |
| yashgaroth | now I have some papers to work with | 00:01 |
| LionClan | http://hmg.oxfordjournals.org/content/12/8/907/F2.expansion.html | 00:02 |
| LionClan | the makers of the original trial were wrong in their hypothesis, so accidentally showed the cure for the 51-55 skip because it was a positive result, their expecting a negative result was irrelevant because their proposed mechanism was not corroberated by observation | 00:03 |
| LionClan | Dystrophin Creation Sequence Interupted By the 51-55 Deletion Is Resumed After Skipping The Missing Sequence | 00:04 |
| yashgaroth | let me see if I can find how they make the drug | 00:06 |
| LionClan | the exact sequence is known | 00:06 |
| yashgaroth | is it just an unmodified oligo, or do they do any wacky shit to it? | 00:06 |
| LionClan | they use a sequencer that is no longer made; I assume there are better ones now | 00:07 |
| yashgaroth | I assume you mean synthesizer, and no one apparently makes synthesizers any more | 00:07 |
| yashgaroth | you can still buy ones used, I might add, or make your own | 00:08 |
| yashgaroth | "They contain a 5 | 00:10 |
| yashgaroth | 0 | 00:10 |
| yashgaroth | fluorescein group (6-FAM), a full-length | 00:10 |
| yashgaroth | phosphorothioate backbone and 2 | 00:10 |
| yashgaroth | 0 | 00:10 |
| yashgaroth | -O-methyl modified ribose | 00:10 |
| yashgaroth | molecules" | 00:10 |
| yashgaroth | whoops | 00:10 |
| yashgaroth | well, those modifications make it a little more difficult anyway | 00:10 |
| yashgaroth | ah 1 sec I found the paper where they describe it better | 00:11 |
| LionClan | the exact sequence is known, it was created with the intent of curing the 51 deletion and failed, and as far as I can see they never follwed up on the positive result for patients with the 51-55 deletion, for which the process was successful | 00:12 |
| LionClan | so they are pursuing a cure they failed at, and ignoring the cure that worked | 00:14 |
| LionClan | because their target was the much larger 51 deletion population | 00:14 |
| yashgaroth | that wouldn't surprise me, but if it gets approved for d51 they might come back and try it for d51-55 | 00:15 |
| yashgaroth | minimizing the risk for another billion-dollar clinical trial etc. | 00:15 |
| LionClan | it doesn't work for the 51 deltion, it lands in an unreadble frame | 00:15 |
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| LionClan | we'd like to bypass the waiting for a 51 deletion cure, and more directly to a 51-55 deletion cure | 00:17 |
| NonFish[ | since when are synths not made anyway? | 00:17 |
| NonFish[ | it looks like they exist. just googling dna synthesizer | 00:17 |
| yashgaroth | no, I mean companies are not manufacturing new ones | 00:17 |
| yashgaroth | synthesis companies that use them just buy old ones or make their own | 00:17 |
| LionClan | someone could end up famous over this, there is a path here to a successful muscular dystrophy cure | 00:19 |
| LionClan | if only for the few where the cause in the 51-55 deletion | 00:20 |
| yashgaroth | I must admit, my own research into MD is only where it overlaps with myostatin | 00:20 |
| yashgaroth | so I can't speak to how effective it may be, but even with the backbone modifications, it wouldn't be too hard to synthesize the oligos | 00:22 |
| LionClan | it's been done, but not on a scale large enough to do more than test it on a toe | 00:24 |
| LionClan | there is proof of concept, and no one is doing a larger systemic test | 00:25 |
| yashgaroth | have you written to any of the researchers and asked why they're not pursuing it for d51-55? | 00:26 |
| LionClan | it is as you said, they wish to find the 51 deletion cure so badly they are ignoring the success shown in curing the 52-55 deletion | 00:27 |
| LionClan | 51-55 | 00:27 |
| yashgaroth | okay, well generating the sheer amounts of the drug they seem to need would require rather a large setup | 00:28 |
| yashgaroth | the clinical trials for the d51 seem to be up to like a gram a week | 00:29 |
| LionClan | they have a successful 51 skip? that would be news | 00:30 |
| LionClan | to me | 00:30 |
| yashgaroth | trials, not necessarily success | 00:30 |
| yashgaroth | I'm referring to http://clinicaltrials.gov/ct2/show/NCT00844597 | 00:31 |
| joshcryer | 15 mins: http://www.spacex.com/webcast/ | 00:31 |
| yashgaroth | oh shit I forgot all about the launch, knew there was a reason I stayed up | 00:32 |
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| joshcryer | yashgaroth :) | 00:32 |
| LionClan | here's a reference to the successful 51-55 skip, though not necessarily the primary article | 00:32 |
| LionClan | http://hmg.oxfordjournals.org/content/12/8/907/F2.expansion.html | 00:32 |
| LionClan | http://hmg.oxfordjournals.org/content/12/8/907.full | 00:32 |
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| yashgaroth | the last one was so disappointing, moreso because I was up til 3 | 00:32 |
| joshcryer | Same here. Hopefully they'll go tonight. | 00:33 |
| yashgaroth | lionclan: did they do any studies in live animals? | 00:34 |
| LionClan | human beings | 00:34 |
| LionClan | in the successful cases, there is restored dystrophin synthesis | 00:35 |
| LionClan | failure of dystrophin synthesis is the cause of muscular dystrophy | 00:35 |
| yashgaroth | indeed | 00:36 |
| LionClan | so it's a cure, if less than perfect | 00:36 |
| NonFish[ | I wrote one of these researchers iirc, to ask if I qualified for an exon skipping trial, giving my deletion location, but nope. | 00:36 |
| LionClan | I assume this is because no one is working on the 51-55 skip | 00:37 |
| yashgaroth | is it super-rare or just rare? | 00:37 |
| LionClan | NonFish[ here has that deletion | 00:37 |
