Sign in or Join FriendFeed
FriendFeed is the easiest way to share online. Learn more »


BioBarCamp: August 6-7, The Institute for the Future, Palo Alto
Pedro Beltrao
Picasa Web Albums - lizfrog - BioBarCamp day2 -
Picasa Web Albums - lizfrog - BioBarCamp day2
Jim H' s photos of BioBarCamp in Picasa - Pedro Beltrao from Bookmarklet
Seems like a wonderful event. I there is another one next year and I find the time to attend. - Daniel Jurczak
Ricardo Vidal
Nano: Bay Area - Michele Cadieux (Room 2)
Nano is big buzzword. $50 b. investment moving into nano industry - Ricardo Vidal
Bio corridor in south San Francisco with mainly bio growth in region. Notice to Roche buying of Genentech and moving from Palo Alto - Ricardo Vidal
Berkeley has a city ordinate that regulates nano industry. Hasn't been well accepted by local nano industries. - Ricardo Vidal
60% of all funding in nanotech from Gov, 40% goes to Silicon Valley. - Ricardo Vidal
Oki asks: What ratio of nano material is biodegradable vs non-biodegradable? - Ricardo Vidal
Main nano applications: biofuels, pharmaceutical delivery, semiconductors, biosensors.... - Ricardo Vidal
Carbon nanotubes going at $1000/gram - Ricardo Vidal
Bay area feeling shortage of engineers - Ricardo Vidal
CNT were at a thousand. Was just talking about the growth of the industry. Single Wall more like $250 a gram, Double wall $250 a kilo. Big differences today. :) - Michelle Cadieux
High precision, multiplexed analytics will, IMO, have the biggest impact on the life sciences - Deepak Singh
Berkeley's ordinance just asks companies to register. Most companies want to do the right thing, for people and the environment. Some businesses just don't want another level of bureaucracy in their business. - Michelle Cadieux
Roche had 56% of Genentech and wanted to buy another 40% but Genentech just turned them down. This is important as there are 1,000,000 sq feet vacant at Stanford Research Park if they move. - Michelle Cadieux
@Michelle, thanks for clearing up those topics I jotted down during your presentation. Interesting details, nonetheless :) - Ricardo Vidal
Since I know people at Palo Alto, continuing to monitor this - Deepak Singh
Genentech turned the offer down? Wow. Now things get interesting... particularly for those of us, ahem, eyeing job vacancies at Genentech. - Bill Hooker Was in the San Jose Mercury today or yesterday. :) - Michelle Cadieux
Attila Csordas
I'm sorry guys for being a bit late here with the administrative rights, just have a minute finally to reflect things and not actually doing them. Seems like you did a pretty good coverage here, great.
I think we can respect that you were actually doing the hard work of keeping the meeting going and we were just having fun. I think it was pretty ok in the end. Again congrats on putting together a great meeting! - Cameron Neylon
Great job, Attila! It was a terrific event. - Michael Nielsen
Thank you guys so much it was just really just a marvellous gathering. My big thanks to all the participants and to the real operational genius behind, that's John Cumbers, and Ying our catering lady, Jim Hardy, the financial chief, and Jamie McQuay, who builds unconferences and software for scientists, also Eva for the stickers amongst others. And thanks to IFTF for being a generous host and the sponsors who gave us enough money to have a seed for BioBarCamp 2. - Attila Csordas
And Deepak: I missed you. - Attila Csordas
You did great job Attila - congratulations! I couldn't attend, but the coverage here at FF and video from Cameron made me feel like almost being there :) - Pawel Szczesny
And I was stupid enough to leave Shirley out of the personal thank list. Thank you Shirley for the essential help and for the great coverage. - Attila Csordas
Missed you all. The Friendfeed and Video made a huge difference. Attila, I think it is safe to say that you and the rest pulled it of. Now this becomes a regular event ... :) - Deepak Singh
// echoes thanks and praise from Cameron and Michael :) Stellar job, Attila! - Kaitlin Thaney
Michelle Cadieux
Pedro Beltrao
The future of science, gradical change, and tools for the people -
Shirley Wu's post on BioBarCamp - Pedro Beltrao
added a long response to David - Deepak Singh
Ricardo Vidal
Jim Hardy - Stem Cells from Perinatal Tissue (Room 3)
Simple and less invasive to use perinatal tissue (ex: placental) than bone marrow and may reduce issues associated to transplant rejection. - Ricardo Vidal
In many cases, it is better than: embryonic stem cs, IPS, bone marrow sc - Ricardo Vidal
Jamie McQuay
It was great to put faces to names.... great job Attila and John! Let's do it again next year!
