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Sunday, January 24, 2010

Biopartnering North and a short break

First off, if anyone is going to BioPartnering North 2010 this week in Vancouver, I'll be there, and would be very happy to talk genomics/biotech and business with you. I was lucky enough to have been found worthy of one of the coveted BIOTECanada bursaries to attend the event, and I plan to get as much out of it as I can. I'll be at the reception tonight, and undoubtedly I'll be around throughout the next few days. (And, if you were wondering, I won't be blogging any talks from BPN.)

Second, I'm pretty sure everyone has noticed that my blogging output has dropped significantly since December, for which there are several good reasons. The first is that I've been quite busy. My personal life is now occupied by event planning, while my work life has been dominated by several major projects, of which I will undoubtedly be "ranting" about in posts in the near future.

However (and thirdly), the other reason I've not been blogging much is that I also had a conversation with a colleague in december about effective communications. He suggested I read a book on "Non-violent communication." I'm working my way through it slowly, and have taken a few suggestions to heart. It's always possible to become a better communicator and, to that end, I'm on a small hiatus while I re-evaluate my use of language. It won't last long - I like having a blog and I'm already itching to write a few more posts, but it's an opportunity to do some personal development.

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Friday, January 15, 2010

Symposium: Advances in Bioinformatics and Genomics - Feb 19, 2010

I just came across a forum that I hadn't heard of before: The 2nd Advances in Bioinformatics and Genomics Symposium, being held in the San Francisco/Bay area in February. Unfortunately, like AGBT, it's been scheduled to overlap with the Olympics. Now, normally I don't care about things overlapping with Olympic events, but this year travel in and out of Vancouver will be a nightmare, and I'm not willing to go through that twice. (Especially for a single day symposium.)

Regardless, if people are leaving from other destinations, or already happen to be in the bay area, this "open access" conference sounds pretty neat. The full schedule isn't up yet - and I have to admit I don't know either of the keynote speakers (my ignorance of the field, I'm sure), but the summary seems to fit my interests pretty well - and likely those of other people who read my blog.

Here's the link:

There's always next year, I suppose. (=


Thursday, July 30, 2009

Science Online 2009 London.

I just saw the most awesome conference in a tweet from Daniel McArthur: Science Online 2009 London. Unfortunately, a) it's in London, UK, which is a little too far for me to walk and b) they're already filled up with registrants. Fortunately, they will be streaming the whole conference on the web, which I'm highly tempted to buy into. (It costs 10 GBP... that's ~$20 CDN, which is vastly more reasonable than flying to London.)

The program has awesome events, including Blogging for impact (Speakers: Dave Munger, Daniel MacArthur), Author identity – Creating a new kind of reputation online (Speakers: Duncan Hull, Geoffrey Bilder, Michael Habib, Reynold Guida - I have to admit I don't know any of them... but I'll go look them up later), and Legal and Ethical Aspects of Science Blogging (Speakers: Petra Boynton, David Allen Green).

In fact, pretty much every session sounds like it will be worth the 10 pounds... If only I were in london


Wednesday, June 24, 2009

CSHL: Personal Genomes

For all that I've been ranting about how much I dislike Cold Spring Harbor's policies on blogging (or at least the rumours about how they'll be changing them in the future), I have to admit that they do have the coolest topics for conferences.

I just received an advertisement in the mail for their upcoming "Personal Genomes" conference in September. I'd like to reprint their ad's description (I'm citing fair use here, just in case any one wonders why I feel free to reproduce it.) for anyone who's interested:
"This second meeting builds on last year's presentations showing a significant milestone in human genetics - the first production of "personal genomes." Ultra high through put swequencing strategies have now been used to study more individual genomes - and yet few scientists and even fewer clinical geneticists, are familiar with the implications of this new data. This meeting will address the issues of individual genomes being part of research and routine clinical medicine within the new years."
Far too cool. Here's a link to the web page.

They have applied for funding to partially support postdocs and graduate students, so you'd better start working on that abstract if you're intersted: they're due July 1st.

