Jason Tsai › Comments

good luck! - Adam Kraut

sounds like a positive development - Mr. Gunn

congratulations! - D0r0th34

best of luck for the new job ! :) - Pedro Beltrao

Way to go. Kudos! Hope you all the best! - Paulo Nuin

Congratulations - I wish you all :) - Lars Juhl Jensen

Nice to hear it's all signed sealed and official now. Exciting ! - Andrew Perry from twhirl

Good luck Neil! :) - Pawel Szczesny

congrats Neil ! - Pierre Lindenbaum

good luck, may the Force be with you! ;) - Yaroslav Nikolaev

congratulations Neil, and best wishes with the new job - Duncan Hull

congratulations, all change for me in 2009 as well. - Frank

congratz!!!!!! :)) - Jason Tsai

Good luck. And hopefully you'll keep on blogging - Deepak Singh

Good luck :) - Jason Tsai

Thanks guys. Fingers crossed everything goes well. - Michael Barton

Good luck! I don't recommend trying to do things the other way around. - Mr. Gunn

Go for it, Michael! - Sally Church

Good luck! - Cameron Neylon

Idem. - Jan Aerts

Good luck :) - Jason Tsai

good luck! - Yann Abraham

Best of luck! Look forward to collaborating soon! - Matt Wood

The recent FF discussions about science communication put me in mind of what I think is perhaps your strongest skill, that of being a communicator. - Mr. Gunn

Thanks guys. (I think you're wrong about my strongest skill, Grady, good communicators are better at smalltalk than me and have more followers on Twitter. Let my employers find out my strongest skill which is more directly innovation related I think.) - Attila Csordas

Good luck! - Chris Lasher

lucky you! - Yann Abraham

that's great news. I remember you asking for interview tips (if atherosclerosis haven't destroyed my memory yet). Good luck with everything. - Paulo Nuin

What team are you in? - Jan Aerts

"smart casual", unless it's a job where you'd wear a suit to work - Neil Saunders

but what is dress up? == suit with tie? I remembered my previous interviews I always felt I overdressed. But I also heard advices that I should wear proper suits, etc. - Jason Tsai

A nice pair of pants and a nice shirt should do it. You can throw a jacket if needed and/or want. - Paulo Nuin

I tend to go with a sports jacket at most - Deepak Singh

For me, "dressing up" means a t-shirt with no stains on it... holes are OK though, right? :-) - Bill Hooker

Shirt, trousers, and perhaps a jacket. Depends on where you are of course. If you are headed for a Wall St. interview, you better wear a good suit :) - Deepak Singh

dress up as much as you feel NATURAL. heck, you want them to hire YOU, not a suit, right ? - General Kafka

If you're interviewing on Wall St. tomorrow, you should dress in a jumpsuit. When they ask you why you dressed that way, straightforwardly reply, "Oh, I'm sorry. I heard you're all getting golden parachutes, so I didn't bother bringing mine." - Chris Lasher

if it's at a company, ask the person who's coordinating your visit. It's in their interest to make you feel comfortable. If it's an academic interview, what Paulo said... - Andrew Su

More seriously, I wore a button up shirt, khakis (both ironed), and no tie to my academic interviews and would say that's perfect. For industry, I have no idea, but I would probably dress the same. - Chris Lasher

East Coast tends to be more formal than West Coast, FWIW... - Donnie Berkholz

punk is good, but go for the classic look -- i.e. east coast US (Iggy, Ramones etc) rather than UK safety-pins, or 90's "gutter punk" look or (heaven forbid) Green Day plastic-punk. on the other hand, if you go for the "raver" look, choose generic UK baggies and soviet surplus gear, avoiding the pacifiers and other baby-kit that is typical of US warehouse parties - Ian Holmes

for industry I would always go for suit&tie. No more than that, no less. at least in Germany this seems the way to go. for academia here I would dress a bit below that, see Deepak's #2 - dK

@dekay "No more" than a suit and tie? The only thing more in Western dress is a tuxedo, right? ;-) - Chris Lasher

it can be suit, tie, vest and gold watch :-) - Paulo Nuin

Sure:- http://www.youtube.com/watch... - Graham Steel

@Chris nah, there is still the 3 piece suit which is still in between. And of course colour is part of those rankings as well. Think black = more formal than grey checkers :) - dK