I think it's a given after the success of this BBC - Deepak Singh
then you should plan to attend now Deepak :-) - Jamie McQuay
Done - Deepak Singh
Yeh, just let me add my congratulations to all the organisers and all the people who in a lot of effort to bring this off. It was a huge success - and something that ought to continue. - Cameron Neylon
Shirley Wu
How should scientific articles be measured / Dealing with noise in science - Peter Binfield (PLoS), Pedro Beltrao
Starts with Albert Einstein: "not everything that can be counted counts, not everything that counts can be counted." - Shirley Wu
Who cares about impact? actually lots of people - public, funders, government, universities, etc - Shirley Wu
how is impact measured today?... with... Impact Factor! :-/ So what's the problem? over-interpretation. Shouldn't assign a paper the impact factor of the journal in which is is published. - Shirley Wu
other problems with IF: influences the publication process, citation behavior differs between fields, it's skewed(e.g. 89% of Nature's IF comes from 25% of its articles.), open to abuse and gaming, etc - Shirley Wu
Proposed alternative: article-level metrics. Ideal attributes: transparent methodology, repeatable / based on open data set, difficult to game, works across disciplines and publishers, be adopted by academia and reported by publishers, based on simple metrics - Shirley Wu
depressing anecdote: some departments require their faculty to publish in journals with IF of at least X. example of how IF is distorting peer review - Shirley Wu
So how can impact be measured? Potentially, where the work is published (traditional IF), citations (scholarly, hyperlinks, social bookmarks, etc), web usage, expert ratings (F1000, peer reviewers, ed boards), community ratings (Digging, commenting, rating), media/blog coverage (how to measure the authority?), policy development? (tangible changes), and more esoteric things like Who published it (institution, lab, previous work), who is talking about it + who is citing it (and what authority do they have?) - Shirley Wu
Web usage as an example. Some considerations: what to measure (if you download a PDF did you read it?)? who is the user? how to capture all usage data? how to compare? is it possible to game the system? - Shirley Wu
Adsense mention :). I am watching between calls - Deepak Singh
suggestion that the google adsense people have solved many of these problems - Cameron Neylon
but then good reasons why it isn't such a good model - Cameron Neylon
There are equivalents to PageRank in science, at least conceptually - Deepak Singh
audience also mentions similarity to Google's PageRank - Shirley Wu
EigenFactor is one. Eric Neumann also published a pagerank like system built on RDF - Deepak Singh
Has to be normalized to size of field as well. a 1000 views on a neuropsychology paper might be equivalent to 1000000 for a genetics of cancer paper - Deepak Singh
potential way to measure impact: "your article received x citations, viewed x times, received x comments, bookmarked x times, rated x by experts, discussed on x "respected" blog, appeared in x news media, etc etc (instead of single "your article was published in journal with IF of X" - Shirley Wu
Chris Patil: any new way of measuring impact is just a different way to substitute judgment? Is measuring impact even necessary/desirable? - Shirley Wu
authority 3.0. how to measure authority? laundry list of potential metrics. - Shirley Wu
Federated ID is essential, IMO and has to be built on top of an INTERNET standard, not some arbitrary scientific standard - Deepak Singh
Some audience discussion about researcher ID, social ID, etc - Shirley Wu
Some discussion about whether people (when searching for papers) look at impact factor before or after they find the papers, if at all, should impact factor come after making an effective search engine for papers? - Shirley Wu
Pedro shows plot of # of PDF downloads correlating with # of citations. Audience comments that # of citations does not indicate quality of paper necessarily. Maybe poor search engine led to crappy paper being read a lot, and you're likely to cite papers you've read even if they're not that good, because you didn't find anything better. - Shirley Wu
Which is why you need markup and have some form of discovery engine - Deepak Singh
Audience: why do we need IF??? some answers: hiring decisions, need a way to filter... etc - Shirley Wu
Goes back to the same point. What is relevance and relevance from what point of view - Deepak Singh
Kaitlin Thaney: impact/popularity != relevance to a researcher's problem - Shirley Wu
Bryan Bishop: we don't need a universal measure. Every search is biased towards the information you want to find. Subjective. Personal filters. - Shirley Wu
Johan Bollen is doing some research around this question:; - Hilary
Jim Hardy
Picturs from Day 2. Group photo after dinner, so only about 15 people. Attila, next year we "must" get a group photo before ending the session! -
Jim Hardy
Hey, where are the pictures from the after party at John's? We had to get back to the hotel in Sunneyvale, so couldn't make it.
Shirley Wu
That's a wrap. BioBarCamp will probably happen in the bay area again next year. Thanks to the sponsors and all the attendees!
Things to think about next year: concrete outputs and records? e.g. a brief to hand off to SciFoo about what happened at BioBarCamp - Shirley Wu
Good length is evening planning + 1 full day - Shirley Wu
Wonderful ... great jobs folks - Deepak Singh
+1 thanks for excellent coverage; I think we've seen the future of conference liveblogging and it is FriendFeed. - Bill Hooker
What a great time! Now I can re-live the whole event on FF. Great note taking Shirley and also thank you for setting up the dinners! - Jim Hardy
Pedro Beltrao
Joseph Perla – Cloud computing, Robotics and the future of Science -
we don't want to do tedious tasks ... - Pedro Beltrao
doesn't automating a cafe take away from the experience? - Jamie McQuay
8-10 years ago C code .. very tedious, needs to tell everything to the computer. the direction in CS has been to make computation less tedious. Example of SAGE - Pedro Beltrao
it is easy to ask the computer to do a task , but it might still take a long long time to process. instead we can take it to the cloud and let it compute. We should not need to know about the details. - Pedro Beltrao
making the argument that spare cycles of every computer can be used - Pedro Beltrao
getting to the problem of parallel processing - Pedro Beltrao
does the national research grid not already fill this void? - Jamie McQuay
the next couple years , due to the multi core processors , programmers need to learn to program for multi core - Pedro Beltrao
Deepak: comment from the audience, tried to get 500 virtual machines for 3 days at Amazon but they were refused (too big) - Pedro Beltrao
DEEPAK - set them straight. - Jamie McQuay
Example of Folding at home (PS3 at people's home) - Pedro Beltrao
Open Mac Grid and SETI@home - Pedro Beltrao
distributed home computing will go away because "normal" people will switch to the cloud with "cloud books" - Pedro Beltrao
