Thanks for visiting my blog - I have now moved to a new location at Nature Networks. Url: - Please come visit my blog there.

Monday, March 15, 2010

Last Post

I'm not sure where "here" really is... but here we are, at the last post of my blog. My 391st blog post! That's actually not so bad for 3 and a half years, now that I think of it.

Anyhow, with Google cutting off ftp publishing, it was time for a move to greener pastures, which in this case is Nature Blogs. I intend to continue discussing the same topics and to continue posting stuff relevant to next-gen sequencing.... or 2nd or 3rd generation, which ever one we're now in. I hope people who've been reading my blog come along and continue commenting at the new site.

For the moment, the new site is a bit plain - Nature is still setting things up, and I'm sure it'll take some time for things to become comfortable over there. I'm going to miss my visitor map, my tag cloud and my many anonymous comments - but these are things I can push for at Nature. They've been fairly responsive to my requests, and hopefully Nature blogs will continue to evolve. Despite the plain looks, I'm expecting great things.

Before I start waxing sentimental about leaving, I'll just invite you to come join me over at my new blog:

Finally, a few last words with which I would like to end this blog:

Thanks to everyone who's read my blog, thanks to those who commented on my posts, and most especially, thanks to everyone who supported me and encouraged me to continue posting. All of which have meant a lot to me. (=


Anthony Fejes


Thursday, February 4, 2010

Why do you blog - part II?

In the first part, I answered the generic "why do you blog" questions. The second part, I wanted to address one of the questions Heather Etchevers asked, because it really is the core reason of why we blog:

Who are you blogging for/who are you talking to?

After much soul searching, I have to answer the reason that probably lies behind all blogs: I blog for myself. If I didn't get something out of it, I wouldn't be doing it. Although, that doesn't mean there's nothing altruistic about the time I invest - there are people who find some of the information I post to be useful. However, it makes me happy to when I get a comment that tells me that something I post made them think, answered a question or just helped them get their computer configured. Yes, I (unashamedly) love to help people, and that is what I get out of blogging.

The less subtle question implied is "who do you think your target audience is?" As to that, I have to admit, I'm not sure. There are several distinct groups who might find information I post to be useful:
  1. People who do Chip-Seq may enjoy the posts on FindPeaks
  2. Next Generation Sequencing related posts may have a broader audience of scientists in the field
  3. People who use Linux probably enjoy the Ubuntu related posts
  4. Grad Students might find my school related posts to be insightful (maybe?)
  5. Anyone who enjoys art might find some of my science art to be unique.
And yes, what that should tell you is that I have a wide, diverse audience. I would suggest that many of the groups above are non-overlapping, so at any one time, I'm probably boring 80% of my audience.

That is the core of the "why am I blogging" question: who am I writing for? Between now and the time I move my blog over to NN (Yes, I think that's where I'm headed), I'm going to try to narrow it down a bit. Some decisions are fairly easy, I'm probably going to drop my linux related posts (there are better forums, and I already participate in them.) and the art/photography is already on the wane. The Grad School posts will probably accelerate for a bout a year (hopefully) and then tail off completely. That should provide a little more focus, in the wake of my scholastic adventures, assuming I can continue blogging once I leave academia - I'll cross that bridge when I get to it.

So, why do I blog? Because I enjoy the conversations and the community. As long as people are reading what I have to say, as long as I get the occasional comment, and as long as there is a reason to keep talking, I'll keep blogging.

Ah... Clarity. (=


Why do you blog - part I?

In light of recent events, this is a question I've had to ask my self. Why am I blogging, and is it worth continuing. Actually, it's not hard to answer, but worth returning to, periodically.

Since I've been thinking about it quite a bit recently, it's no surprise that other blogger's posts on the same topic are of interest to me. One of the blogs I read quite often belongs to Heather Etchevers, and she has an interesting take on it. It's also worth noticing the link on the top of her post to a discussion on it, as well as the answers from other bloggers.

Anyhow, I thought I'd take a stab at the questions myself.

1. What is your blog about?

My blog is generally anything related to next-generation sequencing, the open source science development I do and my journey through grad studies. Anything that catches my eye that's related (sometimes tenuously) to one of those is fair game.

2. What will you never write about?

Anyone who hasn't explicitly agreed to be a part of my blog. I am fantastically lucky to have wonderful people in my life, but their participation in my life isn't consent to being included in anything I write.