| yashgaroth | I gathered that | 00:37 |
| NonFish[ | there is a deletion database if I rem right | 00:38 |
| yashgaroth | I'd need more time to see how effective the drug could be in this case, but assuming it does work, you'd be looking at well over 100 grand for the equipment and reagents | 00:41 |
| yashgaroth | naturally the more people you can treat, the cheaper per patient it becomes | 00:41 |
| LionClan | the idea is to force a jump over the deletion, and land in a readable frame | 00:41 |
| LionClan | if you can force a jump, there is a one in three chance the rest of the sequence is readable | 00:41 |
| yashgaroth | well it's either a 0 or 100 percent chance, depending on the person's gene sequence | 00:42 |
| LionClan | yes | 00:42 |
| yashgaroth | so in nonfish['s case, have you sequenced his dystrophin gene to make sure it'd work first? | 00:43 |
| LionClan | the result is a truncated dystrophin, which is normal dystrophin minus the part coded by 51-55, and minus whatever is skipped | 00:43 |
| LionClan | he has the 51-55 deletion | 00:43 |
| yashgaroth | no I mean the specific bases | 00:44 |
| yashgaroth | (yay rocket launched) | 00:45 |
| LionClan | perhaps my assumption his 51-55 deletion is the same as patient dl 589.2's 52-55 deletion is a hasty generalisation | 00:45 |
| LionClan | perhaps my assumption his 51-55 deletion is the same as patient dl 589.2's 51-55 deletion is a hasty generalisation | 00:45 |
| yashgaroth | it's proooobably close enough | 00:45 |
| yashgaroth | either way, when I say "effective" I mean whether the drug will actually produce a functional improvement in the clinic, regardless of how awesome it should work | 00:46 |
| LionClan | right | 00:46 |
| yashgaroth | and assuming you'd need like 10 grams of it, purified, to have enough to test on one person, you would need many things | 00:47 |
| NonFish[ | http://www.umd.be/DMD/W_DMD/search.shtml is one of the mutation databases | 00:47 |
| yashgaroth | holy damn there's a lot of variants | 00:48 |
| NonFish[ | leiden in .nl has one too, if i refind it | 00:49 |
| LionClan | a lot of variants yes, and the skip over each deletion requires different sequence, if one exists at all | 00:51 |
| LionClan | in the case of the 51-55 deletion, the sequence that forces the skip is known | 00:52 |
| LionClan | 78 exon gene | 00:54 |
| yashgaroth | yeah | 00:54 |
| LionClan | the skip is readable if it jumps some multiple of three | 00:54 |
| yashgaroth | mm, only if the number of nucleotides in the skipped exons is divisible by 3 | 00:55 |
| yashgaroth | but yes | 00:55 |
| yashgaroth | so let's assume your main problem is synthesizing a large amount of this drug | 00:56 |
| yashgaroth | most of the synthesis machines are set up to make tiny amounts of oligos | 00:57 |
| LionClan | the dystrophy caused by the 51-55 deletion is the 12th most common dystrophy caused by a deletion | 00:58 |
| NonFish[ | aha the other db http://www.dmd.nl/nmdb/home.php | 00:59 |
| LionClan | they will get around to that after they find the nonexistent cure for 1-11 | 01:00 |
| LionClan | it's very frustrating | 01:00 |
| LionClan | the funding is going for this hunt, which they have no idea if it will even work | 01:01 |
| LionClan | but they have this accidental proof of theory for a cure for the very few with this exact condition, a 51-55 deletion, his exact condition | 01:01 |
| yashgaroth | could just break into AVI and steal a bunch, but you'd still have to make your own eventually...hmm | 01:01 |
| LionClan | I've made doctors do things they had never imagined before, by doing all the research and preparing copies for everyone and insisting on a case management meeting and presenting everyone with copies | 01:02 |
| LionClan | but this is far beyond the scope of anything I've done before | 01:03 |
| yashgaroth | doctors are terrible at keeping up on research, sadly | 01:03 |
| LionClan | this is more difficult, in that the research is not actually done; what I want to do is outline an experimental treatment plan | 01:04 |
| LionClan | so I need to quantify it; how much money will this take | 01:05 |
| yashgaroth | oh so you want to convince AVI and a doctor and the government to let you try it out? | 01:06 |
| yashgaroth | that's probably actually easier than making it yourself, I'll admit | 01:06 |
| LionClan | this is the only theoretical cure with proof of concept already demonstrated, for any form of muscular dystrophy | 01:07 |
| LionClan | there's a successful human trial, even though it was not the one they were looking for | 01:08 |
| yashgaroth | it does seem odd they aren't pursuing it, even considering how rare this particular variant is | 01:08 |
| LionClan | it was not their target, they seem fixiated on the idea of curing the 51 deletion first | 01:09 |
| LionClan | even though they have had no success at all | 01:10 |
| yashgaroth | well it's not surprising they didn't let him in to the trial if he didn't meet all the conditions, since they can't change the requirements | 01:12 |
| yashgaroth | maybe email everyone involved and ask them personally whether you could work out some sort of one-off experiment | 01:12 |
| yashgaroth | and/or some people with clout in the MDA | 01:13 |
| yashgaroth | must admit I'm not super familiar with how these things work in clinical trials | 01:13 |
| LionClan | I want a doctor with knowledge of state of the art genetic sequencers to propose making a pile of an exact gggtacatggc... strand of rna, and injecting it into each muscle | 01:13 |
| yashgaroth | heh you won't find a doctor with that knowledge; you mean asking him to propose the company makes some, or that he does it himself? | 01:14 |