another possible computer time that we could tap would be webservers - Pedro Beltrao
moving to discussion about lab robotics and automated labs or companies - Pedro Beltrao
fully automated instrumentation in 5 years... yes that is a dream. - Jamie McQuay
Send them to me. - Deepak Singh
I showed him the link. He said that eventually they got the space the needed in a uni cluster. - Pedro Beltrao
Would be interesting to find out when this request was made, cause although sometimes coordination is required, access to a large number of small size instances is usually not an issue. - Deepak Singh
ask him to email me ... deesingh at - Deepak Singh
sorry Deepak, I saw this too late. I don't remember the name know. - Pedro Beltrao
Quite OK ... if anyone else remembers, let me know - Deepak Singh
Cameron Neylon
Recorded video is now available on demand -
If you click on the 'on demand' button at the bottom you will get a selection of the videos where i managed to get the recording going. This includes most of Aubrey de Grey's keynote, sessions on open science, data commons, openwetware and labmeeting - Cameron Neylon
Your video did a great job. Before such experiments like coverage from ISMB and BioBarCamp I wished someone just record the event and post afterwards on the web. Now, I dream about videostreaming and _participation_ via twitter, FF or whatever mechanism (for example to ask questions etc.). - Pawel Szczesny
Awesome. Can't wait to get home next week and take a look at the videos. - Daniel Jurczak
Shirley Wu
Failure in science - Eva Amsen
Talk motivated by fact that Eva has been in school for 6 years and only had one paper, spent 3 years building a system that doesn't work, etc. Tired of feeling like a failure. Can "failure" be redefined? - Shirley Wu
in science, you come up with a hypothesis, if everything works well in about 2 years you get a publication in cell/nature/science. but usually things don't work so well and you just spin your wheels and 4 years later you realize all you have are negative results. whose CV looks better? who worked harder/more? - Shirley Wu
Chris Patil encapsulates: rewards are given based on a whole bunch of factors, many of which are outside an individual's control - Shirley Wu
great topic. Congrats Eva in presenting it. - Jamie McQuay
mention of Journal of Negative Results in Biomedicine, PLoS ONE, Nature Precedings as places you can publish negative results. But still not any of the big 3 or journals with high IF - Shirley Wu
Eva mentions a study that looked at p-values reported in papers. Distributions should be normal-ish. But found that there's a spike right before p=0.05 and a dip right after. People were fudging their data to have "significance" so they could publish in the big journals. Credit Michael Nielsen for the story. - Shirley Wu
Mention that p-value cutoffs are pretty arbitrary. Eva comments that it's because people don't want "failure" that they are driven to manipulate data to get it published in a big journal. Peter Binfield mentions the problem with image manipulation. Chris comments that there's really no such thing as raw data anymore in many cases. - Shirley Wu
Eva now segueing into "alternative careers". Dislike of the term because it's often connoted with "failure" to succeed in an academic career. "Death in the family" response when you tell people you're not going to do a post-doc, etc. - Shirley Wu
a lot of participants feeling like failure is in the eye of the beholder. If you don't feel like you've failed, then you haven't. Do we need to worry about the idea of failure in academia? "alternative" career implies a minority, but it's actually the majority. - Shirley Wu
how to value the work that went into the long and convoluted path that didn't end in a cell nature science paper? this could come out of an in depth interview with the person. But how will that person get an interview? - Shirley Wu
Journal of Negative Results - - Shirley Wu
Would getting your negative results published in PLoS or some other journal be worth the effort of writing up something that's most likely not as exciting to you as a positive result? - Shirley Wu
Of course, publishing negative results is very valuable to science as a whole, avoid wasting resources, greater efficiency, etc. So more altruistic than anything else. Keep someone else from suffering through your pain. (This doesn't necessarily work in the corporate world which is much more competitive) - Shirley Wu
PLoS model - don't determine what is important, just what is valid. In the future, everything will be important to someONE, but we can't know who or when now. They don't want to game their IF at the expense of not publishing science that could help someone eventually. - Shirley Wu
in the life sciences especially, there are so many ways to get things wrong; it's so important to eliminate as many of those paths as possible by getting the negative results out there and published. - Shirley Wu
The perfect paper: negative results + all the things we did to verify the negative result. OR positive results + all the things we tried that didn't work - Shirley Wu
Dangers with publishing negative results: can be very difficult to publish a positive result that contradicts it. What if you just did something wrong? Maybe your result would have been positive too. Things can be negative either because your hypothesis is wrong, OR you did things wrong. - Shirley Wu
Cameron Neylon
Open Science session led by Kaitlin Thaney
FOur principles of open science form science commons - Cameron Neylon
what re the issues? - Cameron Neylon
what are good examples of open science cases? What is your favourite example? - Cameron Neylon
what is a name for these things - Cameron Neylon
to be hoenst will probably cut and paste Kaitlin's notes rather than try to captureeverything as we go - Cameron Neylon
Question again - what are the really good stories. - Cameron Neylon
whatt's in it for me? - Cameron Neylon
has science become more anthropocentric generally? - Cameron Neylon
is this part of the problem - Cameron Neylon
do journals need to mandate more availability - Cameron Neylon
a standard for journals could be written up - Cameron Neylon
avaialability of grey data - Cameron Neylon
*should* be written up - Deepak Singh
sorry - difficult to talk and take notes at same time, but Kaitlin took some down - Cameron Neylon
Cameron, I was referring to the "standard for journals" - Deepak Singh
Ah ok - just finding it hard to follow and keep up, and track camera :) - Cameron Neylon
I think a strong message has been we need more clear statements and standards (which we already knew) - Cameron Neylon
the notes mac so nicely took on this are in the google group ... will post when i get some more bandwidth :) - Kaitlin Thaney
also, here's our blog post pointing to the recommendations and some additional conversation on these issues .. more to come -- - Kaitlin Thaney
Shirley Wu
Panel on biotech startups
Jim Hardy - Gahaga Biosciences, William Anderegg - Fast DNA sequencing technologies, Quinn Norton - science journalist/writer, Alex Bangs - Entelos, Michelle Cadieux - San Jose Business Journal and International society of nanotech/ clean tech nano, Andrew Hessel - Mikana Therapeutics and open source biotech - Shirley Wu