OK I am going to crack and join in. Speaking as an employer many times over, anything so long as it is clean. - Maxine

See? I was right. Holes OK, stains not OK. :-) - Bill Hooker

Awesome... I hope to be in that position soon... - Ricardo Vidal

congrats! - Mr. Gunn

Although it's not necessarily my case, it came across my mind a couple times. Thanks. - Ricardo Vidal

A thesis (in Portuguese dissertacao - no accent here) does not need to be novel, it can be a repetition of some other methodology and results. As Pawel pointed out, it's just a matter of showing you scientific aptitude. On the other hand, a dissertation (in Portuguese, tese) has to be a novel work, and that's why is advantageous to publish in papers as it happens. - Paulo Nuin

Sorry, I just found a PHD Comics about this: http://www.phdcomics.com/comics... - Pierre Lindenbaum

I've just noticed a few projects similar to the one I'm working on and it just ran accross my mind. Anyhow, both Pierre and Nina Jansen have saved the day with phdcomics :) - Ricardo Vidal

and this one: http://www.phdcomics.com/comics... - marcin

They tell us that it needs to be novel and publishable, at least most of it. My dissertation essentially consisted of cutting and pasting my three papers together and gluing them together with some connecting verbiage. I would have hated to be in the position of having my thesis consist of only one publishable unit, and then being scooped on that. - Mr. Gunn

publishable unit, I learn new things every day - Paulo Nuin

My labmate had the similar situation. She submitted way early to Nature but unfortunately got rejected after a long wait. The other group submitted a similar finding to Cell and got accepted. She had to rewrite in a way that her study is independent to the other group and the different/similar results arise from her study compared to theirs. - Jason Tsai

@Paulo: you haven't heard of the least publishable unit? http://en.wikipedia.org/wiki... - Michael Kuhn

Michael, I'm old school :-) - Paulo Nuin

how conserved are the recombination hot spots with the ones in S. cerevisiae ? From that slide they look to be generally conserved. - Pedro Beltrao

very conserved! :) 7 out of 10 hotspots in cerevisiae are found in paradoxus. And this contradicts to theories that hotspots are not really conserved between species. - Jason Tsai

interesting ... I think there was a paper mapping double strand breaks in S. pombe (I think in PLoS Genetics but I am not sure). Since they are supposed to be somewhat correlate with the recombination hotspots maybe it would be interesting to see how conserved those are. - Pedro Beltrao

agreed, coding questions are unlikely. my advice is 1) know your own research inside and out, and 2) asking questions about the interviewer's research conveys interest and enthusiasm. - Andrew Su

don't know how post-doc iv are different, but thats exactly what i've been doing in PhD interviews. - marcin

@enigma I guess it's ok, but you would know his research interests anyway. More like his/her "current" interest. - Jason Tsai

My lab recently interviewed for a postdoc. Our most important criteria, by the time it got as far as an interview, were enthusiasm for the project and fit into the lab culture. - Donnie Berkholz

Understand that you'll be talking to other people in the lab, other people in the department, and maybe even giving a seminar. Don't think that just because these people aren't the PI that their opinion doesn't carry weight! Oh - and this goes for ANY interview - the interview doesn't end when you, say, go out for dinner or a beer... - Todd Harris

Usually, a seminar, talks with everyone and the PI, lunch/ dinner. Be yourself, be curious and seem genuinely ready for responsibility. Its mostly them talking and you listening, other than the seminar. Good luck!! - Aarthy

Don't think about getting the job, just scope out the projects and the people. If you want it for the right reasons, if you're into the work and a good fit with the lab culture, that will be obvious. "Be yourself" sounds trite but it's the best advice there is. You're better off in another job if you'd have to be someone else to get this one! - Bill Hooker

@all thanks for all the advices; @Bill like your last sentence a lot! I'll be myself and hopefully don't laugh too loud after a few drinks... - Jason Tsai

