Forum: Optimal design for bioinformatics "lab" space?
24
gravatar for Casey Bergman
3.4 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

[ Cross posted on r/bioinformatics - some other good replies can be found there.]

While much thought has been put into design for laboratory space and tech companies like Github have put substantial effort into office design for software engineering, most bioinformaticians I've seen (in universities, mainly) work either at desks/benches in wet labs or in open-plan offices (with or without cubicles). Neither situation is optimal for bioinformatics research, since the lab environment can be noisy and distracting but open plan offices don't promote scientific discussion in the way that happens naturally in a lab.

I thought it would be interesting to hear what people's experiences are concerning their bioinformatics workspace, what they think works well/poorly in terms of bioinformatics research space, links to any resources on designing bioinformatics labs, or any pie-in-the-sky design ideas for the bioinformatics dream lab. Hopefully one day, we'll have more places built with these ideas in mind for us to work in!

Many thanks in advance,

Casey 

design forum lab space • 2.7k views
ADD COMMENTlink modified 3.4 years ago by Yannick Wurm2.3k • written 3.4 years ago by Casey Bergman17k
1

Related note. Whiteboard paint has been used around here a bit, which is kind of cool in theory, but for actual writing, I prefer real whiteboards. Maybe it's just the walls here, but it's a little bumpy or something.

ADD REPLYlink written 3.4 years ago by Madelaine Gogol5.0k
11
gravatar for Neilfws
3.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

I'm not really answering the "optimal design" part of the question; I just wanted to note that I was moved to an open-plan environment about 2 years ago. I'd say my productivity is about 10-30% of what it was previously, most days. It is awful.

There's a lot of research and evidence that so-called "knowledge workers" (people who need to sit, think and process data) really suffer in open work environments. I've been collecting articles tagged open-plan at Diigo. Managers of course simply choose to ignore this.

If you're in an environment where you can't work effectively, don't suffer in silence (or should that be, in noise). Tell the boss. And if they're unresponsive, make it clear that you're prepared to act unilaterally and take yourself to a better environment.

ADD COMMENTlink written 3.4 years ago by Neilfws48k
1

I too am a skeptic of "open" work environments. They look like so much fun to Joe Blow Office Schmo, but focus is an incredibly delicate thing. 10-30% of your previous productivity?! Ouch. That's pretty condemnatory of open environments!

ADD REPLYlink written 3.4 years ago by Dan D6.6k
6
gravatar for geek_y
3.4 years ago by
geek_y8.7k
geek_y8.7k wrote:

From my personal experience:

I was sitting along with wet-lab people ( and of different group too ) in open lab. For me, the wet-lab people don't need to think a lot because they follow standard protocols for library prep. The only time they need conc. is when handling large number of samples, not mess with labelling etc. So they used to chit-chat, laugh loudly, speak on phone while pipetting etc.

But we need to think a lot. we need to troubleshoot. we need to understand what a tool is doing and what kind of format it requires and how to get that format by writing a script. While writing a script, which data structures to use, what logic to implement to get things done etc. We have to keep in mind the entire picture of what is happening in the analysis pipeline to interpret the results at each step. The entire process right from the beginning to end requires lot of concentration and thinking.

I used to go out of lab for a walk just to get of noise that was killing my brain cells. 

We need a peaceful environment with some programming books around, coffee, knowledge sharing, a mechanism for regular updates on new tools/pipelines etc etc etc.

ADD COMMENTlink written 3.4 years ago by geek_y8.7k
4

"The only time they need conc. is when handling large number of samples, not mess with labelling etc." Mmm... but that means 90% of the time... Also, a mis-labelling or other mistakes in the lab means at best hours if not days of work and $$$ wasted (assuming you find out there was a mistake, big if). Computer work is more forgiving in this sense (unit test, svn, backups etc.)

ADD REPLYlink written 3.4 years ago by dariober9.4k
1

Totally agree with the thinking part. I sit in a cubicle, and the PI that sits in the office next to me is LOUD. We do a ton of dry runs in our head, so we need to be amongst peers that are either quiet or can be requested to be quiet.

ADD REPLYlink written 3.4 years ago by RamRS17k

Thanks for your comments, I think there are many bioinformaticians in this kind of setting, which I agree is not close to being optimal for the kind of work we do. Do you see any upside to being located inside a wet lab?

ADD REPLYlink written 3.4 years ago by Casey Bergman17k
1

Being located in wet-lab , I understood the library prep protocols. It is very crucial to understand the wet lab protocols to do data analysis. E.g We know exactly what all happened to DNA before it went into sequencer and what to expect. Wether it will have adapters, what kind of adapters, what is the fragment size, is ther a pcr step etc etc. I can quickly go to them ask about the protocols if I have some doubts during data analysis steps, mainly in custom protocols. Knowing wet lab protocols also helps in simulating experiments.