| yashgaroth | you won't need a doctor to do the injection, and any that cherishes his medical license won't do it anyway | 01:15 |
| LionClan | I want to quantify the process, determine what it would cost, in estimate | 01:15 |
| yashgaroth | ah so you do want to synthesize it yourself | 01:16 |
| LionClan | I have the actual sequence around here somewhere | 01:16 |
| yashgaroth | that's not the hard part | 01:16 |
| yashgaroth | you'll probably have to synthesize the nucleotides yourself, since AVI will have them patented no doubt | 01:18 |
| yashgaroth | and making a gram of an oligo out of it would require either a lot of expertise or a lot of money, and even with expertise you'll need money | 01:19 |
| yashgaroth | we're working in this channel on making DIY synthesizers, but even then I don't think we've considering making custom precursors like that | 01:21 |
| yashgaroth | ...not that it's impossible, mind you | 01:21 |
| LionClan | it could be one of the first genetic cures, a precident for many to follow | 01:22 |
| yashgaroth | for diseases curable by that type of exon skipping | 01:22 |
| LionClan | accidentally created a functional truncated dystrophin in patient dl589.2 | 01:23 |
| LionClan | it was still functional at the end of the trial, 6 months later | 01:23 |
| LionClan | maybe still functional now | 01:23 |
| yashgaroth | depends how fast the molecule gets excreted, but maybe | 01:24 |
| yashgaroth | I don't suppose either of you have a background in organic chemistry? | 01:25 |
| LionClan | I have some knowledge of chemistry | 01:27 |
| LionClan | I used to be a genius, now I'm just old | 01:27 |
| yashgaroth | plenty of those in this channel | 01:27 |
| yashgaroth | I can dig through AVI's patents and see if they outline how they make these modified nucleotides, once I've had some sleep/coffee | 01:29 |
| LionClan | there is an abstract explaining the procedure they used to make the sequrence, and the sequence itself | 01:30 |
| yashgaroth | you're referring to the one where they decide which sequence to use, or how to make the precursor subunits? | 01:31 |
| yashgaroth | because that first part is easy | 01:31 |
| LionClan | they had a programmable sequencer | 01:32 |
| yashgaroth | yes but it's loaded with morpholino monomers, which I imagine are not sold, and so you'd have to make them | 01:33 |
| yashgaroth | i.e. http://www.faqs.org/patents/app/20090131624 | 01:35 |
| yashgaroth | so once you can do/find someone to do that process, then it's no problem | 01:36 |
| LionClan | you're the first person I've spoken to that understands what I'm talking about | 01:40 |
| yashgaroth | there's only a half dozen worthwhile biologists in the biohacking community, in my totally unbiased opinion | 01:41 |
| yashgaroth | sadly I'm worthless at organic chemistry, but they seem to lay out the process pretty well, and none of the chemicals needed seem super hard to obtain | 01:42 |
| LionClan | there is a clean bill on toxicity, not toxic | 01:43 |
| LionClan | I believe Mercury and Lead are most often responsible for the deletions, and are widespread and pernicious | 01:44 |
| yashgaroth | you mean the deletions that cause MD? | 01:44 |
| LionClan | the prevailing theory that cosmic rays cause the deletions I consider naive, the energy's would destroy the dna, not nick it | 01:45 |
| LionClan | yes | 01:45 |
| LionClan | I'm not a doctor, I have no credentials | 01:46 |
| yashgaroth | ehh deletions in DNA are caused by any number of factors | 01:46 |
| yashgaroth | regardless...if you had a good organic chemist with lab and a good supply of the precursor chemicals, that's most of your problem solved | 01:48 |
| LionClan | a good organic chemist that is also a grant writer, that would be a plus; I'd like to put together and outline of what I'm proposing | 01:52 |
| LionClan | -d | 01:52 |
| yashgaroth | ha, if you're going for the legitimate approach that's a different story | 01:53 |
| yashgaroth | that'd mean you need to respect patents and such, in which case you should stick with getting a sympathetic doctor to buy some of the drug from AVI | 01:54 |
| yashgaroth | and look into how the FDA regulates such experiments | 01:54 |
| yashgaroth | the stuff about hiring an organic chemist is more of a...black clinic approach | 01:55 |
| LionClan | I'd like to put together a proposed treatment plan and give MDA the opportunity to do their stated mission before someone else does it | 01:56 |
| LionClan | that's one scenario | 01:57 |
| yashgaroth | why does it matter if someone does it before you? unless you're doing lab research yourself, you wouldn't be missing out on some huge amount of credit | 01:57 |
| LionClan | I don't expect credit, I have no credentials | 01:58 |
| LionClan | it's something we'd like to see happen for our own situation | 01:59 |
| yashgaroth | well, find some qualified biologist in the MDA who knows more about the disease specifics than I, and have them validate it, then put that into the plan | 02:00 |
| yashgaroth | that's about the best legal approach I can think of | 02:00 |
| LionClan | we've looked into this for years, since we heard of the research; no one else has progressed in that time | 02:03 |
| LionClan | not on that specific skip | 02:04 |
| LionClan | How did you arrive at the 10 gram esitmate? | 02:05 |
| yashgaroth | dosing regimen for the d51 phase 2 study was something like 50 mg/kg | 02:05 |
| yashgaroth | per week | 02:05 |
| LionClan | let me see that link | 02:06 |
| LionClan | please | 02:06 |
| yashgaroth | http://clinicaltrials.gov/ct2/show/NCT01396239 | 02:06 |
| LionClan | right, I see | 02:07 |
| yashgaroth | naturally you might be okay with a lower dose than that, but 10 grams is still a lowball estimate | 02:07 |