Good luck Jason. - Paulo Nuin

hey - Paulo Nuin

forgot the ! - Paulo Nuin

he said biologist, that's pretty wide definition! - Paulo Nuin

structural/computational biologist here - Donnie Berkholz

compbio - Ian Holmes

Computational Structural Bio (using a broad definition) ... hey! - Deepak Singh

bioinformatics? hey? - Shirley Wu

I assume bioinformatics counts. Hey. - Chris Miller

'hey!' - Richard P Grant

hey! - Yann Abraham

hey! - Pawel Szczesny

Computational biologist. Hey? - Lars Juhl Jensen

hey! population geneticist - Jason Tsai

Me too! (protein chemistry/mol biol/this week's buzzword) - Cameron Neylon

hey! neurobiologist - Björn Brembs

hey! once long ago. (physiology and then biophysics, now I'm a camp-follower) - Maxine

hey! - Marian Siwiak

hey! Genetics, but now mostly bioinformatics - Todd Harris

yup - Maureen

hey! molecular/cell biologist - Ricardo Almeida

used to be molbio & biochem, now bioinformatics. - tim from Alert Thingy

Biochemist then bioinformatics - Pedro Beltrao

hey ! :) former developmental biologist turned bioinformaticist. I'm still a biologist even if I don't set foot in a lab :p - Daniel Swan

neither nor ;) - dK

*raises hand* molecular biologist - Bill Hooker

I'm a biologist. - Chris Patil

biochem/neurosci/genetics? - laura

I'm a biochemist - Sally Church

All things bio folks... or almost. Most of you know what I mean. Thanks for your participation. - Ricardo Vidal

Biochemist, now business development - Jack H. Pincus

Genetics / Dev biology background, turned computational biologist - Oliver Hofmann

Biochemist / Molecular biologist / Biotechnology diagnostics hey, hey, hey ! - Nils Reinton

hey! - Paul Bacchus

hey! from here as well - Jan Aerts

hey! Molecular/cancer biologist and bioinformatician. - Walter Jessen

Could try a speculative phone call? - Michael Barton

PhD physicists, perhaps. Not so much life scientists, but a bioinformatics person really strong in modeling might work. I do think there are unique opportunities that exist now that didn't exist 2 years ago. - Mr. Gunn

Definitely worth a shot if you a hardcore quant. Lots of the same skills - Deepak Singh

I'm not up to date with internets recently, but didn't they go bankrupt this weekend? - Pawel Szczesny

Ooops - yep that was them... - Cameron Neylon

Yup Pawel, they declared bankruptcy protection this morning - Sally Church

Thanks Sally and Cameron. BTW, one of my colleagues was doing molecular modelling and after getting PhD went straight to a broker firm. As far as I heard, it wasn't that difficult to get the job, but on the other hand he doesn't seem to do now any rocket science. I'm not sure about US market, but most of the European finance companies don't do any "cutting edge" or even very sophisticated work in this area. - Pawel Szczesny

People doing cutting edge work in finance or either very rich or very broke. That's too high risk a position for most conventional banks and brokerage firms I think. - Cameron Neylon

Cameron, by cutting edge work I mean doing analysis/prediction better, not with more risk. Or, in other words, there's a reason why competitions in automated trading systems win theoretical physicists not professional trading groups/firms (the latter also participate). Banks are indeed in a different position, but given recent scandal in one of French (if I remember correctly) banks I wonder if all of them are really playing safe ;). - Pawel Szczesny

Thanks! In fact is very close to 10, this is just the date of the official ceremony, not less important whatsoever. - Paulo Nuin

nope .. never - Deepak Singh

Congratulations to you and your spouse! - Chris Lasher

Congrats! - Sally Church

Thanks a lot! I hope I have 100 more of these anniversaries. - Paulo Nuin

Congrats! My one week anniversary is tomorrow! Any required protocol? :P - Todd Harris

Congrats! - Matt Wood

fun ? enjoyable ? :) yes yes ... those are exactly the words most people pick :). Thesis mean different things in different countries. Since I worked in EMBL where people end up defending in many different countries what I found strange during the final process was how different the evaluations are. - Pedro Beltrao

Keep it under revision control. ;-) - Chris Lasher

I went to EMBL once (http://www.flickr.com/photos... - I also met Roland Krause, but I'm sure he doesn't remember me), isn't the thesis a collection of published papers? Here in the UK, you've got three years of funding to do the research and write the thesis. - Michael Barton