Mac Cowell asks: what are the differences between software startups and biotech startups? Jim: no single recipe but typically for both you have to be ok with going for a while without expecting a paycheck to come out of your work. Need a good idea and material to back it up. - Shirley Wu
Initial capital required, investor risk, time to profitability, esp in today's market - Deepak Singh
amongst others :) - Deepak Singh
Be prepared to not get paid for 12 to 18 months. - Ricardo Vidal
Mac follows up: how do you get capital before you get a blockbuster idea? Alex: you need to come up with the blockbuster idea first. Sometimes it takes a while to formulate a really good idea. - Shirley Wu
Andrew: a difference between the two industries - different resources need, much longer time to market, a lot of seed work done in academic environment with funding from the public, unlike software where you can essentially develop everything on your own in your basement - Shirley Wu
I think the investor approach to biotech startups is very random. I wish there were more VCs who understood life sciences and had realistic expectations of risk - Deepak Singh
Quinn: VC for software startups is often very destructive, they often go over the top in their expectations. However, VCs in biotech may be slightly more realistic. - Shirley Wu
I've been around enough VCs in biotech. They are NOT realistic - Deepak Singh
Jim: after you come up with a good idea, sit down and write it up as a business plan before you quit your day job. - Shirley Wu
Question from John Cumbers: these days, a link to an external investment or business is seen as a good thing; but this opens a new can of worms around IP and disclosure. How do you see this relationship between academia and business? is it good? - Shirley Wu
Andrew: it is a problem - makes academics much less willing to talk to each other and share. This is why i'm getting into open source biotech strategies. E.g. nonprofits like OneWorldHealth. - Shirley Wu
It's not necessarily academics. Uni tech transfer offices are always pushing technologies which are not good enough or not ready for prime time. The IP situation doesn't help. Things get protection that should never be protected. - Deepak Singh
@Deepak: Quinn qualified her VC statement by saying that it doesn't mean biotech VCs are that realistic, just compared to the ridiculous expectations of software VCs. - Shirley Wu
New question: is innovation faster in academic environment or startup environment? - Shirley Wu
Answers: lots of tradeoffs. Things can happen really quickly in a business setting that would get bogged down in grant cycles and administration in academia. at the same time, big corporations have the resources but don't necessarily have the interesting ideas, small companies can't necessarily pursue interesting ideas for lack of resources, etc. - Shirley Wu
@Shirley, maybe should just say all VCs are unrealistic, but it's really hard to bootstrap biotech. Much easier to bootstrap software startups - Deepak Singh
Alex mentions some NIH grants that are geared especially for small companies. Not a lot of people applying for them right now, and you can't apply after you've received investor funding, so it's ideal for startup type folks - Shirley Wu
One thing with SBIRs and small grants. Lots of academics set up shell companies to use those grants to get more money and never really use to innovate. We need seed funding. The biotech equivalents of YCombinator, iphone fund, etc. Get people going and fund for 3 years. Enough time to bake and idea and get some idea of potential - Deepak Singh
Mac follows up: can you talk more about the incubators you know of? Are there organizations that help promising startups through the bureaucracy and the process? - Shirley Wu
@Deepak - there are loopholes in all industries.... - Jamie McQuay
There are incubators that provide resources and space but not usually funding. Plug n' Play is an example incubator for software startups. water cooler effect. office space and internet, some biotech incubators have equipment and bio facilities. for a small monthly rent. - Shirley Wu
Jamie ... indeed. There is an incubator at ISB. There was an incubator at Syracuse while I was there, but it was a bit of a sham - Deepak Singh
Curious to see if anyone has worked with iBridge Networks - Deepak Singh
Question: Does location matter? Cambridge, MA, San Diego, SFO seem to be a lot more fertile. Do you have to move there to have a shot? - Deepak Singh
@Deepak - i say yes. I have more contacts in the valley than i ever will being based in Toronto. We are looking to move down the road. - Jamie McQuay
Andrew: $1M is about the minimum you need to start a company with 10 people. - Shirley Wu
Jim: can be desirable to be able to support yourself if you can since VCs complicate everything - Shirley Wu
no VCs in the room... except the guy sitting in front of me ;-) - Jamie McQuay
Question: how does open source biotech change the landscape? - Shirley Wu
Andrew: biotech development always used to be proprietary, now it's not the case. even if it took $1B to develop a drug, it's relatively easy these days for people to raise that much money. - Shirley Wu
New economic model possible with open source biotech. Less overhead on protecting your IP and facilities. Don't need a monopolistic worldview. Can be perfectly successful having just a modest markup/market share. Costs are much lower. - Shirley Wu
Alex: the issue for biotech is both regulatory and risk. Right now everything has to be a home run goal. But what does it actually take to make something that will work and help people? - Shirley Wu
Jim: FDA = pharma, not biotech - Shirley Wu
INCUBATORS: Not sure if there is any room at, but they do have a public tour or you can schedule one for your group. See also And a link to an article on at http://www.sanfrancisco.bizjou... bio-incubator a rival? - says the city supports the idea of a Morgan Hill... more... - Michelle Cadieux
Pedro Beltrao
Joel Dudley & Charles Parrot – Open Access Scientific Computing Grids & OpenMac Grid -
500 cpus on Xgrid - Pedro Beltrao
very easy to share CPU - Pedro Beltrao
scientist can apply for space - Pedro Beltrao
Xgrid is not very good on dealing with files - Pedro Beltrao
bottleneck on the grid is the RAM - Jamie McQuay
they are testing it with ligand docking simulations - Pedro Beltrao
ligand docking, modeling for key/receptor modeling application - Jamie McQuay
they are currently no swamped with requests and they evaluate based on technical criteria and criteria about the users' availability to other resources. If they can have other clusters in their institutions there is no point of using this. - Pedro Beltrao
safety, the Xgrid engine has very low privileges - Pedro Beltrao
What kind of RAM, and what is availability like? Definition of open access? - Deepak Singh
Deepak it is going to any Mac computer. There are ways in Xgrid to ask for some resources apparently and you could test first the resources and go way if it not enough. They have a lot of free space right now. - Pedro Beltrao