| LionClan | researching AVI-4658 | 02:09 |
| LionClan | it's applicable for specific deletions; which ones I wonder | 02:10 |
| LionClan | ah | 02:11 |
| LionClan | it is for deletions of exons 45-50, 47-50, 48-50, 49-50, 50, 52 or 52-63. | 02:11 |
| LionClan | not 51-55 | 02:11 |
| LionClan | so it won't work, though the doasges may be similar | 02:12 |
| yashgaroth | indeed, but it still operates on the same principles | 02:14 |
| yashgaroth | presumably they could tailor any combination of morpholinos to fix many of the exon deletions, but they only get to test one in a clinical trial | 02:15 |
| LionClan | AVI-5038, perhaps | 02:16 |
| yashgaroth | there you go, it's in preclinical | 02:17 |
| LionClan | it doesn't have to be a complete cure to make a profound improvement | 02:19 |
| yashgaroth | indeed | 02:20 |
| LionClan | MD only becomse serious when nearly all of the dystrophin is gone | 02:20 |
| LionClan | if the treatment expresses dystrophin at all, weak muscles are profoundly better than no muscles | 02:22 |
| yashgaroth | try emailing AVI to see if they have any updates on -5038 | 02:23 |
| LionClan | their research confirms my conclusion the treatment is not dangerous and does restore muscle function | 02:28 |
| yashgaroth | ah, good | 02:28 |
| yashgaroth | anyway I'm afraid I need sleep, but I'll be around tomorrow afternoon | 02:29 |
| LionClan | I will likely be around for a very long time | 02:29 |
| LionClan | I'll sleep too | 02:29 |
| * LionClan is LionClan | 02:29 | |
| LionClan | I always use this nick | 02:30 |
| yashgaroth | there's usually a fair number of people in here at normal hours too | 02:30 |
| LionClan | NonFish is always NonFish | 02:30 |
| yashgaroth | good to know; g'night | 02:31 |
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| LionClan | I'll idle here if you don't mind; thanks to whoever has made this room possible | 02:32 |
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| fenn | hmm something got lost in translation. i said "16 microstep" == 0.19 micron step size.. nmz wants to do 256 microsteps for 12nm resolution : | 03:27 |
| fenn | though it's still pretty slow at that resolution, 0.15 in/s | 03:28 |
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| fenn | vs an unusable .009 in/s | 03:41 |
| fenn | 16x microstepping might even be too much. with the screws we are using, 4x microstep is still sub micron (0.79um) and top speed is a reasonable 0.6 in/s | 03:44 |
| fenn | sorry 16 mm/s | 03:46 |
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| kanzure | beeeep | 06:09 |
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| kanzure | how embarrassing: https://wwws.whitehouse.gov/petitions/!/petition/require-free-access-over-internet-scientific-journal-articles-arising-taxpayer-funded-research/wDX82FLQ | 06:57 |
| kanzure | only able to get 6k on that? | 06:57 |
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| kanzure | 8th International Meeting on Substrate-Integrated Microelectrode Arrays (MEA Meeting 2012) | 07:51 |
| kanzure | Location: Reutlingen, Germany | 07:51 |
| kanzure | Date: July 10 - July 13, 2012 | 07:51 |
| kanzure | http://www.nmi.de/meameeting2012 | 07:51 |
| delinquentme | http://taketheflourback.org/ | 07:55 |
| delinquentme | protesters destroying GM crops on the 27ths | 07:56 |
| delinquentme | ( its on the to-address list ) | 07:56 |
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| kanzure | https://groups.google.com/group/brain-training | 11:42 |
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| * NonFish_ looks around | 13:56 | |
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| kanzure | NonFish_: i was hoping my inactivity would spur others to be active instead of me, but it turns out this strategy is flawed | 14:45 |
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| mensch | kanzure: it always is | 15:12 |
| NonFish_ | hello | 15:18 |
| LionClan | hello | 15:21 |
| kanzure | hello | 15:21 |
| NonFish_ | last night there was talk about oligonucleotides for exon skipping.. someone mentioned you kanzure I recall | 15:27 |
| NonFish_ | was that because you're interested/involved in that kind of thing particularly? | 15:27 |
| NonFish_ | or that you're the channel manager? | 15:27 |
| NonFish_ | I was pretty much halfasleep, might be mixed up | 15:28 |
| yashgaroth | I mentioned since he's working on a DIY synthesizer, though it'd be nowhere near the size necessary to make therapeutic amounts of oligos | 15:30 |
| NonFish_ | ah | 15:30 |
| kanzure | yashgaroth: i don't understand. why not just pcr it? | 15:33 |
| yashgaroth | it has a synthetic backbone, normal enzymes won't work | 15:34 |
| kanzure | why would a phosphoramidite machine be able to synthesize that backbone? | 15:34 |
| yashgaroth | you still need to run the reaction, even if you use their precursors and whatever chemicals they use instead | 15:35 |
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| yashgaroth | I'm not sure how different their multimerization reaction is from normal pamidite chemistry | 15:35 |
| kanzure | right, okay. was just curious how you made that leap. | 15:35 |
| kanzure | because right now it technically doesn't synthesize anything at all :) | 15:36 |
| kanzure | much less oligos, much less modified oligos | 15:36 |
| yashgaroth | heh | 15:36 |
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| Burninate | I want a combination of this: http://www.leapmotion.com/ this: http://www.kickstarter.com/projects/1104350651/tiktok-lunatik-multi-touch-watch-kits this: http://www.brothershopping.com/products/Galactus---Cellphone-Watch-With-Video-Camera-and-Media-Player.html , a solar band, and a waterproofing twist-bezel in front to hide the uUSB/SIM/uSD | 15:42 |
