BioBarCamp

There are some pretty active groups and IMO flickr rocks around events (thanks to tagging) - Deepak

Correct, tagging makes it the best during events. - Bora Zivkovic

I find Flickr somewhat difficult to fathom as a community. Groups and events are good, but building community/traffic around your own work is really difficult. Perhaps because there are so many photos and users - many of whom are talented professionals showcasing their work. It's hard to get noticed in such a crowd, even if you think you're quite good :) - Neil Saunders

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

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

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

Who cares about impact? actually lots of people - public, funders, government, universities, etc - Shirley Wu

live video feed at http://www.mogulus.com/cameron... - Cameron Neylon

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

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

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

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

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

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

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

Kaitlin Thaney: impact/popularity != relevance to a researcher's problem - Shirley Wu

Good length is evening planning + 1 full day - Shirley Wu

Thanks for the coverage guys; great work. - Neil Saunders

Wonderful ... great jobs folks - Deepak

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 http://www.sagemath.org/ - 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

http://news.cnet.com/8301-1384... - Deepak

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

ask him to email me ... deesingh at thatbigretailsite.com - Deepak

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 - http://www.jnrbm.com/ - 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

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

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

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

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

amongst others :) - Deepak

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

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

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

http://www.oneworldhealth.org/ - Jamie McQuay

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

@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

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

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

Curious to see if anyone has worked with iBridge Networks http://www.ibridgenetwork.org - Deepak

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

@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

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

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

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

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

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

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

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

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 peopl