Ah ... its a "G" grid - Deepak Singh
Is it 500 CPUs or 500 cores - Deepak Singh
Shirley Wu
So you want to live forever: why you should care about the biology of aging - Chris Patil
distinction between biogerontology and gerontology. Biogerontology = intersection of genetics, genomics, systems bio, all these new life science technologies. Study of the biology of aging. Lots of work in model systems, etc - Shirley Wu
"Lifespan regulation" - some people have asked him, why would i want to live longer it sounds boring (answer: then don't take the medicine), and also why would i want to spend longer being frail and sick? (answer: we're not trying to add on the years at the end, we're trying to add on years in the middle) - increase healthspan - Shirley Wu
why study aging as opposed to more immediate diseases like heart disease or stroke? --> Age is the primary risk factor for so many of these diseases. If you combat aging, you will make the biggest % increase in lifespan. Curing anything in particular or even all cancers, heart disease, etc, you'll only make incremental increases - Shirley Wu
compares increase from curing various diseases to increases that have come from research on aging - Caloric restriction is first, with a bigger but still somewhat incremental increase in lifespan. Then the best mouse lifespan achieved (extrapolated to human lifespan) is a big increase. The best worm lifespan increase achieved dwarfs all other increases. (mouse and worm lifespans achieved simply from knocking out a single gene - a growth hormone receptor). - Shirley Wu
multiple gene knockouts + caloric restriction in worm = 10X lifespan increase - Shirley Wu
while before the study of aging consisted of isolated groups studying independent aspects, it is starting to come together into a cohesive picture - Shirley Wu
conclusion: resource allocation - small red sliver is for National Institute on Aging (but this goes towards design of wheelchairs, ramps, etc), tiny sliver goes towards studying the biology of aging, and an invisible sliver goes towards foundations like the Methuselah foundation. Are we spending our money in the right ways? - Shirley Wu
Question: science as a quest for knowledge vs science as a goal-driven enterprise? Answer: most people are in it to discover the mechanism, not to intervene. Second question: aging is endemic to our species, is "curing" aging more destructive to our society than beneficial? Answer: no attachment to what is "natural", our definition of "natural" changes all the time. Also, any change (social, demographic, economic, etc) will happen gradually and we will have time to adapt. - Shirley Wu
interesting horror story scenario: if we get things wrong, someone could end up with the body of a 16 yr old but a mind made of swiss cheese - Shirley Wu
Cameron Neylon
Video is back, not sure how well the whole, giving my talk and livecasting it will go
Cameron is giving is talk: "Building the data commons" - Pedro Beltrao
we know more or less what needs to be done, "clear blue skies ahead" - Pedro Beltrao
a resource that is held in common for use - Pedro Beltrao
John Wilbanks - This is not about copyright, data is public domain data is not free, science costs a lot of money. - Pedro Beltrao
making data available is not cheap (although we heard yesterday from Google that there are ways to make data available to a large scale) - Pedro Beltrao
we need a minimum "standard" to promote the data commons. Data availability could be this minimum standard. - Pedro Beltrao
We need to have the raw data, protocols, processed data made available to be able to reproduce it - Pedro Beltrao
issues of policy (mandates for open data, with provisions to help make the data available). issues about funding (the cost to make the data available - 2%-3% of research costs) - Pedro Beltrao
instead of funding the research , funding could target the availability of data - Pedro Beltrao
Scientists, as a community and field, need to start thinking hard about the mechanics and operational infrastructure for data distribution - Deepak Singh
issues about Motivation. Altruistic reasons ? a good tech company needs to satisfy at least one of the deadly sins :) .. so maybe we need the same in science. - Pedro Beltrao
we know that there are positive benefits to availability ... should we use pride to lure scientists or let them see the benefits with time - Pedro Beltrao
We need better tools - Pedro Beltrao
a quick comment on semanatics, instead of adding semantic annotation for publication, it should be captured by the instruments - Pedro Beltrao
mission statement: adding value to current data production to make it available. There could be easy economic arguments to make the case for the availability of data, enabling re-use - Pedro Beltrao
question about incentives, incentives from data usage outside of papers. discussion on microcredits etc - Pedro Beltrao
Jamie McQuay
Cameron Neylon - Building the Data Commons (room 1)
title slide.... clear blue skies ahead... - Jamie McQuay
data is the public domain. - Jamie McQuay
none of this is free... science costs money. a lot of money. - Jamie McQuay
data commons - public domain, useable, and re-useable. - Jamie McQuay
raw data from a published paper should be made available. - Jamie McQuay
"i don't have any original thoughts, i'm in open science so i just borrow everything". - Jamie McQuay
data commons - adding value to what we are already doing. - Jamie McQuay
data commons is not - a walled garden, cheap, easy, a forgone conclusion. - Jamie McQuay
Cameron Neylon
Open Source Biotech
Pink Army - open source drug development for cancer - Cameron Neylon
love of DNA and computing (shows picture of HAL) - Cameron Neylon
dna was not much use on its own - needed computer science - Cameron Neylon
developed computer software for genomic mapping - Cameron Neylon
hired by Amgen to develop software for handling their genomic data - Cameron Neylon
in Amgen had experience of drug development pipeline - Cameron Neylon
very profitable protein drugs - 92% return on production costs - probably similar to printing money :) - Cameron Neylon
Talk by Andrew Hessel - Ricardo Vidal
talking about current drug development pipeline , leads , pre-clinical etc - Pedro Beltrao
$300M for preclinical testing, $600M for human testing, $95M for post approval following of outcomes - Cameron Neylon
But look at Amgen today!!! - Deepak Singh
10.000 to 30.000 substances to get a single molecule in the market (typical 10 years) - Pedro Beltrao
thousands of compounds reduced to one lead by development people (who are not scientists - more like accountants) - lots of paperwork involved over ten years - Cameron Neylon
compare that to genbank - used to have it on a floppy, since grown super exponentially - Cameron Neylon
look at the ten year in the past for what genbank/proteomics/whatever data, and then think about what is coming as we develop the next generation of drugs - Cameron Neylon
(if someone wants to make questions we can relay them) - Pedro Beltrao
introduction to cancer - Pedro Beltrao
general description of background to cancer - arms race between cancer and the treatment - Cameron Neylon
