On a boat – and starting new things.

Well, it’s a ferry.  Does that count?

My new commute plan takes me from Oakland to South San Francisco by boat, across the bay on the ferry, with a short bike ride on either side.  Given that this is still day 2 of taking the ferry, I’ve still got that warm glow of disbelief that I get to watch the sunrise and sunset from a boat.  Too cool.

Anyhow the important thing is why I’m doing this, which should obviously be because I have a new job.  After three and a half years with Fabric Genomics, it was time to move on.  I left all of my work there in good hands, and the projects I wanted to finish were all wrapped up… and now I’ve got an opportunity to do some real bioinformatics, and not just engineering.  That’s a huge draw for me, really.  I miss doing algorithm design and working with the data, which is pretty much the part of bioinformatics that drew me to the field in the first place.  It’s nice to know that I can do kick-ass engineering, but it’s hard to see myself doing it much longer.

Anyhow, I’m very excited about my new job at Tenaya Therapeutics, and super thrilled to be working with a really awesome group of people.  Unlike many pharmaceutical companies, they’re thinking about their data right from the start.  That may seem obvious, but it honestly wasn’t – I’ve spoken to a lot of companies that had grown to 300+ people, with tons of research programs, and were just now thinking that they should hire someone who understands large scale data.  At that point, it’s way way way too late.  No matter how fast you’ll run, one bioinformatician will never be able to keep up with 60+ scientists generating data.

At any rate, I’d love to say more about what I’m doing, but that’s a conversation I’ll have to start up.  As I’ve learned over the years, surprises aren’t good.for anyone, unless it’s a birthday.

Stay tuned for more.

I’ve landed.

So, I think it’s time to return to blogging.  I’ve started in a new group and have begun feeling my way around in a new area – so, for those who followed me for Next Gen Sequencing in the past, you may be surprised that it’s likely to play a diminished role in my new position.  I don’t think I’m done in NGS, but it looks like I’ll have a little break from it, until it my new group completes a few upgrades, at least.

Are you curious?  I’m working at the CMMT in Vancouver, in the Kobor Lab.  I can’t say enough how awesome this group is, and how welcoming they’ve been (and I don’t even think they read my blog…).  I’ll also likely be collaborating with a few other groups here – but the extent of that is yet to be determined.

So what will feature prominently in my blog?  Well, that’s a good question.

It seems like Chip-Seq will come back.  I don’t think I’ll be returning to FindPeaks – I’ve got better ideas and more interesting plans that I hope to move forward on. It seems likely that I have more to contribute in this particular area, so I expect I’ll be starting a new code base that deals a bit more with the statistics of Chip-Seq.  The findpeaks code base has become a bit too big for rapid prototyping, so it’s time to step out of it to move forward.

I’m sure that epigenetics will take a front row seat in my work. That’s a major focus in this group, both for histones and DNA methylation, so I can’t see it not playing a significant part.  (I’m looking forward to working with methylation, which I’ve never done before…)

I’ll probably be working with Python – I’ve been thinking that it’s time to move away from Java.  Not that there’s anything wrong with Java, but I’ve heard really good things about Python, and I’m excited to start a language that seems to fit a little more naturally with the way I’d like to approach the problem.

I’m hoping to work with Open Source..  well, that hasn’t been discussed much yet, but I still believe strongly in the open source philosophy – particularly in the academic world.  I’d rather not work on closed source code in this environment.

I’ll also likely be working with a bit of Yeast genomics – it’s a great model system, and there’s still a lot to learn about regulation and epigenetics in that particular organism.  And there’s always the tie in to beer.  That doesn’t hurt either.

At any rate, things are still evolving, and I have a 500Mb stack of papers to read (yes, I’m saving paper), but I think that I’m back.  I may do a few reviews of the subjects I’ll have to read up on, which include the epigenetics of healthy ageing and childhood development.  Oddly enough, I think we can learn things at both ends of the human age spectrum, so why not?

And yes, I’ll try to keep the disparaging comments about Denmark to a minimum from now on, but I can’t promise there won’t be any.  Not, at least, till the lawyers finish working out who’s owed what.

Blogging about your own work.

Ok, so my titles aren’t nearly as inspired as Cath’s are.  This week hasn’t exactly been encouraging for puns, unless you consider massacring Danish pronunciation as a very complex linguistic joke.

Actually, I only have a glimmer of an idea tonight – but I’m writing because I need something to do to keep me up for an hour or so.  Sorry for the bad pun, but the clock *is* ticking and it’s only three weeks till I’m supposed to be in Denmark – and I still don’t have movers.  It’s driving me completely around the bend.  So, as a therapeutic device, I’m going to write my glimmer of an idea.  Please don’t be too harsh on it.