3. Have you ever considered leaving science?

Yep - After leaving my start-up company, I briefly toyed with the idea of doing other things and just starting fresh in another field. In the end, my love of science won out.

4. What would you do instead?

Oddly enough, I'd probably have done photography. I'm content to let it be a hobby, for now, but Travel photography is really a passion of mine, and I'd love to do more of it. Incidentally, I started the blog about the same time, because I had initially intended to use it to display my pictures. Interesting how things work out...

5. What do you think will science blogging be like in 5 years?

Not all that much more different - just a lot more condensed. Twitter is becoming an alternative to blogging, and I think the two will converge somewhere for most people.

6. What is the most extraordinary thing that happened to you because of blogging

Wow... that's tough. All the really cool people I've met has been an incredible bonus that I never expected. The fact that people read my blog at all never seizes to amaze me. Anytime I'm at a conference and someone recognizes my name, I'm thrilled - and that's more than extrordinary enough for me. (When they actually pronounce it correctly, it blows my mind)

7. Did you write a blog post or comment you later regretted?

Of course... but most of those were done early on in my blogging days, on a blog that's no longer visible (thank goodness!) I've pissed off friends, insulted people, and even annoyed people in my own lab. My first blog taught me a LOT about what not to do on line. I hope I've learned most of those lessons.

8. When did you first learn about science blogging?

Long after I started posting science on my blog, really. People started telling me that I should take a look at other blogs, and the more I read, the more I discovered there was a community out there.

9. What do your colleagues at work say about your blogging?

Not much, really. Occasionally, one of them will comment on something I wrote, or offer me advice on something I've discussed, but for the most part, it doesn't come up much in conversation. Although, there is the "blog effect", where people around you suddenly know things going on in your life/research that you are sure you didn't tell them. It's somewhat creepy, and it has taught me not to tell stories to people who read my blogs - they already know what I have to say on some topics.

10. How the heck do you have time to blog and do research at the same time?

Code, commit, run, wait... wait.... (blog)... wait... RESULTS!


Tuesday, February 2, 2010

The end is near...

Well, here we are, nearly 350 posts into my blog, and I have to say, I think it's coming down to the end. This isn't something I was contemplating until about 15 minutes ago, so it's a bit of a surprise to me. I should start at the beginning, however, and explain what's going on.

About 6 months ago, I received an invitation to join the Nature Networks blogs, which really appeals to me, in that they have a fantastic community going over there. There are a lot of advantages to participating in such neat group of people who all share a common interest in science. So, pending a few changes at NN, I thought I'd move my blog over there at some point, or at the very least, associate my blog with my NN account.

And then, just this morning, I got an email from blogger/google letting me know that they are going to drop support for FTP published blogs. I have until the end of March to step in line and move my blog to their server, because supporting FTP-based blogs publishing is no longer cost-effective for them. Unfortunately, the only reason I had picked blogger in the first place was because they supported FTP publishing, which leaves me somewhat in the lurch.

Regardless of what I do next, this blog will have to go through some major changes in the next month. There are three changes I can see might solve the issue:
  1. change back-ends and migrate away from blogger (eg. try out wordpress)
  2. change servers, and set up a "custom domain" (eg, use blogger's servers)
  3. move my blog to a completely new venue (eg, start fresh with Nature Blogs.)
Each of the above options will take a lot of work. At the very least, I'll have to archive the current blogs and comments, and then likely be forced to turn off commenting unless I pick option #2. However, with that said, I'm thinking it's time to just bite the bullet and move on to a completely new blog, and Nature Blogs does seem like a good place. For the moment, it is the most appealing option to me.

On the bright side, if I do start a new blog, maybe I can come up with a slightly easier to say name. (Yes, Fejes is actually pronounced as "fey-esh".) Unfortunately, on short notice, the best new blog name I can come up with is "Blog-seq". If anyone has better ideas, I'm definitely open to them. (=

Well, here's to the closing of one chapter, and opening a few new doors... I don't know where this will take me, but as always the journey should be fun!


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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Wednesday, December 16, 2009

post on blogging

I received an email from a friend last night, who read my post on committee meetings. First, I'm thrilled that someone is reading my post, but the content of the email (roughly paraphrased, since I haven't asked his permission to quote the email) was something like this:
You're writing about real people and not everything you say will be taken in the best possible light. Since people who will be considering you for future positions will be reading your blog, should you be posting in this tone? Will having a blog hurt your future career?"
His point was far more articulate than that, but that gives you the idea. He was able to pick out a few examples of things I've said that could clearly be taken in a bad light - and I can certainly see why they might be taken that way. So, I thought I should explain a little.