By the way, the conference runs from Sept 14-17, 2009.


Wednesday, June 17, 2009

More on conference blogging...

If you've been following along with the debate on conference blogging, you've surely been reading Daniel McArthur's blog, Genetic Future. His latest post on the subject provides a nifty idea: presenters who are ok with their talks being discussed should have an icon in the conference proceedings beside the anouncement of their talks so that members of the audience know it's safe to discuss their work. He even goes so far as to present a few icons that could be used.

On the whole, I'm not opposed to such a scheme - particularly at conference like Cold Spring, where unpublished information is commonly presented and even encouraged by the organizers. However, Cold Spring is one of the few rare venues where the attendance is "open", but the policy on disclosing the information is restricted. It's entirely regulated for journalists, but in the past has not been an issue for scientists. However, if a conference begins to restrict what the scientists are allowed to disclose outside of the meetings, the organizers are really removing themselves from the free and open scientific debate. A conference that does that isn't technically a conference - at best it's a closed door meeting - and the material should explicitly be labeled as confidential.

Assuming that the vast majority of presentations can't be discussed without explicit permission is quite the anathema of science. If you look at the way technology is handled in western society, you'll see a general trend: The patent system is based around the idea of disclosure, copyright is based on the idea of retaining rights after disclosure, and even our publication/peer review system demands full disclosure as the minimum standard. (Well, that plus a wad of cash for most journals...) For most conferences, then, I suggest we use a more fitting model than opting-in to allow disclosure, as proposed by Daniel. Rather, we should provide the opportunity to opt-out.

All presenters should have the option of choosing "I do not want my presentation disclosed." We can even label their presentation with a nice little dohicky that indicates that the material is not for public discussion.

Audience members who attend the talk then agree that they are not allowed to discuss this information after leaving the room. Why operate in half measures? It's either confidential or it's not. Why should we forbid people from discussing it online, and then turn a blind eye to someone reading their notes in front of the non-attending members of their institution?

Hyperbole aside, what we're all after here is a common middle-ground. Science Bloggers don't want to bite the hands of the conference organizers, and I can't really imagine conference organizers not being interested in fostering a healthy discussion. After all, conferences like AGBT have done well because of the buzz that surrounds their organization.

As I said in my last post on the topic, Science does well when the free and open exchange of ideas is allowed to take place, and people presenting at conferences should be aware of why they're presenting. (I leave figuring out those reasons as exercise to the student.)

Lets not throw the blogger out with the bathwater in our haste to find a solution: Conferences are about disclosure and blogs are about communication: aren't we all working towards the same goal?

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Saturday, June 6, 2009

Once more into the breach...

I haven't been able to follow the whole conversation going on with respect to conference blogging, since I'm still away at a conference for another day. Technically, the conference ended a on thursday, but I'm still here visiting with some of the more important people in my life - so that is my excuse.

At any rate, I received an interesting comment from someone posting as "such.ire", to which I wrote a reply. In the name of keeping the argument going (since it is such a fascinating topic), I thought I'd post my reply to the front page. For context, I suggest reading such.ire's comment first:

click here for his comment.

My reply is below:


Hi Such.ire,

I really appreciate your comment - it's a great counter point to what I said, and really emphasizes the fact that this debate will have plenty of nuances, which will undoubted carry this conversation on long after the blogosphere has finished with it.

To rebut a few of your points, however, I should point out that your examples aren't all correct.

Yes, conferences are well within their rights to ask you to sign NDAs as an attendee - or to require that confidentiality is a part of the conference - there is no debate on that point. However, if you attend a conference that is open and does not have an explicit policy, then it really is an open forum, and they do not have the right to retroactively dictate what you can (or can't) do with the information you gathered at the conference.

I think all of us would agree that the boundaries for a conference should be clearly specified at the time of registration.

As for lab talks for your lab members - those are not "public disclosures" in the eye of the law. All of your lab colleagues are bound by the rules that govern your institution, and I would be surprised if your institution hadn't asked you to sign various confidentiality rules or policies about disclosure at the time you joined them.