@Chris http://michaelbarton.lighthous... and http://github.com/michael... - Michael Barton

I don't know anybody who thinks writing a thesis is fun. It's not like a publication. You're writing a document that your committee will spend five minutes looking at, and that you will never look at again (most likely). - Todd Harris from twhirl

At the time I wrote mine there was a transition between the old type to the new one where chapters were papers, so I mixed and matched. Also I didn't have a series of published papers to present as a thesis (nor I do have them published now). In Brazil, you got 4 years of fund to research and present it, but now it is getting down to three. - Paulo Nuin

Tips from my advisor: vomit it out. If you get stuck, just write.It won't write itself, so set a time to write everyday. Get in the zone and get it done and get on to more meaningful things :) Oh, and have fun! - Todd Harris from twhirl

The "set a time to write" is a good advice. I used to do that, have some fun/work done in the morning and write a lot after 12 pm. - Paulo Nuin

Seconding the advice to barf it up in one big lump. Braindump first, edit second. Also, if you're like most people, don't try to do bench/lab work at the same time -- different zones, hard to switch between 'em. Also, exercise: get some, regularly, it'll keep you (relatively) sane. - Bill Hooker

treat it like a novel - write lots, write consistently, edit later. I wrote my introduction last, I still maintain this was a good idea... - Daniel Swan

I absolutely agree that you should write as much as possible as fast as possible and only edit it later. Also, don't try to do other work in parallel - I personally stayed at home while writing up to not have colleagues disturb me. - Lars Juhl Jensen

Hi Michael, are you thinking of writing the paper format thesis or the traditional way (one big intro, one big result chapter.etc.)? I am currently writing results->method-> discussion->intro. Where are you heading next? - Jason Tsai

Most pleasurable thing I have ever done ... and I agree with Bill - Deepak Singh

if I may speak from the other side (trying to squeeze thesis out of students) I also second Bill's approach. Far better to have rubbish to edit than a blank slate - Cameron Neylon

I was fun when over and enjoyable when finally submitted!! Congratulations on the milestone!! - Aarthy

What I did was to take my papers and essentially cut and paste them in, making each a separate chapter and then just doing a little introduction, conclusion, and textual filler/glue in between. Having something on the page kick-starts the writing process. - Mr. Gunn

It's been said by pretty much everyone above, but I'll say it again: Just brain dump it onto the page, then edit it afterwards. I wish someone had told me this, since I took far too long to write. The most time you will ever waste is if you try and write it 'perfectly' first time and sit around waiting for inspiration. Once there is something on the page, it's very easy to fix up, and suddenly, you have a great working draft. - Andrew Perry

The other strategy that I used was time tracking, with estimates and actual time taken, broken down into very small tasks (eg by Figure) .. I used http://voo2do.com , but you can do it in a spreadsheet or whatever. It helped me get better at making time estimates, and motivated me to not procrastinate so I could meet my projected targets. - Andrew Perry

latex latex latex. But you knew that already http://freelancingscience.com/2008... - Duncan Hull

Thesis writing is probably the pinnacle of mental anguish. Thankfully, you will never experience anything as traumatic and soul-destroying for the rest of your career. Just think of it as the start of the descent into mental disorder that characterises most working scientists. - Neil Saunders

If you need a latex template, "MUTHESIS" http://www.google.co.uk/search... (Manchester University Thesis) might be handy - Duncan Hull

Yeah, must of the stuff has already been said, latex, revision control and just keep writing. It is also good to get at least a couple of people to look at each chapter, not just your supervisor. Get your self a personal account with Starbucks for al the java, and be prepared to put about 3 stone in weight. Oh yes start writing in year 1 :) - Frank

Good luck! We'll be sharing the pain with you (virtually) - Duncan Hull

Thanks you everyone for your over whelming response. This has prompted me to start seriously about trying to make a dent in the writing now, rather than later. Fingers crossed, in eight months time I'm done. I will share my agony on twitter. Would be interesting to connect a blood pressure monitor to the twitter API. - Michael Barton

15 now - Michael Barton

Loading... - Michael Barton

I'm microblogging a loading webpage. My life is becoming everything I ever dreamed it would be. - Michael Barton