The idea for the post came from reading Jacquelyn Gill’s blog post, “Why did I start blogging?”  (By the way, please go vote for her to win CollegeScholarships.org Blogging Scholarship. She clearly deserves it!) Her post isn’t quite related, but at the same time, it is – you can go read it to see why, if you’re interested.

One of the things I struggled with for the past two years has been blogging about my own work. Of course, I interpret this as blogging about what you’re currently working on, not the stuff you finished months ago, which is always fair game.  (Blogging your own publications always struck me as blatantly endorsing yourself – something only politicians should need to do.)

Anyhow, blogging your own current work, showing the bumps and warts of science is something I love to do, and as a scientist, something I want to do as often as I can.  However, there are several problems with it.  It tends to tip your hand to the whole world about what you’re working on and that can have some disastrous consequences.

First, if you’re in a medical field, it can be difficult to talk about cases you’re working on, if there’s any form of patient confidentiality.  Many of the projects I’ve been involved in have required me to maintain complete silence about the nature of the project.  Blog + confidentiality = Instant ethics issues, methinks.

Second, if you’re working on a manuscript, presumably you’re going to have to keep everything you do quiet.  Heck, I’ve got a paper in the works for which the journal sent instructions that require absolute silence on whether it’s even been accepted or not, let alone contemplate communicating anything about the topic.  If I say any more about this, I’ll either jeopardize the publication or wind up in jail.  (Have I already said too much?)

Third, if you aren’t working on a manuscript, you’re either not an academic, or you’re working on an open science project.  I was fortunate enough that I my own project was open, allowing me to talk about my Chip-Seq work for the first three years of my PhD – but alas, that work never cumulated into a second paper.   That’s another rant for another day.

That leaves scientists in the awkward position that they either:

  1. blog about someone else’s work – as if they were journalists, describing their own fields,
  2. blog about their own work in vague terms so that their competition doesn’t scoop them,
  3. blog about work they’ve already published.
  4. blog about the unimportant stuff – or the stuff that they don’t plan to publish.

I can think of one exception: Rosie Redfield, who does a good job of writing about what she’s working on, although her recent work has all been about rehashing and verifying (or more accurately not being able to verify) someone else’s results.  (Yes, I’m referring to the arsenic bacteria fiasco.) I have to admit, I don’t follow any other bloggers who discuss their own data in public, but I’m sure there must be some out there…

Still, if this is a problem for academic bloggers, industrial bloggers face an even harder battle to discuss their own data.  I can think of Derek Lowe over at In The Pipeline as a great example of a blogger from industry.  I used to read his blog daily, and back when I was an avid reader, I seem to recall my favorite posts of his were from the lab – but were all about the strange mishaps and challenges faced by chemists, drawn mostly from the past.  Absolutely none of his current work was discussed, unless it ended in spectacular failure. (Those were good stories too…)

So, I often find myself wondering, when I hear people say that scientists should blog more about their own work, who exactly do they expect to follow that advice? (Btw, It’s something that pops up in conversation frequently, although I couldn’t think of a blog entry that makes that case specifically, off hand. If you need a citation, you’ll just have to settle for “personal correspondence.” Sorry.)

Are there a group of scientists who are willing to blog their own work at the expense of getting publications or being fired from their jobs?  Somehow, I have yet to meet this clique – although if I did, I’d have a lot of questions.  And I can’t imagine they’d be in a position to do this for very long.  You don’t get grants renewed without publications – and you wouldn’t have a workplace for very long either, if you kept blogging the secret sauce recipe.

Maybe, however, this is why some scientists chose to leave the lab bench to pick up the mantle of journalism.  Cue Ed Yong, for instance.  So, the solution isn’t that we need more scientists blogging about their own work, but that we need more scientists to leave science to blog about other people’s work…. or perhaps we should just ask them to stay in science and blog about other people’s work already.

Ahem.  Status quo wins again!

Updates – Oct 2011.

So, my thesis with the requested changes has gone back to my supervisor.  The process we have going is pretty…  unstructured.  At this point, I’m not sure what happens next.  In theory, it should now go to my committee, but who knows when that will happen. My external examiner isn’t scheduled to get it until mid december, which means my thesis defense can’t be scheduled until February at the earliest. Thus, I more or less have  4 months of thumb twiddling penciled in, unless my committee decides they want me to do another experiment. (And I’d probably have some choice words about that plan.)

So, with that said, I have a couple projects to “wrap up”, if you consider it wrapping up to be a) starting a project that won’t appear in my thesis, and b) doing some maintenance work on an open source project that my committee disregards because its not biology.  At worst, that’s about a week’s worth of programming (probably 10-15 hours, really), and getting things organized for someone in the lab.  (Hopefully a few emails I can take care of this afternoon.)