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| Burninate | that would give you life logging, minimal PDA/MP3/ipod functionality, and cell service | 15:45 |
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| kanzure | "If the only way to get to Disneyworld was to spend $20,000,000 and ride a thirty-year-old over-sized Russian vibrator, Disneyworld wouldn't exist either." | 16:54 |
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| yashgaroth | I really hope that's a metaphor for space travel | 17:00 |
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| kanzure | yashgaroth: yes | 17:06 |
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| kanzure | i am somewhat disappointed that the venter institute transfers genomes by email. | 18:04 |
| kanzure | http://xkcd.com/1058/ | 18:04 |
| kanzure | apparently they just have mountains and mountains of unmaintained perl cruft. | 18:05 |
| nmz787 | thats not truth | 18:05 |
| nmz787 | i mean, you're not basing that statement on that comic are you? | 18:05 |
| joshcryer | can you really synthesize a genome yet? | 18:05 |
| nmz787 | didn't you read the venter paper? | 18:05 |
| kanzure | joshcryer: yes, it just takes forever and costs a buncch | 18:05 |
| nmz787 | http://en.wikipedia.org/wiki/Mycoplasma_laboratorium | 18:06 |
| kanzure | more like mycoplasma laborious :( | 18:06 |
| joshcryer | I'm impressed | 18:09 |
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| kanzure | nmz787: the perl statement is based on talking with jcvi programmers | 18:14 |
| nmz787 | what about genomes being emaile | 18:15 |
| nmz787 | dd | 18:15 |
| kanzure | just from the comic. | 18:15 |
| kanzure | i don't know though. | 18:15 |
| yashgaroth | nah they use zip disks for some reason | 18:15 |
| kanzure | "WE TOTALLY FTP IT TO DROPBOX" | 18:16 |
| audy | ginko bioworks synthesizes genomes in 6 months (says their website) | 18:16 |
| audy | I hope they MD5'd that human genome after emailing it | 18:17 |
| audy | just to make sure | 18:17 |
| ParahSailin | someone needs to write a better global sequence aligner | 18:19 |
| -!- Netsplit *.net <-> *.split quits: augur, splicer | 18:19 | |
| audy | ParahSailin what's wrong with needleman wunsch? | 18:20 |
| nmz787 | ParahSailin: next-gen sequencing people are probably doing that now | 18:20 |
| * ParahSailin is a next-gen sequencing peopleguy now | 18:20 | |
| nmz787 | i know there is a need for new methods with the pac-bio systems | 18:20 |
| kanzure | ParahSailin: and what's wrong with all the open source alignment software? | 18:21 |
| -!- Netsplit over, joins: splicer | 18:21 | |
| ParahSailin | bwa doesnt catch everything | 18:21 |
| ParahSailin | i dont have much experience with bfast, bowtie and the others | 18:21 |
| kanzure | ah. bowtie/crossbow is where i'd start looking. | 18:22 |
| ParahSailin | im probably not allowed to be more specific until they publish a paper | 18:22 |
| ParahSailin | novoalign might be a good one to try out | 18:23 |
| kanzure | what's your fragment size? | 18:24 |
| ParahSailin | read length? we go as cheap as possible on gaIIx, typically 36 or 50 | 18:24 |
| -!- Netsplit *.net <-> *.split quits: splicer | 18:25 | |
| kanzure | erm wait, was your company the one that takes in data from others and provides alignment as a service, or are you doing in-house sequencing too? | 18:25 |
| ParahSailin | eureka has a bay area wet lab with next gen sequencers | 18:26 |
| superkuh | It's weird that only one person in this channel split. | 18:26 |
| superkuh | Oh. Geez. Nevermind. | 18:27 |
| kanzure | bay area doesn't sound like the best area to host a wetlab | 18:27 |
| kanzure | in terms of cost efficiency? i mean you don't need your superbrains working in it do you? | 18:27 |
| audy | ParahSailin you work for Eureka Genomics? | 18:28 |
| ParahSailin | yes | 18:28 |
| ParahSailin | bay area is where you get vc for wetlabs | 18:29 |
| audy | Neato. Hire me :) | 18:29 |
| ParahSailin | what can you do? | 18:29 |
| nmz787 | heh, hire me | 18:29 |
| ParahSailin | i've been here less than a month | 18:29 |
| audy | I do mostly metagenomics, 16S rRNA, bacterial genomes | 18:29 |
| ParahSailin | when i've been here longer, i can probably push through resumes | 18:30 |
| ParahSailin | audy, wet or silico guy? | 18:30 |
| audy | I used to be wet | 18:30 |
| nmz787 | sounds good, I think I'm full til september | 18:30 |
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| audy | but now it's all silico | 18:30 |
| audy | I like doing both | 18:30 |
| ParahSailin | where are you located? | 18:30 |
| audy | Florida | 18:30 |
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| kanzure | ParahSailin: haha all the bio guys are about to ask you for a job | 18:31 |
| audy | haha | 18:31 |
| ParahSailin | ok lets linkedin | 18:31 |
| ParahSailin | send me names in pm | 18:31 |
| roksprok_ | is bio employment always kind of sucky? or is it just now? | 18:31 |
| kanzure | from what i can tell it's always sucky | 18:31 |
| kanzure | unless you start your own company | 18:32 |
| roksprok_ | well it seems like the suckiness for employers is the inverse of the suckiness for employees | 18:32 |
| roksprok_ | the problem of course is you need money to start a company | 18:32 |
| roksprok_ | and a job to get money | 18:32 |
| kanzure | you don't need much money to start a company. depends on what you're doing. | 18:33 |
| roksprok_ | speaking of money what would be a good estimate for bay area living costs? | 18:33 |
| nmz787 | roksprok_: it depends | 18:33 |
| kanzure | at least 1500/mo in rent, or possibly 1100/mo in rent if you want roommates | 18:33 |
| ParahSailin | cool | 18:33 |