Well at least you're not microblogging a battering running ou - Cameron Neylon

Time's up - Michael Barton

Get someone currently at ISMB to publicise it for you - Duncan Hull

evoldir? - Jason Tsai

Is there anyone at SMBE who could mention this around? - Michael Barton

@Jason Would you be able to mention this on evoldir? - Michael Barton

reshared to ISMB 2008 room - Duncan Hull

Hmm, the ISMB room probably wouldn't cut it - do you have a print out? If you send a PDF, I am happy to take care of posting it. Many of the great IT specialists of The Future look at the notice board. - Roland Krause

done. should be up in the daily post tomorrow - Jason Tsai

I have just posted the survey to the Scandinavian bioinformatics mailing list - Lars Juhl Jensen

posted on a Brazilian list. - Paulo Nuin

Thank you everyone for your help with publicising the survey - Michael Barton

Yeah, there is a lot of comments/rumours about different type of next generation technologies. Too bad most of them are published in big named journals (so lack of methods..) It would be nice to confirm that - Jason Tsai

You might be interested in the following from Nature Methods: http://www.nature.com/nmeth... Apologies if you've already seen it. - Mr. Gunn

I've got some related links here: http://www.connotea.org/user... - Mr. Gunn

For the next few years I am interested in studying the evolution of signaling systems in yeast. Most of my work will be computational but I am starting to work also on genetic interaction screening in different yeast species. - Pedro Beltrao

I'm a neurobiologist and electrophysiologist, currently studying the regulation and physiological roles of transient receptor potential (TRP) channels in various neuronal celltypes. - NatBlair

Currently sequence-structure relationships in proteins, bacterial membrane, secretion and infection, this year p-p networks (interactions, metabolism, etc), in a near future protein design and bioengineering - only at keyboard - Pawel Szczesny

I work in a company specialized in genotyping (Illumina, snplex ...). I'm in charge of the database management , programming tools, creating web interfaces. - Pierre Lindenbaum

Wet lab; currently: molecular biology of Myc/Max related transcription factors; previously: mol basis of human iron homeostasis, fine details of HIV reverse transcription, PCR assay for Pneumocystis, candidate vaccine antigens from schistosomes. - Bill Hooker

No direct science anymore, just for fun. Marketing/strategy/BD in life science software companies. Personal background is in electronic structure theory, protein structure prediction, molecular simulation, drug design. Work has ranged from molecular modeling software to genomic data management especially for pharmacogenomics. Current geek interest: Distributed data - Deepak Singh

I don't know what I am currently working on, basically it is a annotation, microarray creation for some bacteria species on a metagenome/pan-genome project. My main interests are more bioinformatics focused, no wet-lab involved. I am very interested in evolution, phylogenetics, population genetics, bioinformatics education, translational research, databases, programming and interface development for applications (web and standalone). - Paulo Nuin

I think I've lost track - still mostly wet lab though. Bit of directed evolution, bit of protein ligation chemistry, bit of structural biology (protein-DNA complexes and membrane proteins methods development), bit of analytical methods development mainly high throughput. I've had projects crash and burn in most of these areas and got some results in most of them - Cameron Neylon

No wet lab work here. I'm a geek at a supercomputing center working under a PI who's a chemist (think big calculations on small molecules). I work on molecular modeling, protein structure prediction, enzyme design, QM/MM simulation, and just about anything that catches my interest. - Adam Kraut

I work on evolution of yeast spcies. Basically relating everything that has been found in yeast onto its new resequenced genomes. Daily task involves copy and pasting perl codes - Jason Tsai

I work on the structure and function of outer membrane proteins from mitochondria and bacteria, specifically those involved in outer membrane beta-barrel folding, insertion and assembly. My time is split about 70 % wet lab, 30 % dry lab these days. - Andrew Perry

100% computational, but formerly biochemistry/molecular microbiology. General theme just now is computational prediction of protein-protein interaction from a structural standpoint; especially protein kinases and their substrates. Real passion is anything to do with microbial genomes and any computational method that provides insight into them. Plus a general interest in better ways to handle biological data of all kinds. - Neil Saunders

I head up the Production Software team at the Wellcome Trust Sanger Institute. We provide informatics support to the various genomic projects within the Institute, including Illumina sequencing and genotyping platforms. - Matt Wood