When writing a blog, there are three things that are never far from your mind - anonymity, veracity, context.

The first is anonymity: both my own identity and those of the people who participate in my life. Personally, I've made the choice to blog as an individual - so people who read my blog can figure out who I am. I ensure that I don't discuss my family or friends on the blog, as they have not explicitly consented to participate in this project. However, the identity of the people who interact with me in my daily life, particularly at work or school, where the bulk of the blog-related topics occur, is a fine line. I would hate for people to stop talking with me because they're afraid I'm going to blog something that's inappropriate.

So the point about my committee meeting post is quite valid - my committee members did not agree to be discussed on my blog. And yet, committee meetings are a core activity in all PhD studies, so talking about the lessons I'm learning from it is something important to me - as long as I am careful not to infringe on the privacy of the committee members themselves.

In terms of veracity, a good lesson from this blog has been that idle speculation is a "Bad thing" (tm). Going out on a limb where people can Google what you've speculated about can lead you to a boat load of trouble - and it stays on the web for a long time. Consequently, it's important not to exaggerate or speculate needlessly - and certainly slander is a terrible blog-crime.

In the example of my committee meeting post, I have to be careful not to dwell on my interpretations of comments, but just refer to the facts as I see them. However, the blog *is* about my interpretation of events - to which I'm entitled, and which I'm allowed to discuss so long as it doesn't violate the anonymity of the participants or misrepresent events.

The third point is context. In a conversation, it's easy to clarify a context if someone misinterprets what you've said, however blogs require that each entry be atomic and self-contained. If I miss the context in the post, the reader will walk away without knowing what I had in mind. However, this is difficult to do - and it's what separates the good bloggers from the bad. (And clearly, I'm still learning.)

With those three points in mind, here's an example from the post, describing how your PhD committee interacts with you:
"They may be friendly with you, but they're not there to give you friendly advice and guide you through your PhD. Instead, they are really engaged in an adversarial relationship in which they are the gate keepers that will decide when you can leave this pit of doom, and they are the ones that will open the door at the end when they believe you're ready to depart. Yes, they do have the roadmap to letting you out, but they would much rather you figure it out yourself instead of asking them to help plan it."
When I wrote that, I meant for it to describe the relationship that is mandated by the committee - not my relationship to my own committee members. Personally, I think I get along well with them, for the most part - although if they misinterpret that particular paragraph, that might change!

In reality, I have a cordial relationship with my committee - they do give friendly advice (particularly when discussions occur one on one), and they are all wonderful people. And while I may be guilty of some hyperbole (grad school isn't actually a pit of doom), the actual purpose of the committee is fairly accurately described. If you want advice, you should talk with your committee members - not wait for a committee meeting. And, in fact, I'm going to stand by my point that they want you to figure out the roadmap. Every student and every project is different, and there is no single way to get out. It's your advisor/supervisor's job to help you plan your exit - not your committee.

So, was I overly harsh? Perhaps - but it was all about making the point about committees, not about individual committee members. Having gone over the rest of the article, I can tell I've done a poor job of explaining the difference between committee members and a committee, so I'll make a few revisions to reflect that. That clearly shows I goofed on the point of context.

At any rate, that's why I love feedback so much - thanks to my friend's email, I've had the opportunity to re-evaluate and clarify the three points (anonymity, veracity, context) that underpin responsible blogging. And, of course, to learn from a valuable experience from excellent feedback.

To my anonymous friend who took the time to email me, THANKS!


Monday, August 24, 2009

Science Online 2009 London blogs

I had several cool ideas for blogs this morning; I was going to illustrate the physics of how I think water flow impacts the height of a splash when doing a "human cannonball" into a swimming pool... and I had a great idea of writing up another cartoon style "how a sugar rush affects the human body and the longevity of your life...", but then I got distracted by the Science Online London 09 blogs.

Unfortunately, I'm on the wrong continent for attending it... and frankly, I had other things to do at 2am on a sunday morning. (Yes, I was asleep...), but the beauty of blogging conferences is that people do actually blog them.

While I missed out on the content firsthand, there are plenty of commentaries, reviews and discussions about the conference.