herceptin, pre-genomics drug 30% breast cancers, $5000 for diagnostics to check if you can use it. - Pedro Beltrao
6 companies are profitable above 5 billions (5 billions looks like a lot). The industry as a whole never made money - Pedro Beltrao
biotech has limited number of targets (needs to go for blockbusters) , it is way behind tech development. cannot support personalization (blockbusters again). it has not cured cancer :) - Pedro Beltrao
discussion of hte business - not profitable industry - Cameron Neylon
I have to jet out, but at the opportune time, could someone ask him what he thinks about plans by certain big pharma to essentially become virtual companies as well as the program Allan Roses is running at Duke - Deepak Singh
finally, a sub conversation in the same room :-) - Jamie McQuay
whats to make safe and effective drugs fast, state of the art (not 10 years old), failure tolerant, personal (cancer is personal) and global. - Pedro Beltrao
leading up to synthetic biology ... DNA synthesis - Pedro Beltrao
steve jobs in the most powerful tool in biotechnology.... oh, the laptop... - Jamie McQuay
talking about Drew Endy's work on standards for synthetic biology. plot of cost of DNA sequencing and synthesis - Pedro Beltrao
introduction to oncolytic virus (, infects cancer cells but not normal cells - Pedro Beltrao
personalized drug pipline, good to think different. - Jamie McQuay
video seems to be back on for the moment - Cameron Neylon
looks like a sales pitch to build a genomics company built on top of an "open source" community of parts , cheap personal genomic testing , and cheap synthesis of viral therapy - Pedro Beltrao
tricky part regulatory part .... interesting idea, total personal treatment does not/cannot be tested in clinical trials, does not make sense (it makes sense to me I was just relating how he said it :) - Pedro Beltrao
Pedro, if you perform the test on yourself you would bypass this problem. - Jamie McQuay
business structure used: co-opt, similar capacity as a corporation ,IP is regulated, non-profit. - Pedro Beltrao
asking for participation - Pedro Beltrao
he makes money by selling speaker fees back to amgen :) - Cameron Neylon
Deepak - don't think there is time to ask your question - will try to ask him later out of the session - Cameron Neylon
if regulators in Canada do not allow them , they can move it - Pedro Beltrao
Ricardo Vidal
DIYbio - Mac Cowell (room 2)
give us some feedback on the session Ricardo - Jamie McQuay
Discussion regarding safety - Ricardo Vidal
Ignite international DIYbio movement: need to provide 1) reagents and biomaterials, affordable equipment, expert knowledge and nurturing public experimental spaces (ex: techlab) - Ricardo Vidal
General interest in registry of parts and the iGEM binders with DNA samples. - Ricardo Vidal
Jamie McQuay
Alex Bangs - Personal Health Simulation (Room 3)
PhysioLab Platforms, virtual patients for simulation - Jamie McQuay
possible to build virtual populations - Jamie McQuay
Cardivascular modeling, specific, do not have to model bones etc... - Jamie McQuay
environmental conditions to genetic decomposition play a role in the modeling - Jamie McQuay
Nonlinear ODE modeling.... i've been there, complex stuff - Jamie McQuay
fitting algorithms can have up to 1000 state variables - Jamie McQuay
Could be even more if we had the measurement tools - Deepak Singh
the virtual patients are validated against clinical trail data - Jamie McQuay
how to make sense out of a battery of tests? - Jamie McQuay
virtual population size in the 1000s - Jamie McQuay
which tests are important to me? - Jamie McQuay
modeling results can give the value of the tests to the patient (i.e. what tests are more important to be done). - Jamie McQuay
Shirley Wu
Keeping Stalin out of science - Jeremy England, Joseph Perla, Mark Kaganovich (Labmeeting)
Discussion about the future of science, where we're heading and how do we get there - Shirley Wu
Two drivers that will continue to advance: Internet improving communication, technology improving science experimentation. - Shirley Wu
Projects that 4 things will change: how science is funded, who plans experiments, what carries them out, what publication/review process ensues - Shirley Wu
changes in science: how science is funded, who plans the experiments, what acarries them out; the publication/review process - Pedro Beltrao
"people in brazil funds thinker in India that directs robots in Germany. information published immediately to be reviews by the community" - Pedro Beltrao
Radical vision for the future: _soon_, people in brazil send $ to thinker in india who directs robots in germany to do experiments so she can write paper that is published immediately so it can be reviewed by whole research community - Shirley Wu
(Under)current - a lot of reform is needed in the way science is funded, carried out, and reviewed - Shirley Wu
Chris Patil comments: must be careful not to conflate governmental policies for funding etc with agovernmental policies for scientific review and publication - Shirley Wu
Essentially, Internet is a platform for distribution of information, information is fluidly defined. Alex Griekspoor (Papers) mentions that ultimately all the money comes from the public, they should have some say in how it is used. Jeremy says yes, but it shouldn't be funneled through only a very few channels. - Shirley Wu
Michael Nielsen asks: so how much money in the US should be used towards creationist research? (reflecting the fact that there is vocal support from "the public" for it) - Shirley Wu
Hilary Spencer (Nature) comments that it's because of publicly funded (through government taxes) science that we are able to argue effectively for open access and mandate it. If you take it away this public funding aspect you may undermine openness. - Shirley Wu
Chris Patil objects to calling Germans "robots" ;) - Shirley Wu
Argument for how these changes SHOULD occur: science relies on trust, trust only remains intact when change occurs through consensus, change through consensus is inherently gradual. - Shirley Wu
point about trust is key - I'm not sure I agree with a lot of the other things said but that is really at core - and that consensus is important - Cameron Neylon
Conclusion: the first step is to create incentives for individual scientists to voluntarily start doing the same everyday things on the same web platform. - Shirley Wu
Problem: there is no central place on the web where scientists do these things. Little benefit to be the only one or the few in any one place. Hard to motivate people to join these places if little benefit. - Shirley Wu
finding key issues that will give incentives to use of web tools ... I also don't agree with a few things they said. - Pedro Beltrao
Potential solution: create something that will benefit the individual (for now), or individual labs. -- gradual, incremental. Does not require a large user base, only needs you to benefit you. - Shirley Wu
Audience comment: may need to incentivize even more - what will get people to try a new tool? Answer: empirical approach. Identify what it is people want or need, develop something to solve that, analyze what aspects they find most useful, improve. Vivek follows up: identify the burning need. - Shirley Wu
