Living on the edge of academia

http://www.drmaciver.com/2008/12/living-on-the-edge-of-academia/

by hhm • 18 years ago

45 34 18 years ago

cowmoo3• 18 years ago

If you graduated college, consult with your college librarian. The chance is, most journals have online subscription deals and they are accessible via VPN/proxy through your school's subscriptions. If this doesn't apply, go to a local University's library or research hospital in your area, most of these subscriptions are validated through universities' ip addresses - so any computer on campus will do. Trust me, I do this all this time even though I graduated already.

ojbyrne2• 18 years ago

Great minds think alike.

lliiffee3• 18 years ago

There are also certain public libraries (I believe the NY public library is one) that have access to these databases, and allow residents from anywhere in the country of world to get a library card. (You may have to get the library card in person, however.)

ojbyrne2• 18 years ago

The solution to the "Academic Firewall of Doom" is to get a degree, and then you can generally go back to your alma mater and get some kind of library account that will let you access the stuff behind the firewall (generally from within the library only, of course). Of course its been over a decade since that loophole worked for me, might have been closed up by now. Or it might have expanded.

DaniFong• 18 years ago

I recall some kind of problem when I attempted to do this at Dalhousie, but I can't remember what it was. Maybe I'll try again soon.

scott_s• 18 years ago

The ACM's copyright form states that author's are legally allowed to put a copy of the paper on their personal website. Really, you don't need to pay any subscription. If you know the author's names for a paper, chances are one of them will have it on their personal page.

Most of this is findable in Google within 30 seconds. Often when I search for a paper's title, I get a pdf from the author's site before an official ACM or IEEE listing.

newt0311• 18 years ago

CiteseerX is also a good source of papers though not as good as an ACM subscription.

timr3• 18 years ago

This article fairly accurately sums up the process of doing research: you read about some idea, work like crazy for a few days/weeks/months to try a variant of it on your problem, discover it fails, and repeat the process. For the rare thing that actually does work, you rush to publish it, then quickly move back to the grind. There's no time to polish software for distribution, when the reward is entirely based on the number of documents you produce in a year.

This is why it amuses me when people stereotype academic scientists as impractical dreamers -- anyone who has stuck with the process of completing a PhD has demonstrated him or herself to possess a truly super-human tolerance for drudgery.

(Public service announcement: Hire a PhD! They need the work!)

cowmoo3• 18 years ago

Coming from someone who's considering going back to school (grad school) for Bioinformatics/Comp Bio, I have always thought that Bioinformatics wasn't like "traditional" academia because so much of it is "Run n' Gun" programming/statistical analysis of the latest data-set or with a new mining algorithm. Or at least, this is what I envision to be (if you will, the dawn of a major field, like the 1960-1970's of Computer Science research).

Would you care to shed more light onto doing Comp. Bio research as a graduate student for someone who's seriously considering taking on 6-8 years of indentured servitude into the field?

timr3• 18 years ago

Most scientific and engineering research follows the same pattern: you spend a lot of time setting up an elaborate thingamajig to test a hypothesis, then you run the experiment, and spend months analyzing the data. Then you discover that you've failed. Lather, Rinse, Repeat. Data-mining research just uses computer software as the thingamajig, so maybe you do a few more failure cycles per unit time than the guys down the hall (who are building a nuclear accelerator to find the anti-bozon -- but hey, at least they get to play with lasers!)

As far as practical advice for someone contemplating a PhD in bioinformatics, mine would be: don't get a PhD in bioinformatics. There are no jobs, and a PhD is generally just a fantastic waste of time (unless you want to be a professor, and are comfortable with the numerous, well-documented drawbacks of that lifestyle). If you feel that you must explore the field, go far enough to get an MS, then quit.

I realize that's harsh, so I'll add some slightly softer, less-valuable advice: if you must get a PhD in bioinformatics, at least have the good sense to do it in a computer science department, so that you can go back into software when you find there are no jobs in bioinformatics. It's a dangerous mistake to get a PhD in bioinformatics from a biology department (ahem...do as I say, not as I do.)

Failing all of that advice, if you really, really want to be in bioinformatics, despite all good advice to the contrary, then make sure that you spend equal amounts of time at the bench and at the computer. If you want to be respected in the field, you have to have experimental results to back up your computer models, and the best way to do that is to run the experiments yourself. Run away from any program or professor who won't let you work at the bench.

JunkDNA• 18 years ago

I'll second what timr says, I think a PHD in Bioinformatics is possibly a waste of your time. I got into the field in 2000 immediately after undergrad. Since then, I've been working in industry and did my masters in bioinformatics at a top notch school. I've always had a pretty good feel for where new technology is going, how things are going to advance, etc... but I called bioinformatics completely wrong. I really thought it was going to be much more important than it has actually been. Over the last year or so I started looking for a new job in the field and they are REALLY hard to come by (especially industry jobs in the US). In the end, I managed to get a good position (much more medical informatics that bioinformatics actually). I am very aware that I got super lucky. In fact, I was VERY close to pulling the plug on the whole field and trying my hand at a startup (mostly because I hang out here too much :)).

