Jeremy Leipzig › Likes

I work at a small biotech company and as Neil said, access to journals is the biggest issue. We are associated with a university so when I'm there I can access journals, however normally from the company building I can't. The delay is frustrating. In terms of commercial tools/databases, currently I would like access to Genelogic gene expression database and Biobase transcription factor database and analysis tools. - Greg Tyrelle

Another small biotech here, and yes, access to journals is a huge pain. - Bill Hooker

I'm currently at a university, but was considering being an independent scholar for year or two (= a homeschooling mom with a research rather than a knitting hobby). Resource problems I anticipated: access to journals, Scopus subscription, Web of Science subscription. - Heather Piwowar

Thank you all - just as I expected: access to journals (and ways to find journals/papers) is the most expensive and most difficult to get thing if one is outside of University. How about space for office (lab?), equipment (poster printer?), software - if you were a researcher at home (freelance scientist) what would you need that costs? - Bora Zivkovic

Depends what kind of research. I'd need a biosafety hood, liquid nitrogen storage, glassware, balances, electrophoresis equipment, culture incubators, autoclave, chemical store... :-) - Bill Hooker

Software is the other bit. Biotech's tend to be a lot more budget constrained than many academic labs. - Deepak Singh

Access to journals and availability of equipment are both big deals, but whereas some equipment can be obtained from ebay or a local lab equipment company, academic literature database subscriptions can't be obtained at a discount rate. (AFAIK) - Mr. Gunn

For journal access, try getting yourself an unpaid appointment as affiliate faculty (aka courtesy appointment) at your local university. I've known a couple of people who have done that. - Donnie Berkholz

Lab space outside of a university or big company is very difficult to find. The so called "incubators" are expensive. It is still unclear to me what the rules are for running labs in commercially-zoned properties. - Jeremy Leipzig

Access to journals is a huge issue. My biggest expense for freelance science (computational biology) is the computing equipment; second would be software. - Walter Jessen

As I'm considering becoming an independent scientist (again!), some time ago I did back-of-the-napkin calculations and it turned out that I might need ca. $100 (reliable internet connection) + $500-1000 (per article payments, no subscriptions) + $500-1000 (computing cloud, storage and calculations) a month to work comfortably outside of academic infrastructure (without spamming all my... more... - Pawel Szczesny

Access to journals is the biggest issue. Obtaining this access by being an adjunct faculty is much more valuable than the salary they pay for your services. Obtaining funds to attend scientific meetings and to cover publication costs isn't far behind. Not always trivial to convince business types there is value in publishing your basic research. - Jeff Habig

Donnie, good to know re: affiliate positions, thank you. - Heather Piwowar

and you can order that latte with amazing accuracy. - Mickey Schafer

Please delete this post - it could be infectious. All it takes is for a few undergraduates to get wind of this and you could tip over the whole apple cart. - Jeremy Leipzig

Too late, don't tell my PI (Steve Koch) but I'm leaving the lab now. I knew I didn't have to work for free for a chance to be successful! - Anthony Salvagno

with or without a frothy introduction... - Mickey Schafer

Why do mathematicians need PhDs? Discussion from diybio.org: http://groups.google.com/group... - Mackenzie Cowell

@Mark, another idea before its time: http://testingtfv.blogspot.com/2007... - Steve Koch

Thanks, Pierre. Been working hard to make the jump between experimental biology & bioinformatics - Attila Csordas from iPhone

Congrats! Sounds like a great opportunity. - Heather Piwowar

congrats! - imabonehead

Congrats! Great news: welcome to the Silicon Fen. - Matt Wood

congrats, Attila! What will you be working on? - Mr. Gunn

Congrats Attila !! - Khader Shameer

Thanks, appreciate the support, it's definitely a proteomics job, exciting horizon - Attila Csordas from iPhone

Congratulations! Where will you be based? - Berci Mesko, MD

Congratulations!! - Yann Abraham

congrats :) - Pedro Beltrao

Congratulations! - Ruchira S. Datta

Woot - glad to see that the mass take over of EBI continues apace... - Cameron Neylon

How so take over? Is there anything you do not like about the EBI that requires take over? - Egon Willighagen

No, no. Just that we seem to be gradually getting people we know into positions there. Duncan, Nico, now Attila...not so much a takeover as an _enhancement_ - Cameron Neylon from twhirl

Congrats - Abhishek Tiwari

Thank you all! (Berci: EBI is @ the Genome Campus in Hinxton, we'll be based in Cambridge) Looking forward to meet all the Cambridge/Sanger/EBI people there - Attila Csordas

Congratulations! - Kubke

Congrats Attila :) - John Cumbers

Great! Congratulations! - Konrad Förstner

And of course my congratulations too, Attila.....looking forward to meeting you in person (finally)... - Nico Adams

thanks again to everyone, accepted the offer today with an April start date. - Attila Csordas

Congrats Attila! Read this on my handheld and thought you said the "FBI" instead. Does this mean the next BioBarCamp will be in the UK? - Jim Hardy

Nice, congrats! - Sung W. Lim

HI/congrats!--I think my friend John Tate works there...if so tell him I said hi! - Mary Canady