Cameron says: it's all about $$$$. Money is a huge incentive. - Shirley Wu
Hilary asks: if you have distribution of funding how do you determine data/research ownership? Jeremy comments: it's more about openness, choice, transparency, at least you will know who's funding it and what strings are attached if any. - Shirley Wu
Chris Patil asks: what makes us believe that direct democracy (the people who vote American Idol as the best show on television) is a better way to do resource allocation than the current system? - Shirley Wu
Vivek comments: opening up the way funding is allocated is tricky. Marketing can aggregate funds towards pretty much anything (friendship rings for De Beers) if you have enough money to campaign. - Shirley Wu
Nikesh comments: for individual scientists, it's not usually about money. - Shirley Wu
Michael Nielsen comments: people should have a lot of incentive to save for their own retirement, but they usually don't and the government usually steps in for them. Interesting precedent to think about if you start talking about people investing money in other things that may or may not have direct benefit to them in their lifetime - Shirley Wu
we could have discussed the issues that scientists need to solve, those would be the ones that these tools should focus on - Pedro Beltrao
Pedro ... agreed. and I don't think change has to occur through consensus. You almost always follow the Crossing the Chasm adoption curve ... - Deepak Singh
Jamie McQuay
adopting web 2.0 - room4
IFTF uses a drupal based website :-) - Jamie McQuay
web 2.0 - who controls the information? - Jamie McQuay
moderating blog comments is acceptable.... i beg to differ... - Jamie McQuay
Shirley Wu
Using online communities to share resources efficiently - Vivek Murthy (Epernicus) and Ricardo Vidal (OpenWetWare)
Getting started now, a bit behind schedule - Shirley Wu
Lots of tools popping up solving slightly different problems. Question is, how do we leverage these tools and the online communities using them? - Shirley Wu
Overview of Epernicus: Specific problem they tried to solve - if you need to find a person with a specific skill or knowledge or resource. This should be quick and easy, not the challenging goose chase it is now. Often times the person you need to find is someone you _already know_, you just didn't know they were there, or that they could help you. - Shirley Wu
Epernicus: problem to solve: find a person close to your social network that has the skills or tools that you need - Pedro Beltrao
Started about 6 months ago at MIT with a few seed labs, has grown lots since then (unofficial estimate Vivek gave me yesterday was from a couple hundred about 3 months ago to a couple thousand now), but only about 10-20% of where they want to be - Shirley Wu
Epernicus lets you search your network online for people who might have the expertise you need. Does example search for "stem cells" in the Epernicus system - finds 114 people over all networks, narrows down to just people in his network (35 people). You can then quickly screen these folks for how they are connected to you, can briefly scan their profiles to learn more about them (CV type thing, scientific genealogy, and listed assets) - Shirley Wu
The genealogies and networks are populated automatically based on a few connections each person lists. Natural networks include labs (people with the same adviser), departments, schools, other groups in which you claim membership - Shirley Wu
BenchQ: a tool to broadcast requests to a large number of people. It is not email so you only check when interested - Pedro Beltrao
What if you don't find exactly what you're looking for, or get too many people from your search (and don't want to bug all of them)? Use BenchQ - send a question to network(s). People in that network can view those questions whenever they want and can reply if they want. - Shirley Wu
While most networking sites you try to amass as many contacts as possible, with Epernicus you already have large natural networks and the idea is the leverage your networks better. - Shirley Wu
Overview of OpenWetWare (OWW): also an online community, but offers lots of tools. E.g. group websites/wikis, online lab notebooks (also wiki-based) - Shirley Wu
Demo - creating an individual's lab notebook. Just type in the type of notebook and the name of it. Generates a wiki template that you can modify. - Shirley Wu
Shows examples of existing notebooks from iGEM project (international genetically engineered machines competition). Dozens for 2008. Shows page from Peking University. Can view by date. Individual team members and groups within the team also have pages. - Shirley Wu
Kerfuffle about the fact that anyone can edit anyone else's wiki/notebook (disincentive to use?) - Cameron says, should the question be about whether anyone can, or whether anyone does? Audience members still very incensed about that. Will take discussion offline - Shirley Wu
Anyone can edit the wiki pages. This started an discussion here on other people editing personal lab notebooks - Pedro Beltrao
Another big aspect of OWW is the protocol repository. Protocols can be commented on, annotated, etc. "Talk" page is connected to each protocol where you can discuss the protocol without editing the protocol. - Shirley Wu
Now talking about integrating the different tools so there is a central place a person can go to find what they need, whether it be paper management, tools and protocols, or network and communication. Vivek just quotes, 95% of Epernicus(?) members have never heard of FriendFeed even though it is useful. - Shirley Wu
John De la Cruz asks: what about data portability? Newton Chan mentions some upcoming events/meetings focused on this topic. Pedro says the "social graph" at the very least should be integrated. - Shirley Wu
Jeremy England asks: are there any problems with adoption of the wiki format for lab webpages/notebooks for most scientists? Cameron says that it's true, it's hard to sell markup languages to lay scientists, but the OWW wikis are actually a really really easy way to set up a group website. Ricardo says they try to minimize the amount of "screw up" possible but the wiki lets people still have control over things if they want to. Jeremy just iterates that some people's eyes glaze over if they see code at all - Shirley Wu
Chris Patil comments: the adoption issue with the older generation of scientists is "nearly calamitous". He implores us to essentially evangelize, market expressly to traditional scientists, have testimonials, success stories, etc; win over that population in order for these approaches to take off. He's interested in hearing more about how you might transition from nothing to everything. - Shirley Wu
Chris comment: We need success stories of older generation starting to use these tools and found them useful. - Pedro Beltrao
Jamie McQuay
opening up the data to invite cross-disciplines to bring different perspectives to the problem.
Cameron Neylon
plans for the next session?