Martin Fenner (Gobbledygook) has so far put together the most comprehensive list of posts on Science Online London 09 that I've found so far.

One of my favorite reviews (at least, one of the most topical for me), is at the mind wobbles, which provides a summary of Mark Henderson, Dave Munger and Daniel MacArthur's "Blogging for Impact" talk. I found the points are really quite useful - as always.

Since it's still just early morning here, I'm WAY in catching up on the blogosphere... I guess I'll have to save my illustrated posts for another day. So many blogs to read, so little time!


Monday, August 17, 2009

301st blog post.

This is my 301st post to my blog - an impressive number considering that I had originally started with the idea of using it to publish my photography - and have since put almost no photography on my blog. Even more impressive, to me, is that I don't seem to have run out of things to talk about yet. Hopefully I still have another 300 posts in me over the next year or so.

Ironically, three things have been popular over the course of the blog: My posts on AGBT 2009, my summary of how Eland works, and finally, the all-time most popular posts ever have been the ones with the 4- and 5-way venn diagrams. I never would have predicted that any of those articles would have so much of an audience, but hey, I'm very pleased that people have found my blog to be useful.

Well, here's to hoping that I can find 3 more useful articles in the next 300. (-;


Sunday, July 26, 2009

PHP script for latest twitter tweet in HTML

One of my (many) projects this weekend was to sign up for twitter and then use it as a means of making micro updates to my web page. Obviously, it shouldn't be hard, but I had a lot of details to work out, and several tickets to have my hosting service upgrade to PHP5, and install the curl library (both of which were necessary for this hack to work).

Since it's all working now, I thought I'd share the source. This can obviously be modified, but for now, here's the script that's doing doing the job. Yes, bits of it were pulled from all over the web, and some of it was cobbled together by me. Obviously, you'll need to put the correct source for the feed, which is marked below as ""


$curl = curl_init();

curl_setopt($curl, CURLOPT_URL, "$
curl_setopt($curl, CURLOPT_RETURNTRANSFER, 1);
curl_setopt($curl, CURLOPT_CONNECTTIMEOUT, 0);

$xmlTwitter = curl_exec($curl);


$xmlObjTwitter = simplexml_load_string( $xmlTwitter );
$item = $xmlObjTwitter -> channel -> item;
$title = substr_replace($item -> title,'',0,8);
$url = $xmlObjTwitter -> channel -> link;
echo "Anthony tweets: {$title}";

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Friday, July 17, 2009


This week has been a tremendous confluence of concepts and ideas around community. Not that I'd expect anyone else to notice, but it really kept building towards a common theme.

The first was just a community of co-workers. Last week, my lab went out to celebrate a lab-mate's successful defense of her thesis (Congrats, Dr. Sleumer!). During the second round of drinks (Undrinkable dirty martinis), several of us had a half hour conversation on the best way to desalinate an over-salty martini. As weird as it sounds, it was an interesting and fun conversation, which I just can't imagine having with too many people. (By the way, I think Obi's suggestion wins: distillation.) This is not a group of people you want to take for granted!

The second community related event was an invitation to move my blog over to a larger community of bloggers. While I've temporarily declined, it raised the question of what kind of community I have while I keep my blog on my own server. In some ways, it leaves me isolated, although it does provide a "distinct" source of information, easily distinguishable from other people's blogs. (One of the reasons for not moving the larger community is the lack of distinguishing marks - I don't want to sink into a "borg" experience with other bloggers and just become assimilated entirely.) Is it worth moving over to reduce the isolation and become part of a bigger community, even if it means losing some of my identity?

The third event was a talk I gave this morning. I spent a lot of time trying to put together a coherent presentation - and ended talking about my experiences without discussing the actual focus of my research. Instead, it was on the topic of "successes and failures in developing an open source community" as applied to the Vancouver Short Read Analysis Package. Yes, I'm happy there is a (small) community around it, but there is definitely room for improvement.

Anyhow, at the risk of babbling on too much, what I really wanted to say is that communities are all around us, and we have to seriously consider our impact on them, and the impact they have on us - not to mention how we integrate into them, both in our work and outside. If you can't maximize your ability to motivate them (or their ability to motivate you), then you're at a serious disadvantage. How we balance all of that is an open question, and one I'm still working hard at answering.

I've attached my presentation from this morning, just in case anyone is interested. (I've decorated it with pictures from the South Pacific, in case all of the plain text is too boring to keep you awake.)