So, that has left me pretty focused on the post-thesis phase.  While I do have plans, I’m just waiting for an airplane ticket to be booked before I announce things. Until there’s an actual date, I’m not sure I feel comfortable spreading the news just yet, just in case everything suddenly crashes down and things don’t work out the way I expect them to.  All I can say, for the moment, is that I’m incredibly excited by the job description and the opportunity to work with the people I have already met, and of course, to meet everyone else there.

(I should mention that I was horribly jet lagged when I met them all the first time, but they all left a great impression, even if I’ve forgotten a few names…)

So, on to blogging, which is the next big thing that I’m mulling over.  First, I haven’t discussed blogging with my prospective employer, so I’m quite sure where things will go.  Of course, I don’t think it’s appropriate to blog about one’s workplace in any great detail, but some corporate bloggers have done a great job of it by discussing issues important to the work place.  In any case, I can see myself doing a few things:

  1. Continuing along the same path, and blogging about next gen sequencing – with a slightly more corporate bent. (which is a hint about what I’ll be doing next.)  There will be plenty of NGS related topics that I’ll be watching, and I’m certain to have an opinion on many of them.  (Who’da guessed?)
  2. Continuing along the same path, but diversifying to other topics in science so as not to focus on science tangential to my work.
  3. Adding on new topics about moving to new lands (is that a hint?).
  4. Adding on new topics about things more personal to me. (photography, music, etc.)

yes, my version of foreshadowing is a bit heavy handed.

And, last but not least, the other two things on my mind:

I’m seriously considering releasing drafts of my thesis on the web.  Now that my supervisor has agreed that my biology project is not likely to lead to a publication (and yes, that was the bulk of my work for the past year), it’s unlikely to meet much resistance.  I won’t do it until I get a go-ahead from those affected by the work, but it’s a project I’m working on, as I’d love to get more feedback.

And, finally, I had plans to write out summaries of some of the papers I’ve read on my way to wrapping up my thesis.  I haven’t decided if I’ll do this yet, but it would probably be a great way to help study for my defense.

In any case, that’s what’s on my mind this afternoon. And now that I’ve gotten it all down, I can clear my mind and get back to some of the other things I’ve been neglecting this past week.  Whee… errands!

Recap for August 2011

So I’m back.  Finally.

About 4 weeks ago, I cut off all of my “time wasting” interests for the sake of completing my thesis and then went all out in writing the damned thing.  As it happens, it was a great way to work.  No twitter, no blogging… no distractions.  I simply sat and wrote for 6-8 hours a day for 3 weeks and two days and banged out a version of my thesis to hand to my supervisor.  Given that I’d already written about 80 pages before pulling the internet plug, that was roughly the equivalent of 100 pages in ~15 days. I’m not unhappy with that.

But, of course, life doesn’t stop while you’re working on your thesis.  I’ve had to do a number of other small projects in the meantime, and a few big projects as well.  The biggest is that I have figured out where I’ll be going after I defend my thesis.  The open question is when that will be, as I still don’t have a defense date, but I am going to push for it to happen as quickly as possible.  For now, I’m going to keep the specifics quiet, but I’ll let everyone know in a few days.

Otherwise, I do know that my wife and I will be moving out of Vancouver, so we’ve begun the process of winnowing down our possessions.  I’ve given away a few potted plants, sold a lot of stuff on craigslist, emptied out drawers, recycled a ton of paper and even had a (very poorly attended) garage sale.  The fun never ends!

More noticeably to the internet, I’ve also switched internet service providers.  Despite the fact that we’re moving, our previous provider was unwilling to extend our current contract, and instead wanted $50 a month more for the same level of service, which just annoyed me – so I made the call to their competition.  Unfortunately, I didn’t realize that the new ISP actively blocks port 80, which took down my website. By pure fluke, I already had a hosting plan that I had been planning on canceling and they had recently started offering wordpress blogs – So, what you’re now seeing is no longer hosted from the computer in my living room. A big thank you to the staff at namespro.ca who helped make the transition reasonably seamless – other than having to wait over the long weekend for the right staff to come back to work to migrate my account. (=

Of course, the other internet change is that my email is no longer hosted from my home computer anymore – but that’s another long story. (However, the experience of running your own email server is pretty awesome – I highly recommend it if you have the opportunity.)  More to the point: If you tried to reach me over the past week and didn’t get a reply, that was the reason.  Sorry!

I also discovered that 4 weeks of isolation is great for reminding you of all of the blog topics that you should write about.  I have a couple more days of web site migrations to do (such as re-uploading the missing pictures from the blog, moving a few other hosted pages to the web server, etc), but once those are completed, I’ll be back on the blogging band wagon – and I have lots of ideas to write about.

In any case, thanks to everyone for their patience during my disappearance – and thank you for everyone who supported me while I was hunkered down and busy writing.

>Last Post

>I’m not sure where “here” really is… but here we are, at the last post of my fejes.ca 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 fejes.ca, I’ll just invite you to come join me over at my new blog: http://blogs.nature.com/fejes.

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

>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!