| kanzure | if you move further out from SF, it gets a bit cheaper- maybe 800/mo with roommates | 18:33 |
| roksprok_ | would you be able to get to public transport? | 18:34 |
| nmz787 | i think mainly on size of company... smaller companies can give you more responsibility more quickly... larger companies i would think forget having fun unless you have a phd and 5-10 years of industry experience | 18:34 |
| ParahSailin | wetlab employment is a carefully guarded cartel | 18:34 |
| ParahSailin | computer stuff is more meritocratic | 18:34 |
| kanzure | roksprok_: public transport is all over the place in SF, so yes | 18:34 |
| nmz787 | you can find berkeley housing for <$800 in efficieny studios, or cheaper if you rent a room | 18:34 |
| nmz787 | publiuc transport from outside the SF peninsula is expensive tho | 18:35 |
| kanzure | ParahSailin: yeah, so i don't see any /reasonable/ job involving wetlab work | 18:35 |
| roksprok_ | its mostly buses right? | 18:35 |
| * ParahSailin escaped from PhD program doing wetwork to code | 18:35 | |
| nmz787 | no monthly passes and bulk ticket purchases only dicount you 6.25% | 18:35 |
| kanzure | halcyon molecular had some interesting machining+wetlab work, but they paid very low | 18:35 |
| ParahSailin | wetlab work is very easy relative to the extreme cost of the capital | 18:35 |
| kanzure | the "capital" is mostly madeup costs | 18:35 |
| ParahSailin | such an industry lends itself well to monopolies | 18:35 |
| kanzure | "$500,000 thermocycler!" | 18:36 |
| ParahSailin | oh of course | 18:36 |
| ParahSailin | but the barriers are real | 18:36 |
| ParahSailin | time for 3d printers to make patents unenforceable | 18:36 |
| kanzure | patents are already "unenforcable" in that sense | 18:36 |
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| kanzure | roksprok_: also, california has a state tax | 18:37 |
| ParahSailin | it just isnt that widespread yet, kanzure | 18:37 |
| roksprok_ | kanzure: you mean income tax? | 18:37 |
| kanzure | yes | 18:37 |
| kanzure | state income tax. | 18:37 |
| ParahSailin | once it becomes trivial to get your $1000 next gen sequencer, its over for those bio cartels | 18:37 |
| roksprok_ | don't most states? | 18:38 |
| kanzure | roksprok_: not texas (where i live) | 18:38 |
| nmz787 | only other state i've heard of with no income tax is New hampshire | 18:38 |
| yashgaroth | washington | 18:38 |
| nmz787 | man i need to add crap to my linkedin page | 18:38 |
| kanzure | i think my linkedin profile says "director of pixie dust at fuck you inc" | 18:39 |
| nmz787 | i've worked about 3X more jobs/research positions than i have listed | 18:39 |
| kanzure | nobody looks at linkedin anyway | 18:39 |
| nmz787 | we just did | 18:39 |
| nmz787 | its 'cool' | 18:39 |
| nmz787 | :P | 18:39 |
| kanzure | http://www.linkedin.com/pub/bryan-bishop/8/397/3a6 | 18:39 |
| roksprok_ | Parahsailin does :-) | 18:39 |
| ParahSailin | i got into linkedin because i was job-hunting for about 6 months | 18:40 |
| yashgaroth | oh kanz I'm gonna add you on there real quick | 18:40 |
| roksprok_ | did it help much? | 18:40 |
| roksprok_ | ParahSailin | 18:40 |
| ParahSailin | nope, i found this job on craigslist | 18:40 |
| kanzure | yashgaroth: go right ahead | 18:40 |
| kanzure | yashgaroth: http://heybryan.org/ lists my other accounts | 18:41 |
| yashgaroth | I mainly want to find out how you're a 3rd degree with someone I have added already | 18:41 |
| kanzure | pfft, i'm only a 3rd degree with you? how lame is that | 18:41 |
| kanzure | you don't even know anyone else in here? | 18:42 |
| yashgaroth | I've only added coworkers so far | 18:42 |
| yashgaroth | (ex) coworkers | 18:42 |
| yashgaroth | aight I'll find the rest of you then | 18:42 |
| kanzure | my google+ profile seems to be more popular (5000 followers) | 18:42 |
| yashgaroth | that's because you have a lot of nerd friends | 18:42 |
| kanzure | https://plus.google.com/102967708777429109844/posts | 18:42 |
| nmz787 | i never started google + | 18:43 |
| nmz787 | i got enough socializing | 18:43 |
| ParahSailin | heh i heard of pico money the other day, and i just realized i had the founder linkedin | 18:44 |
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| yashgaroth | only 3 of the 20 people that got laid off with me have new jobs | 18:45 |
| kanzure | awesome. | 18:46 |
| kanzure | audy: i heart your profile pic, great beard going on there. | 18:46 |
| kanzure | the bike's a bit too hipster though :p | 18:46 |
| roksprok_ | yashgaroth: do you think a master's degree improves things at all? | 18:47 |
| yashgaroth | nope | 18:47 |
| yashgaroth | every single person I've talked to says they're useless | 18:47 |
| yashgaroth | several have had violently negative opinions | 18:48 |
| kanzure | yashgaroth: our shared (distant) connection is ratha grimes. she used to live in austin. she and i met when we were setting up the austin hackerspace. | 18:48 |
| roksprok_ | and my understanding of a phd is you either have to be lucky or network hard....is that correct? | 18:48 |
| yashgaroth | that's true even without a phd, but yeah | 18:49 |
| yashgaroth | not to mention enduring 8 years of bitch work to get it + a postdoc | 18:49 |
| audy | kanzure it's not a fixie | 18:49 |
| audy | kanzure nothing hipster about bike commuting :) | 18:49 |
| audy | maybe bike + beard | 18:49 |
| audy | + thick rims | 18:49 |
| kanzure | well, if you were wearing flannel in that pic, then i'd totally identify you as hipster | 18:50 |
| audy | kanzure you just can't see it | 18:50 |
| kanzure | yashgaroth: your contacts look very uh, clean | 18:50 |
| yashgaroth | heh | 18:50 |
| yashgaroth | it's all ex-work people | 18:51 |
| kanzure | i know all these lame journalists that keep trying to get a story | 18:51 |