Here it is (it's about 7Mb.)

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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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Tuesday, March 3, 2009

Update to blog url

Just a quick admin note - I'm finally going to make the blog the default page on my domain, so for people who have this page bookmarked, you'll want to drop the "blog.html" part of the URL.

As far as I can tell, people aren't spending a lot of time looking at my photography, so I may as well let the blog tell the main story here.

Just in case you find yourself at the blog.html page, and aren't sure where to go, just follow this link to


Saturday, February 14, 2009

Collection of all of the AGBT 2009 notes

I've had several requests for a link to all of my notes from AGBT 2009, so - after some tweaking and relabeling - I've managed to come up with a single link to all of the AGBT postings. (There are a few very sparse postings from AGBT 2008, but they don't contain much information that's really useful.

Anyhow, if you'd like the link to all of my notes, you can find them here:


Friday, February 13, 2009

Time for a new look

For people who read my blog on my web page, rather than through feeds, you might notice that my page looks different today. I had some feedback from other bloggers at AGBT (in particular, Daniel MacArthur of Genetic Future), who made some suggestions that should have been simple to implement. Unfortunately, my template is so customized, it's nearly impossible to make the changes without breaking the layout.

So, I figured the best thing to do is clean up and start from scratch. If you notice odd changes in the template, that would be why. (=

In the meantime, there's lots of good FindPeaks news - including controls, which are starting to work, new file formats, and a HUGE speed increase. (Whole genome runs in 6 minutes with a control... wow.)

Anyhow, I've got lots to do - and don't mind the blog template tinkering, 6 minutes at a time.


Friday, February 6, 2009

Site Feed changes

I'm never one to shy away from changes, even when I should probably know better. One of the things that came up yesterday while talking to the other (read: much more professional) science bloggers was that I should be monitoring my rss feeds, and they all unanimously suggested feedburner.

Of course, I've never set it up before, so I'm still in the process of trying to figure out how it works - but hang in, I've still got another half hour before the first session starts. That should be more than enough time, right?


Friday, November 28, 2008

It never rains, but it pours...

Today is a stressful day. Not only do I need to to finish my thesis proposal revisions (which are not insignificant, because my committee wants me to focus more on the biology of cancer), but we're also in the middle of real estate negotiations. Somehow, this is more than my brain can handle on the same day... At least we should know by 2pm if our counter-offer was accepted on the sales portion of the transaction, which would officially trigger the countdown on the purchase portion of the transaction. (Of course, if it's not accepted, then more rounds of offers and counter-offers will probably take place this afternoon. WHEE!)

I'm just dreading the idea of doing my comps the same week as trying to arrange moving companies and insurance - and the million other things that need to be done if the real estate deal happens.

If anyone was wondering why my blog posts have dwindled down this past couple of weeks, well, now you know! If the deal does go through, you probably won't hear much from me for the rest of this year. Some of the key dates this month:
  • Dec 1st: hand in completed and reviewed Thesis Proposal
  • Dec 5th: Sales portion of real estate deal completes.
  • Dec 6th: remove subjects on the purchase, and begin the process of arranging the move
  • Dec 7th: Significant Other goes to Hong Kong for~2 weeks!
  • Dec 12th: Comprehensive exam (9am sharp!)
  • Dec 13th: Start packing 2 houses like a madman!
  • Dec 22nd: Hannukah
  • Dec 24th: Christmas
  • Dec 29th: Completion date on the new house
  • Dec 30th: Moving day
  • Dec 31st: New Years!
And now that I've procrastinated by writing this, it's time to get down to work. I seem to have stuff to do today.

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Monday, September 22, 2008

Two milestones reached

Two of my three projects have met significant milestones this weekend, which I thought were worth sharing.

The first one is that FindPeaks had it's first official patch submitted to me from developers outside the Genome Science Centre, on sunday night. Thank you very much to the submitters! I'm very glad to see someone using (and playing with!) the code. While the patch was minor, it tells me that there is definitely use in having released it to the wild.

The second milestone is for my blog, and while it's not officially a "project" in the academic sense of the word, has consumed enough of my time that it starts to feel like one. The milestone? There are now as many people coming here directly as there are finding it through google. It's not a huge number of hits, but it's nice to know there's an audience who's enjoying my random rants. (-:

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Thursday, June 26, 2008

Hello to Oregon State University.