Department seminars are somewhat different - if they are advertised outside the department to individuals that are not members of the institution, then again, I would suggest they are fair game.

I don't blog departmental talks or RIP talks for that reason. They are not public disclosures of information.

Finally, my last point was not that journalists and bloggers do anything different up front, but that the method of their publishing should have a major impact on how they are treated. Bloggers can make corrections that reach all of their audience members and can update their stories, while journalists can not.

If a conference demands to see the material a journalist publishes up front, it makes sense. If they demand to do the same thing for a blogger, it completely ignores the context of the media in which the communication occurs.

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Thursday, June 4, 2009

The Rights of Science Blogging

An article recently appeared on scienceweb, in relation to Daniel McArthur's blogging coverage of a conference he attended at Cold Spring Harbor, which has raised a few eyebrows (the related article is here). Cold Spring Harbor has a relatively strict policy for journalists, but it appears that Daniel wasn't constrained by it, since he's not a "journalist", by the narrow definition of the word.  More than half of the advice I've ever received on blogging science conferences comes from Daniel, and I would consider him one of the more experienced and professional of the science bloggers - which makes this whole affair just that much more interesting.  If anyone is taking exception to blogging, Daniel's coverage of an event is guaranteed to be the least offensive, best researched and most professional of the blogs, and hence the least likely to be the one that causes the outcry.

As far as I can tell from the articles, Cold Spring is relatively upset about this whole affair, and is going down the path that many other institutions have chosen: Trying to suppress blogging, instead of embracing it.
Unfortunately, there really very few reasons for this to be an issue - and I thought I'd put forward a few counter-points to those who think science blogging should be restrained.

1.  Public disclosure

Unless the conference organizers have explicitly asked each participant to sign a non-disclosure agreement, the conference contents are considered to be a form of public disclosure.  This is relevant, not because of the potential for people to talk about it is important, but because legally, this is when the clock starts ticking if you intend to profit from your discovery.  In most countries, the first time an invention is disclosed is when you begin to lose rights to an invention - broadly speaking, it often means that you have one year to officially file the patent, or the patent rights to it become void.  Public disclosure can be as simple as emailing your invention in an un-encrypted file, leaving a copy of a document in a public place....  the bar for public disclosure is really quite low.  More crucially, you can lose your rights to patenting things at all if they're disclosed publicly before the patent is filed.

Closer to home, you might have to worry about academic competition.  If you stand up in front of a room and tell everyone what you've just discovered (before you've submitted it), any one can then replicate that experiment and scoop you...  The academic world works on who has published what first - so we already have the built in instinct to keep our work quiet - until we're ready to release it.  (There's another essay in that on open source science, but I'll get to it another day.)  So, when academics stand up in front of an audience, it's always something that's ready to be broadcast to the world.  The fact that it's then being blogged to a larger audience is generally irrelevant at that point.

2.  Content quality

An argument raised by Cold Spring suggests that they are afraid that the material being blogged may not be an accurate reflection of the content of the presentation.  I'm entirely prepared to call B*llsh!t on this point.

Given a journalist with a bachelors degree in general science, possibly a year or two of journalism school and maybe a couple years of experience writing articles and a graduate student with several years of experience tightly focussed on the subject of the conference, who is going to write the more accurate article?

I can't seriously believe that Cold Spring or anyone else would have a quality problem with science blogging - when it's done by scientists with an interest in the field.  More on this in the conclusion.

3. Journalistic control

This one is more iffy to begin with.  Presumably, the conference would like to have tighter control over the journalists who write articles in order to make sure that the content is presented in a manner befitting the institution at which the conference took place.  Frankly, I have a hard time separating this from the last point:  If the quality of the article is good, what right does the institution have to dictate the way it's presented by anyone who attended.  If I sit down over beers with my colleagues and discuss what I saw at the conference, we'd all laugh if a conference organizer tried to censor my conversation.  It's both impossible and violates a right to free speech. (Of course, if you're in russia, or china, that argument might have a completely different meaning, but in North America or Europe, this shouldn't be an issue.)  The fact that I record that conversation and allow free access to it in print or otherwise should not change my right to freely convey my opinions to my colleagues.