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| roksprok_ | kanzure: is that how you met the biopunk guy? | 18:52 |
| audy | kanzure why don't you have your own wikipedia article yet? | 18:52 |
| kanzure | roksprok_: no, i met marcus at harvard | 18:52 |
| kanzure | audy: because i haven't written it, or other people haven't written it | 18:52 |
| kanzure | audy: also, most of the diybio thunder hasn't been directly referencing me, so i'm a wee bit scarce on news resources | 18:53 |
| kanzure | roksprok_: he knew me from the diybio group over the interwebs, and plus people involved in diybio know me, so they probably mentioned me to him | 18:53 |
| kanzure | hahah | 18:54 |
| kanzure | yashgaroth: so.. joseph replied. http://www.youtube.com/watch?v=kmTNtSs1UQY | 18:55 |
| kanzure | oh wow he has it on his youtube account | 18:56 |
| kanzure | damn, i feel so lame now | 18:56 |
| yashgaroth | dude says 'lol' a lot for someone that went to harvard | 18:56 |
| kanzure | http://www.youtube.com/watch?v=TsbaBv9rmeY&feature=plcp | 18:56 |
| kanzure | yeah, but you should read his journal articles | 18:56 |
| kanzure | "Thanks the "secret" is it usually takes about 10 years to build a foundation of muscle and 10 weeks of hard dieting to show it off with very low fat. This was really the first time in 13 years that i got "ripped."" | 18:56 |
| kanzure | "I put on a lot of size fast, like age 12-16 but only after a decade of training did I figure out how to bring out the details, diet properly, etc. You can build a decent physique during the teenage years but it also takes time to fill out." | 18:57 |
| kanzure | "A lot of military presses, bench press. Heavy shrugs for traps." | 18:57 |
| kanzure | his account is http://www.youtube.com/user/philosopherbody apparently | 18:58 |
| yashgaroth | well then | 18:59 |
| kanzure | it seems he didn't associate it with his /name/ though | 18:59 |
| kanzure | so, it's still legit to keep it hosted there | 18:59 |
| yashgaroth | you don't need a name with bilateroids that ripped | 19:00 |
| kanzure | i hosted the video on my youtube account as a sort of public shaming for ever putting a 'muscle montage' on his facebook account (who does that??) | 19:01 |
| kanzure | i mean, he took it down, so then i put it back up | 19:01 |
| kanzure | i'm a little disappointed that he wasn't on steroids | 19:02 |
| kanzure | what sorta transhumanist is this | 19:02 |
| roksprok_ | kanzure: I was looking through the logs and saw you helped delinquentme with an email to send out to get work on life extension stuff....did that work well? | 19:05 |
| kanzure | no | 19:06 |
| kanzure | the email was about 10x more ridiculous than yours :P | 19:06 |
| kanzure | but i helped him touch it up a bit | 19:06 |
| kanzure | the problem is that there's really no *good* outlet for transhumanist progress at the moment, it's just *us* | 19:07 |
| kanzure | he wanted to get into a lab where he could be paid to make lab automation tools to advance longevity research | 19:07 |
| kanzure | but there's really no lab that wants that. | 19:07 |
| roksprok_ | what about stuff like SENS? | 19:07 |
| kanzure | ParahSailin: that's your expertise | 19:08 |
| kanzure | roksprok_: ParahSailin worked at SENS for quite a while. until they fired all their biologists. | 19:08 |
| roksprok_ | i guess that would explain that | 19:08 |
| kanzure | like, they axed rob, lorenzo, wtf :( | 19:08 |
| roksprok_ | is the email asking for a job just not a very good way to get one? | 19:09 |
| kanzure | for a job that doesn't exist? email is probably not the best way to make that happen | 19:09 |
| kanzure | especially not a ranty, 10-paragraph email | 19:09 |
| roksprok_ | hah and you said mine was long at like 4 | 19:10 |
| kanzure | yeah, you also berrated yourself and made it sound like you were a runt, but you're awesome dude | 19:11 |
| roksprok_ | yea i took your advice and took out all of that | 19:11 |
| roksprok_ | but ironically people still don't want to pay me | 19:11 |
| kanzure | i'm really really cynical about biology-related jobs, sorry | 19:11 |
| roksprok_ | actually its funny you say that because the more bio-focused places i emailed i got 1 response and it was 'thanks but no thanks' while software places all emailed me back | 19:12 |
| kanzure | yeah, software is hiring like crazy | 19:12 |
| kanzure | fresh grads out of college are being offered (on average) at least $90k from google, facebook, apple or possibly microsoft (not so sure about ms' pay scales at the moment) | 19:13 |
| roksprok_ | which is good, but i enjoy the 'tedious' parts of bio more | 19:13 |
| ParahSailin | yeah i never got paid to do computer shit before this | 19:13 |
| kanzure | roksprok_: the tedious parts.. that should be automated? | 19:14 |
| roksprok_ | and i figure you need a bit of leverage before you get to say 'no i only do interesting stuff' | 19:14 |
| kanzure | i mean.. the tedious stuff is being done by people getting paid $8/hour for life | 19:14 |
| kanzure | doing 5 years of tedious work is not leverage | 19:14 |
| ParahSailin | SENS did not fire all their biologists | 19:14 |
| kanzure | ParahSailin: tell us the story | 19:14 |
| kanzure | what's the deal with letting lorenzo go? | 19:14 |
| ParahSailin | just at least two that i know of, myself included | 19:14 |
| kanzure | and you? | 19:14 |
| kanzure | i know they just got that extra $500k from last summer | 19:15 |
| kanzure | so they aren't strapped for cash entirely | 19:15 |
| ParahSailin | lorenzo and gouri did not get along | 19:15 |
| kanzure | gouri was his manager? | 19:15 |
| roksprok_ | didn't they spend like 1.x million last year? | 19:15 |