I love google analytics, but I always forget to look at it. It's such a fantastic interface. Unfortunately, I can't see the individual IP addresses of the people who are hitting my blog, but I can see the cities from which I'm getting traffic.

Can you believe nearly 1/2rd of my traffic comes from Corvallis, Oregon? Something like 25 hits a day. (Yes, I average around 50 hits a day on my blog.) So, what's in Corvallis? The only thing I can find is the Oregon State University - which incidentally has a Center for Genome Research and Biocomputing, where they do some Illumina related Sequencing. Coincidence? Maybe.

Anyhow, I just thought I'd say hi to whoever it is in Corvallis that likes my blog. (=


Thursday, February 7, 2008

AGBT post #1.

I'm here.. and online. I almost didn't make it, thanks to bad weather in florida, but at least the car we rented didn't break down on the road, the way the other group's did. Apparently the police saved them from the aligators and wild pigs... No one can say AGBT hasn't been exciting, so far.

Anyhow, lots of good topics, and meeting interesting people already. (I'm even sitting beside an exec from Illumina, in the ABI sponsored lunch.. how's that for irony?) Anyhow, I'm excited to start the poster sessions and get some good discussions going.

Unfortunately, I missed two of the talks this morning, while I negotiated with the good people at United airlines to have my bag delivered. The three others I've seen so far have been good. Some interesting points:

The best graphics are the ones with the two DNA strands shown separately. Too cool - must include that in my FindPeaksToR scripts.

Loss or gain of homozygosity can screw up what you think you have, compared to what's really there. Many models assume you have only one copy of a gene, or just don't really do much to make sense of these events.

From David Cox, I learned that Barcoding isn't new (it's not), but that it usually doesn't work well (I can't prove that), but hey, they got it to work (and that's good!).

And yes, my favorite line from David Cox's presentation was something like: 900 PCR products, 90 people['s samples]... 1 tube. Make sure you don't drop it!

Anyhow, I'm getting lots of ideas, and I'm thoroughly enjoying this conference. I'm saturated in next-gen sequencing work.

Anyhow, if anyone else is reading this, My poster is #38... feel free come come by and talk.

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Thursday, September 20, 2007

Textbook Chapter

Lately I haven't had much to write about, as is clearly shown by the complete lack of content for the past month. I've been too busy to do much photography (I haven't even put up my most recent shots onto my web page)... but I have figured out some of what I'd like my blog to be, and I'm going to put some effort into breaking it up into two sections: photography and Grad School.

Of course, that will have to wait until I come back from my trip - oh, right - I don't think I mentioned I'll be in England, Scotland and Wales for about 10 days. This trip has been in the works for two years, so you can imagine that I've been looking forward to it... just a little bit. (-;

Anyhow, before I go, I have a few things to finish, once of which is a textbook chapter. I agreed to take this project on about a month ago, and since it's on an area in which I'm actively working, I thought it would be a good idea.

The topic of the chapter is a method or protocol called ChIP-Seq (or ChIPSeq, or ChIP-Solexa, or a few other things, actually), which is a combination of chromatin immunoprocipitation and a so-called "next-generation" sequencing technology. (If anyone wants to know more, send me a message, and I'll do a post on it.)

At any rate, when I was first approached about it, I was in the process of rewriting all of the production code that's being used to analyze the results - so I'm now intimately familiar with how that works. And, once that was done, I spent the next week doing a scholarship application, for which I had to do some lit review.. and finally this week, I got to working on the chapter.
I spent a few days reading, a day outlining, and a few hours here and there doing some writing. It's slow work, to be honest, but it's getting there.

The funny part is that I found a great paper yesterday, that would have pointed me to the right place, and has a great introduction. Where did I find it, you ask? On my desk. I've had it for about 2 months - it's the paper on ChIP-Seq written by the guy who sits across the cubicle wall from me.

Anyhow, That's life. Now I just need to sit down and write like mad - I'd like to get a draft out before my vacation starts.

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Saturday, January 20, 2007

One more "little" change..

Alright - one more change. I've just moved to the "new blogger" from the old one (where I've been since 2001-ish). I wish I could say that I have a good reason for it, but it's midnight, I'm addicted to bleeding-edge packages and I've already broken apache on my home computer. Doesn't that scream that this is the perfect time to try an upgrade that I don't need?

If you said no, you have way more common sense than I do. Else, I'm just itching to press the "publish" button, and see what this does to my web page! Lets go!