A few years ago, you could count on finding a job at one of the major Pharmas or in a software shop that serves one of them. But many of the pharmas are cash strapped and have been cutting "luxuries" like bioinformatics and software. My experience is that many biotechs are so small and narrowly focused, they often don't benefit from too much bioinformatics work. That leaves academia, but even there, the supply of PHD scientists is way higher than the number of jobs (this is actually a more general problem than in just bioinformatics).

I've often regretted that I didn't just go for a straight CS masters so that I could beef up some of those CS concepts you always avoid when your programming for fun.

I think you need to decide what your ultimate career goal is. If you want to be a PHD scientist getting grants and doing work at a university, then you have to go the PHD route. But if you think you want to work in industry, I would strongly urge a different route, one that doesn't paint you into a corner too much.

Herring• 18 years ago

Something I've always wondered about- is there no value in failed results? I'd think people would benefit from knowing what approaches have failed. How is that information communicated?

lliiffee3• 18 years ago

It basically isn't, which I suspect is a huge collective waste of effort. I have several times had what I thought was a reasonably obvious idea that was "sure to work" which I was baffled that I couldn't find in the literature. Then, after spending a lot of time pursing it, I find it didn't work (for non-obvious reasons). I suspect I am one in a line of many people that have gone through that process.

d0mine• 18 years ago

It is called publication bias. http://en.wikipedia.org/wiki/Publication_bias

tokenadult• 18 years ago

"Something I've always wondered about- is there no value in failed results?"

Peter Norvig has some great comments on the problem of NOT communicating failed results in his article on interpreting research.

http://norvig.com/experiment-design.html

oldgregg• 18 years ago

oh, that's so cute! it's almost like he's pretending that academia isn't a soul-less abyss controlled by self-aggrandizing profiteers.

gnomic_conic• 18 years ago

Ugh, seriously. Academia isn't the place for people with 'Big Ideas' anymore (or was it ever?)

You find most of the innovation and creativity out in the startups and small businesses.

wheels• 18 years ago

I end up needing a lot of research papers for the work that I'm doing. My solution is kind of lo-fi crowd sourcing. I'm usually in a few channels on Freenode and when I hit a paper that I'd like to have and can't hit with a few well-crafted Google searches I just ask if anyone around has access to them. Usually gets me the copy I need within 10 minutes or so.

Now, what's really annoying is market research. Friggin' Forester and their hundreds of dollars per paper. Hrmf.

11ren2• 18 years ago

Some university libraries have a public terminal or two (mine does), which has access to all the electronic journals they are subscribed to (ACM, IEEE, JSTOR, Springerlink etc).

They don't advertise this; you have to ask.

albertcardona• 18 years ago

It's a current tragedy in computer science research: authors release a matlab blob (no source code) or no implementation at all. When asked, I've encountered these answers:

1) An implementation is not important. We developed an algorithm!

2) Uh... the student who made the program already left and we can't find it.

3) [the student] I can no longer find my notes on which parameters I used to make the figures of the paper.

Very rarely, nearly never, does one encounter a proper software release.

Why? Many reasons--the key point is that only a handful of research institutions have technical staff on board to collect and curate software produced in house.

marcus• 18 years ago

The process the author describes is almost identical to the one I've experienced, despite the fact my area of research is different than his (machine learning), but his analysis of the results drastically differs from mine

Its true, 90% of the stuff doesn't work/isn't applicable and I have spent more money on buying papers than on rent in the past year, and I spend many days working on stuff that often has little or no positive effect. But its still the most cost effective research you can do, after you factor in the value of your time.

Every new idea I develop on my own takes far longer to develop and test, and trying to get better results than everyone else is a lot easier when you're basing your progress on the cutting edge instead of something that is a decade old.

puzzle-out• 18 years ago

For journal access, consider some part-time lecturing / mentoring at your nearest university. I mentor a group of business students once a week, and aside from the extra money and overall enjoyment, get a university email and athens account - as I'm undertaking market research for a new startup, this is saving me A LOT of money.

parenthesis• 18 years ago

I pay a fee to have access to my local university library. (As a graduate of said university I get half price, but full price (160GBP) is still reasonable.) This gives me book-borrowing rights, and reference access to printed copies of journals, (but not electronic access).

bbgm• 18 years ago

There is a lot of value in failed results, especially in science. What doesn't work is critical, if for nothing else, than for protocol and experiment design. Freeing up negative data is a huge motivation behind Open Notebook Science(1) and a subject of much discussion on the science blogosphere(2)

1. http://en.wikipedia.org/wiki/Open_notebook_science 2. http://network.nature.com/groups/harvardpublishingforum/foru...

Living on the edge of academia

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