If I'm theonly one recording which is the session most worth recording? I was thinking the open science one is probably best? - Cameron Neylon
Sounds good, I will probably be at the online communities one so I can liveblog there - Shirley Wu
cool - would like to track that one - Cameron Neylon
i'll be recording in room 2 on the scibarcamp twitter account - Jamie McQuay
is someone close enough to ask Attila to give us moderator access to the room? Then I think we can subscribe the room the Jamies' twitter stream - Cameron Neylon
@Cameron, will you live webcast your own talk? I'm interested in attending Eva's failure session - Shirley Wu
will aim to do my own somehow - I'm not sure exactly how - Cameron Neylon
Jamie McQuay
i'm tweeting on the scibarcamp account on twitter for the Toronto bunch
can we re-aggregate? Subscribe the room to your twitter account? - Cameron Neylon
i'll try to get that done now... i'll ask attila - Jamie McQuay
Shirley Wu
Aubrey de Grey keynote
Options for his talk (we get to vote on which 2 or so he gives): How to be a successful heretic, SENS overview, how to obviate mtDNA mutations, how to eliminate intracellular junk, how to really really prevent cancer, and longevity escape velocity - Shirley Wu
Aubrey starts at 9:36AM with beer in hand :) - Shirley Wu
we get to pick what he will be talking about - Pedro Beltrao
The two picks: How to be a successful heretic and how to really really prevent cancer - Pedro Beltrao
First talk - Not the TED commandments (or How to be a successful heretic) - Shirley Wu
Derides the TED commandments as being so over the top that you can't tell if they're joking or not. Prefers some wisdom from successful heretics instead (Gandhi, Haldane, etc). But there are lots more unsuccessful heretics. How to be successful? - Shirley Wu
why are there so many unsuccessful heretics? - Cameron Neylon
1st rule to be a successful heretic: "Be Right" :) - Pedro Beltrao
get the details right, they are important - Cameron Neylon
There is a lot of crap in theoretical biology ... to be a good heretic you need to know about the current state of the art - Pedro Beltrao
Quote from Sean Carroll, Edge 2008: "Heresy is more romantic than orthodoxy.... but casual heretics can't be bothered [with the details?]... Galileo knew the reigning orthodoxy of his time better than anyone so he was better able to see beyond it" - Shirley Wu
Rule 3 - Be a doer (as well as a talker) ... (I missed the 2nd rule) - Pedro Beltrao
Rule #3 = be a doer (as well as a talker). (what was rule #2? - Doh, missed it too..) - Shirley Wu
Rule #2 Be boastful (about your subject) - Cameron Neylon
talking about the methuselah mouse prize - another example of prize money as a way of motivating scientists when you can't acutally fund the research - Cameron Neylon
Rule 4: be indomitable (?) - Pedro Beltrao
(if not invincible ;) - now showing examples of criticism against his science. - Shirley Wu
Rule 5: be diplomatic (maybe not all the time) - Pedro Beltrao
Rule 6: Be everywhere - Pedro Beltrao
(a pint is worth 1000 words) - a conversation over alcohol can make all the difference - Shirley Wu
to respond to critics he says running around conferences is important - Pedro Beltrao
Rule 7: have a sense of humor (?) showing a clip of him with Colbert in Colbert report - Pedro Beltrao
rule 8: be inspirational - Pedro Beltrao
The Colbert Report clip was an example of Rule 7: be pithy (under pressure) - Shirley Wu
Rule 9: Be selfless (control is only a means to an end). Basically get out of the way when the idea grows - Pedro Beltrao
It seems Aubrey gives about 40 talks a year. That's a lot of talk/travel - Ricardo Vidal
Rule 10: reiterates rule 1 - Be right - with an emphasis on effective communication to both experts and laymen - Shirley Wu
comments on the importance of proper organisational structure and good management. Richard Branson when asked about his successs said 'detailed management accounts' - Cameron Neylon
Second half of keynote: How to really really cure cancer. Claims that cancer is the hardest part of aging to solve. We can probably solve other aspects of aging pretty soon, add decades to human life. But if we don't cure cancer, we'll just die later, and die horribly. - Shirley Wu
Why is cancer the hardest part to solve? Cancer is the only part of aging that has natural selection on its side. "The smarter we get, the smarter it gets." 6Gb of DNA is a lot to play with. Treatment selects for mutants that resist treatment. Is there a cleaner solution than drug/treatment "cocktails"? - Shirley Wu
cancer is the only aging related problem that has evolution on its side.Each cancer cell is an evolutionary (?)furnace - Pedro Beltrao
is there are 'clean' approach to cancer treatment or are we stuck with 'cocktails' such as HIV treatment - Cameron Neylon
proposal he is going to make is not what he wants to happen - therapy of last resort. What is being worked on at the moment might work and that would be better - Cameron Neylon
He is thinking of a last resort solution to cancer , not what he wants to happen - Pedro Beltrao
selection can only do so much - the problem with cancer is that it works by doing some rather easy and common - changing gene expression levels. But what about gene existence changes? - Cameron Neylon
Proposed therapy: WILT - Whole-body Interdiction of Lengthening of Telomeres - Shirley Wu
Proposal is to re-engineer a person every decade of so with stem cells that are delted for telomerase and ALT genes - ok he said it was radical - Cameron Neylon
Here are a couple photos: - Ricardo Vidal
current treatments only try to restrain metastasis - by removing telomerase cancers don't make it through crisis stage - Cameron Neylon
4 paths: Without any cancer treatment, cancer activates telomere elongation, malignant metastasis, death. With current and foreseeable treatment, you just cycle back to the start of malignancy but usually can't regress for sure. With just telomerase deletion you get indefinite regression but eventually your renewable tissues stop renewing (aging). WILT is the 4th option, combining telomerase deletion with indefinite replenishment of renewable tissues - Shirley Wu
Question: there might be other functions of telomerase that are important. - Pedro Beltrao
Question: is "heresy" the right term to describe controversy between scientists and the rest of the scientific community? (examples of Galileo and Gandhi were battling against external pressures, differences in morality). Anyone catch the answer? - Shirley Wu
Other ways to read this feed:Feed readerFacebook