Watching now. BTW, you've convinced me to try "hundreds of slides" approach some day - I wasn't sure it works in more scientific talks. - Pawel Szczesny

Pawel, I wasn't sure either, but I've had a chance to do deeper dives now (at Supercomputing) and it seems to work, especially as I get more comfortable talking science in this format. If I had to choose an alternate one it would be a pure storytelling/figure format, i.e. about some of your core results and work backwards if required. - Deepak Singh

that was a really great talk! - Jeremy Leipzig

fortunately a relative will be at the Airport and will wait for me. Jan, FYI I'll land in Tokyo tomorrow 14th at 14H00. - Pierre Lindenbaum

Ha! Is the "I know what I've seen" one a reference to "Watchmen" or "Twilight Zone"? - Chris Lasher

Take the Bus. There is a bus service that takes from from Narita into Tokyo hotels (by zone). Narita is a ways away from tokyo, so DO NOT TAKE A CAB. - Deepak Singh

I remember when BIND went commercial ..all sorts of web-services suddenly broke(changed URLS )and were partly inaccessible. Its sad that we have free web-email but no money for persistent hosting of these resources. Maybe we should assemble a bioinformaticians-sans-frontier to rescue these services and port them to the cloud ( google-app-engine , amazon and other such services) - Hari

@Hari Wouldn't it be nice? - Chris Lasher

How'd you pay for cloud resources? - Rajarshi Guha

It'd be good to repeat this kind of survey now (that data is from 2005). Maybe a good Biogang project? Get all the databases from six months of Bioinformatics (or pick a NAR databases issue) from, say, three years ago and see how they're doing? - Euan

@Euan Wasn't it done last year ? I don't remember who's done the job. - Pierre Lindenbaum

we started just to check if they were online and if they worked but we never finished. - Pedro Beltrao

NIH has an active PA for "Continued Development and Maintenance of Software" (http://grants.nih.gov/grants...) which even dates back to 2002. Wonder how many grants have been funded off of it... - Andrew Su

Great data point... Agreed with Euan that this kind of survey needs to be repeated. Ideally, one would re-contact the databases contacted in 2005 in order to update the data, and then also contact databases mentioned in a new collection of issues. - Hilary

One could create a shared spreadsheet on google-doc, with each database and its current status. - Pierre Lindenbaum

It's almost worse if a one-off database stays up abandoned with old data. I bear some major guilt here - the Alternative Splicing Gallery (my thesis project) is still running with ESTs from 2003 and consistently gets 130 unique visitors a month. There is no simply no mechanism (guilt doesn't count) to maintain a program that is created for the purpose of getting a paper published. - Jeremy Leipzig

@Pierre @Hilary Something like Michael Barton's survey? http://tinyurl.com/6gs6pq - Chris Lasher

Duncan, is your thesis available somewhere as a pdf document ? I've the feeling it contains many things I'd like to learn about taverna, biomoby etc.... - Pierre Lindenbaum

Likewise, but at the bottom of the page it says Duncan says he'll publish it soon, he just has to make final corrections. - Chris Lasher

I'm also very interested in giving this a read. Please let us know when it's available :-) - Ricardo Vidal

@Duncan , that would be great: plindenbaum yahoo fr - Pierre Lindenbaum

@Duncan chris DOT lasher <AT> gmail TOD com - Chris Lasher

wouldn't it be great if we created an email list? - pn

Excellent idea, Paulo. Any ideas (interested) FF'ers as to how best to take this forward? - Graham Steel

It is possible to create a simple mailing list and have full access by everyone of everyone's info. - pn

I've set up a Mailman server before. I don't know if that does what you want. It sounds more like you're looking for an email registry. FWIW most of us have our email listed somewhere on one of the services published through FriendFeed. - Chris Lasher

yes, we do, but if we need access to someone else's email we don't have it at hand. I have a mailing list in my ISP's server, but that's not handy. - pn

Google groups? - Rajarshi Guha

Nice one, Rajarshi, didn't know about Google groups http://groups.google.com/ - Graham Steel

Rajarshi may be on to something. Groups provides mailing list support, as well as support for wiki-like pages. We could choose to publish our emails on that. Still, my Spidey Sense says we're re-inventing the wheel. - Chris Lasher

Most of us are connected threw LinkedIn. The e-mail are available to the direct contacts. - Pierre Lindenbaum

maybe a Ning network would solve this problem - Jeremy Leipzig

or someone with a daring sense of humor :-) - Björn Brembs

Neither silly nor embarrassing... just very, very funny. - Richard P Grant

I've heard politics described as a dog and pony show... - Richard Akerman

sighs - Graham Steel

Ooooops: http://www.timesonline.co.uk/tol... - Bora Zivkovic

@Bora Yikes I'm surprised it made the Times. Ouch. - Richard Akerman

Something to point to, next time the argument comes up about Nature (or any journal) accepting or refusing papers in order to please advertisers. Pretty clear that the editorial hand has no idea what the advertising hand is up to. :-) - Bill Hooker

Wow...definitely a sily mistake but...damn - Rah-PM 2012