Thus, I would argue you can either have a closed conference, or an open conference - you have to pick one or the other, and not hold different attendees to different standards depending on the mode by which they converse with their colleagues.

4. Bloggers are journalists

This is a fine line.  Daniel and I have very different takes on how we interact with the blogosphere.  I tend to publish notes and essays, where Daniel focusses more on news, views and well-researched topic reviews.  (Sorry about the alliteration.)  There is no one format for bloggers, just as there isn't one for journalists. Rather, it's a continuous spectrum of how information is distributed and for journalists to get upset about bloggers in general makes very little sense.  Most bloggers work in the niches where journalists are sparse.  In fact, for most people, the niches are what making blogs interesting.  (I'm certainly not aware of any journalists who work on ChIP-Seq full time, and that is, I suspect the main reason why people read my feeds.)

Despite anything I might have to say on the subject, the final answer will be decided by the courts, who have been working on this particular thorny issue for years.  (Try plugging "are bloggers journalists" into google, and you'll find more nuances to the issue than you might expect.

What it comes down to is that bloggers are generally protected by the same laws that protect journalists, such as the right to keep their sources confidential, and bound by the same limits, such as the ability to be sued for spreading false information.  Responsibility goes hand in hand with accountability.

And, of course, that should be how institutions like Cold Spring Harbor have to address the issue.


Treating science bloggers the way Cold Spring Harbor treats journalists doesn't make sense.  Specialists talking about a field in the public is something that the community has been trying to encourage for years: greater disclosure, more open dialog and sharing of ideas are the fundamental pillars of western science.  To force the bloggers into the category of the journalists in the world of print magazines is utterly ridiculous: bloggers articles can be updated to fix typos, to adjust the content and to ensure clarity.  Journalists work in a world in which a typo becomes part of the permanent record and misunderstandings can remain in the public mind for decades.   The power to reach a large audience exists - but only bloggers have the ability to go back and make corrections.    Working with bloggers is a far better strategy than working against them.

No matter how you slice it, institutions with a vested interest in a single business model always resist change - and so do those who have not yet come to terms with the advances of technology.  Unfortunately, it sounds like Cold Spring Harbor hasn't yet adapted to the internet age and are trying to fig a square peg into a round hole.  

I'd like to go on the record in support of Daniel McArthur - blogging a conference is an important method of creating dialog in the science community.  We can't all attend each conference, but we shouldn't all be left out of the discussion - and blogs are one important way that that can be achieved.

If Cold Spring Harbor has a problem with Daniel's blog, let them come forward and identify the problem.  Sure, they can ask bloggers to announce their blog urls before the conference - allowing the organizers to follow along and be aware of the reporting, I wouldn't argue against that.  It provides accountability for those blogging the conference - which serious bloggers won't object to - and it allows the bloggers to go forth and engage the community.  

To strangle the communication between conference attendees and their colleagues, however, is to throttle the scientific community itself.  Lets all challenge Cold Spring to do the right thing and adapt with the times, rather than to ask scientists to drop a useful tool just because it's inconvenient and doesn't fit in with the way the conference organizers currently interact with their audience.

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Saturday, November 22, 2008

Is medicine ready for 2nd Generation Genomics?

Yesterday was the second day of the 10th Annual B.C. Cancer Conference, which draws in researchers, practitioners and cancer survivors from around BC and the world. It also draws in a lot of drug companies, but that's somewhat besides the point.

One particular part of the conference caught my eye as a must see: the Cancer Genetics Laboratory Open House. This event was a set of posters and hands-on demonstrations for how genetics can be used to help cure cancer. Since that's essentially my thesis project, I figured I absolutely had to attend it.