50/50 wet/dry lab: studying protein dynamics, folding and interactions with solution NMR. current focus - leucine zipper domains from transcription factors cJun and GCN4. /// overall - am slowly shifting to silico-lab - Yaroslav Nikolaev

I'm a ring-in. I'm a theoretical physicist who now works fulltime on open science. But I enjoy biology :-) - Michael Nielsen

I'm an chemist specialized chemometrics and chemoinformatics, now in metabolomics research, working on open source chemo- and bioinformatics software, such as CDK, Bioclipse, MetWare, and with a strong interest in the semantic web technologies as means of improving the amount of information we use from measurements. - Egon Willighagen

I'm a biochemist but long gone from the lab. These days I'm more interested in the theoretical aspects of biochemistry and molecualr biology as it pertains to oncology and improving cancer treatments - Sally Church from Alert Thingy

@kambiz There are plenty of field biologists, but I don't think they're big computer users :) - Neil Saunders

@kambiz I was just kidding :) I suspect though that there are more bioinformaticians on FriendFeed than ecologists. - Neil Saunders

Running a molecular biology diagnostic lab (wet lab, I guess). Testing for bacterial/viral pathogens and human genetic markers. - Nils Reinton

I work on adult stem cells and tissue repair. My dissertation is on the the repair of bone by MSCs and their interaction with bone-destroying cancer. Attila is currently in our group, but he'll be leaving soon, as will I, because my defense is coming up! - Mr. Gunn

Currently finishing PhD on RDF-based integration of pathway data, with a sprinkle of data mining gene expression for pathway activation and genetic polymorphisms (all through relational or RDF triple databases)... dreaming to work for Google when I grow up - well anywhere with lots of geeks around the workspace. Used to be molecular biologist without having done a single PCR - doing fluorescence photography to localize proteins in cellular compartments, lots of geeky stuff there too for image processing.. - Ntino

I'm in science publishing. I like to pretend I'm still a bioinformatician, though. - Euan

I'm completely dry. I am in the early stages of a PhD focusing on protein dynamics using hybrid computational-experimental techniques. Simply, it's MD simulation using non-calssical NMR restraints. I hope to do some wet lab experiments as relying on collaborators for data is becoming quite frustrating BUT my PI is very reluctant for me to get wet. - Mitchell J Stanton-Cook

Mitchell, I can understand your PI being uncomfortable with you getting wet around the computers :) The project sounds cool though. What kinds of data are you looking for? Any interest in large scale size/shape constraints? - Cameron Neylon

These days doing wet lab work in synthetic organic chemistry making anti-malarial agents - from a larger perspective I am interested in the automation of science and Open Science - Jean-Claude Bradley

I'm between wet and dry labs. I do in vitro selections (using mRNA display) and do computational work to interpret the selections as well as investigate other questions. - Matthew D. Smith

It all started with a genetics degree then a proteomics PhD; half in the lab and half modeling the data (reporting standards) and knowledge (ontologies) produced as a result. Now it is 100% computational, modeling data and knowledge for neuroscience. I wonder what I will do next? Maybe a synthetic biology ontology... - Frank

Like Euan, I am in science publishing and like to pretend that I am still a chronobiologist. PLoS Online Community Manager, science blogger, organizer of ScienceOnline (formerly Science Blogging Conference), series editor of The Open Labarotory (anthology of science blogging), OA evangelist, telecommuter.... - Bora Zivkovic

Protein structure, combination of crystallography and modelling. For the main part my Ph.D. work, I'm enhancing some structural modelling and refinement programs to use less "ideal" information when reality doesn't act ideal in many cases. On the crystallography side, I just got a paper accepted last week to JMB about atomic-resolution catalysis in glutathione reductase! - Donnie Berkholz

Namely, but not only, studying extra/intracellular cell biology, Glycobiology, Proteoglycans (especially Heparan Sulphate) and Glycosaminoglycans, etc. Involved in networking between us public, scientists, researchers, physicians, Journals etc. OA evangelist - Graham Steel

Former wet lab biologist for my PhD (genetics of neurotransmission), turned bioinformaticist and designer. I'm the project manager and lead developer of WormBase. I also assist on analysis and visualization for a number of large scale genomics projects. - Todd Harris