| kanzure | and at some point i think john schloendorn was doing things, but i can't recall the specifics | 19:15 |
| ParahSailin | gouri was hired on about last august as the lead sciencer | 19:15 |
| kanzure | how many other biologists or who's still there? | 19:16 |
| kanzure | i know there's a lot of people that seem to come out of arizona state university.. not sure why | 19:17 |
| roksprok_ | is SENS pretty good at bootstrapping? I recall seeing a vid from BIL talking about how they got a lab up for lysoSENS really cheaply | 19:25 |
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| audy | to bed I go | 19:31 |
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| kanzure | damn. only 51 vim shortcuts/min | 19:39 |
| kanzure | https://www.shortcutfoo.com/app/drills/4fa9868ee1fbd4001b00000f/quick | 19:39 |
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| kanzure | 58 shortcuts per minute. this is hard. | 19:47 |
| ParahSailin | my coworkers use the arrow keys with vim | 19:48 |
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| -!- Netsplit over, joins: splicer | 19:55 | |
| jrayhawk | the shame can be generalized to "my coworkers use navigation keys to navigate with vim" | 19:55 |
| kanzure | gah why can't i get above 58 :( | 19:57 |
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| kanzure | maybe it's a limit to their javascript or something | 20:11 |
| kanzure | or my ability to recognize the line of text they are showing me | 20:11 |
| kanzure | it's too bad that my 180+ wpm doesn't apply to vim shortcutting | 20:12 |
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| joshcryer | 180wpm? wow | 20:12 |
| kanzure | joshcryer: http://www.seanwrona.com/typeracer/profile.php?username=kanzure | 20:13 |
| nmz787 | i prob suck at typing | 20:14 |
| nmz787 | lots of typos | 20:14 |
| joshcryer | Woot, I just won a race. | 20:14 |
| joshcryer | 80 wpm :P | 20:14 |
| nmz787 | i will have to play this | 20:15 |
| nmz787 | even sounds decent on the evo (phone) | 20:15 |
| kanzure | joshcryer: http://play.typeracer.com/?rt=12i3080y8q7pz | 20:15 |
| kanzure | nmz787: click that too | 20:15 |
| kanzure | blah it wants me to prove i'm not a bot | 20:16 |
| nmz787 | i have no idea what just happened | 20:16 |
| yashgaroth | 82 damn | 20:16 |
| kanzure | 156.. but i aced the "prove you're not a bot" with 184 | 20:17 |
| kanzure | you can edit your nick by going to "sign in" and clicking "guest nickname" | 20:17 |
| kanzure | 161 :( | 20:18 |
| kanzure | what's up with me and 160 tonight :/ | 20:19 |
| * n_bentha is a bot | 20:20 | |
| ParahSailin | your name sounds like a robot name | 20:20 |
| kanzure | 169.. that's slightly better? | 20:22 |
| nmz787 | man i suck | 20:28 |
| kanzure | the important thing is that you know you have a typing problem :P | 20:29 |
| kanzure | typists anonymous | 20:29 |
| ParahSailin | the bottleneck for me in coding or writing is not the manual part | 20:29 |
| kanzure | it is for me :( | 20:30 |
| kanzure | it's all manual labor | 20:30 |
| kanzure | otherwise the compooter would be doing it | 20:30 |
| ParahSailin | i mean manual as in mano = hand | 20:31 |
| joshcryer | I BEAT KANZURE (OK I think he got d/c'd... heh). | 20:32 |
| kanzure | no, i failed pretty hard on that one | 20:33 |
| kanzure | she tied WHAT to a chair?? | 20:33 |
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| joshcryer | it said you were averaging 129 wpm tho | 20:34 |
| kanzure | maybe i should sit up straight. | 20:34 |
| joshcryer | I have no real ability to sit up straight | 20:43 |
| joshcryer | I mean, I don't have a desk to put stuff | 20:43 |
| joshcryer | so my lap is my desk kinda | 20:43 |
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| nmz787 | http://nopr.niscair.res.in/bitstream/123456789/4384/1/IJFTR%2034%282%29%20149-154.pdf http://nopr.niscair.res.in/bitstream/123456789/4384/1/IJFTR%2034%282%29%20149-154.pdf | 21:24 |
| nmz787 | Electromagnetic shielding effectiveness of copper core yarn knitted fabrics | 21:24 |
| nmz787 | sorry those links are the same | 21:24 |
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| nmz787 | kanzure: http://www.dovermotion.com/Downloads/KnowledgeCenter/Accuracy.pdf -- ACCURACY IN POSITIONING SYSTEMS | 21:56 |
| nmz787 | can you bookmark that in the laser projcet | 21:56 |
| kanzure | alright | 21:57 |
| nmz787 | any ppl in here can get me papers? http://jcer.com/index.php/jcj/article/view/194 | 22:07 |
| nmz787 | "Hypothesis on the Central Role of Serotonin in Biological and Anthropological Creation" | 22:08 |
| nmz787 | http://journals.lww.com/health-physics/Abstract/2008/10000/Quantitative_Evaluations_of_Mechanisms_of.1.aspx | 22:08 |
| nmz787 | "Quantitative Evaluations of Mechanisms of Radiofrequency Interactions With Biological Molecules and Processes" | 22:08 |
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| Steel__ | kanzure | 23:02 |
| kanzure | what. | 23:03 |
| Steel__ | who should I talk to in DC besides HacDC | 23:03 |
| kanzure | ask yashgaroth | 23:04 |
| yashgaroth | why me | 23:04 |
| kanzure | is jigsaw in dc? | 23:04 |
| kanzure | no, i guess not | 23:04 |
| yashgaroth | for the last time washington state is not DC | 23:04 |
| kanzure | yes i know | 23:04 |
| kanzure | just not sure which things are at which place:) | 23:04 |
| yashgaroth | ah well anyway I don't know any h+ etc types in DC | 23:05 |
| Steel__ | found one | 23:06 |
| Steel__ | looks sing heavy tho | 23:06 |
| kanzure | are you in dc now? | 23:06 |
| Steel__ | I will be moving down a week from sat | 23:07 |
| Steel__ | Starting work June 4th | 23:08 |
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| --- Log closed Wed May 23 00:00:18 2012 | ||
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