Unfortunately, I was rather disappointed in the scope of the work they do, though not because they do poor work, but rather that my expectations were too high. For breast cancer, they only screen people who have a family history of breast cancer, and even then they only look for two markers in BRCA1 and BRCA2. That's not a bad thing, though - those two genes make up a significant portion of the hereditary breast cancer risk for women. What surprised me was how reactive the technology was - the lab only screens patients with a high likelihood of carrying the mutant genes, and only patients referred to them by physicians who suspect the familial disease association. Again, this is pretty standard, so there's no criticism meant.

However, what concerns me is whether these people will be ready for the onslaught of information that's about to hit them. Ina couple of years, genetics researchers will be handing off the testing of tens of thousands of simultaneous genes, gene splicing defects, and complete analyses of transcriptomes/genomes, which are currently being done in the lab, as we speak. This is a far cry from doing PCR on two genes to look for SNPs, with a massive technology gap in between.

The Cancer Genetics Lab appears to have 15 doctors and technologists, which is a small staff to support a whole city of several million people, let alone the whole province. I have to wonder if any of them have any experience with 2nd-generation sequencing, seriously high throughput genetic screens, or even the concept of how to do genetic councilling about risk factors in the "whole genome diagnostics" age. Of course, I didn't spend too long at the session, so I don't know if anyone there is an expert, however the few people I spoke to weren't really talking about the upcoming changes to their discipline, so I'm a little skeptical.

In any case, I do have to wonder how this pandoras box of information we're unleashing about the makeup of patient's cell and heredity will effect the downstream medical practitioners, and how well they are prepared to deal with it. Are the seminars to bring these people up to speed on what's coming at them? Are the agencies ready to shell out the money for the infrastructure they'll need? Are the people writing the textbooks that educate these people including chapters on the subject?

It's all nice that I talk about trying to understand how a cancer works in the lab through 2nd-generation sequencing, but I have to wonder what we should be doing in the meantime to prepare them from the firehose of information that we're going to point at them and let loose. The personal genomics revolution is poised to land on these people like a ton of bricks, and with about as much mercy.

Then again, lest we be smug about it, how many of us are writing aligners for SMRT sequencing that's already on the horizon in our own field. Preparing for the future is definitely hard when we're still coping with the present. I'm sure it's no different for the Hospital Genetics Labs, even if they're 15 years behind the cutting edge.

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Monday, April 28, 2008

I've spent the last week madly putting together a poster for the "Reasons for Hope 2008" conference this past weekend, which focuses on breast cancer science, treatment and quality of life research. So, you'll notice (shortly), a new poster in my poster section. It was a educational experience, and I must admit I learned a lot. Not so much in the areas that I need to learn for my own research, but about physiology, psychology and general health research. And that's even considering how few talks I went to!

Still, I highly recommend dropping into talks that aren't in your field, on occasion. I try to make a habit of it, which included a pathology lecture just before xmas, last year, and this time, I learned a lot about mammography, and new techniques for mammography that are up and coming. Neither are really practical skills for a bioinformatician, but it gives me a good idea of where the samples I'll be dealing with come from. Nifty.

Anyhow, I had a few minutes to revisit my ChIP-Seq code, FindPeaks, and do a few things I'd been hoping to do for a while. I got around to reducing the memory requirement - going from about 4Gb of RAM for a 12M+ read run down to under 1Gb. (I'd discussed this before in another posting.) The other thing I did was to re-write the core peak-finding algorithm. It was something I'd known was not-optimal for a while, but re-implementing a core routine isn't something you do without a lot of thought. The good news, it runs about 2x as fast, scales better on multiple cores and guarantees not to produce any of the type of bugs that have been relatively common in early versions of FindPeaks.

Having invested the 2 hours to do it, I'm very glad to see it provide some return. Since my next project is to clean up the Transcripter code (for whole transcriptome shotgun sequencing), this was a nice lesson in coding: if you find a problem, don't patch the problem: solve it. I think I have a lot of "solving" to do. (-;

For those of you who are interested, the next version of FindPeaks will be released once I can include support for the SRF files - hopefully the end of the week.

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