Bioinformatician who work completely separated from wet-lab ( like who work in data analysis companies, where they don't do wet lab at all) lack this knowledge and they may blindly follow standard pipelines and end up in poor quality data analysis.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by geek_y8.7k

In my own experience it is always very difficult to make wet lab people tell you exactly what protocol they've used once you get the data. Even worse, once you get the protocol the next run will always be performed with a modified protocol, different adapter sequences, etc. So I strongly believe the problem is not separation, but the fact that a bioinformatician needs a concise description of library prep, preferably in a written form :) While we use version control system for our scripts, I don't think such system for web lab protocols is a common practice.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by mikhail.shugay3.3k

as a wet scientist I feel like I should take offense to this...But I guess it is just a matter of not really knowing/understanding "the other side"

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Whetting1.5k

Don't. We are here because we're making the best of our lack of people skills. Hence the reduced banter frequency :)

ADD REPLYlink written 3.4 years ago by RamRS17k
5
gravatar for Dan D
3.4 years ago by
Dan D6.6k
Tennessee
Dan D6.6k wrote:

Great topic!

I'm rather fond of my current workspace, It's glass on most sides, so people can see if I'm busy without entering my "bubble." It's separate from the lab, but not distant. Easy interaction with wet lab scientists is definitely a must, for me at least.

I don't care about lounge areas, pool tables, beer taps, whatever. If I need a break I'll go outside and take a walk. That's just me. I worked in restaurants and factories (two distinct circles of the same general hell) from my 16th birthday through the following ten years, so I have that "blue collar" mentality about work being for work and then making the most of my time away from it.

Other musts:

  • The space needs to be quiet and free of unnecessary traffic.
  • Any individual's space should have room for at least two monitors.
  • It's impossible to have too many chalk/whiteboards.
  • A separate, enclosed area for discussion and collaboration.

Ten years ago I would have insisted on a good collection of books, but that's largely a moot point today with more journals being open-access, sites like Biostar, and services like Safari e-books.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Dan D6.6k
2

I like this answer a lot and wanted to second "A separate, enclosed area for discussion and collaboration". We have a big conference room nearby, but it was pretty heavily used by ours and other groups for big lab meetings and such, and we recently got a smaller conference room with a big TV + computer and about 5 chairs around a table. This has been very useful for smaller consultation type meetings with collaborators.

ADD REPLYlink written 3.4 years ago by Madelaine Gogol5.0k

Thanks for all these comments. Dan. I agree with all of them. I hadn't thought about the issue of glass walls, which I can see would lead to fewer interruptions. To put things in more context, how many people do you share your workspace with?

ADD REPLYlink written 3.4 years ago by Casey Bergman17k
4
gravatar for Yannick Wurm
3.4 years ago by
Yannick Wurm2.3k
Queen Mary University London
Yannick Wurm2.3k wrote:

Standing-sitting desks for everyone. 

ADD COMMENTlink written 3.4 years ago by Yannick Wurm2.3k
3
gravatar for Casey Bergman
3.4 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

In Manchester to have dedicated bioinformatics space, with labs and PI offices interdigitated based on a design by Terrri Attwood who was involved with the planning of our building. The labs are 3.5mx5m (11.5ftx16.5ft) and hold up to 6 people. One door (solid with window) opens into the lab that can be closed to hall traffic. Desks are around the perimeter, with shelves above, and small filing cabinents under desks

Pros:

  • Quiet
  • Few ambient distractions
  • Good space for books, personal belongings
  • No lab noise from lab equipement, deliveries, etc.
  • Limit on number of people in the room.
  • we are in the same building as wet-lab scientists and located near the cafe

Cons:

  • Not a lot of room for people to move around
  • People at the desks near the door get disrupted everytime some comes in/out.
  • No free wall space for white boards (only white board is on the door under the coat hook so it doesn't get used much)
  • Wireless signal spotty
  • No space for spontaneous discussions that don't impact whole lab
  • Circulation can be poor in summer (better with door open, but this infringes on one workspace

To have a place to talk/diagram ideas, I installed one big whiteboard in the hall. This has been good for getting noisier discussions out of the lab proper. But having the whiteboard in the hall is not ideal, since this is a "public" space, leading to many weird looks and people closing doors because they don't want to hear about Drosophila genomics. Also, pens and erasers go missing.

We also used to have a small "break-out" room with whiteboard/projector (dedicated, non-reservable) that was useful for having spontaneous conversations. but this got converted into office space.

Overall, I'd say we are pretty lucky (maybe lucky is not the right word since the space was designed by a bioinformatician) that we have good space computing, but our labs are probably too small and/or we don't have the right common space to promote dynamic scientific interaction. 

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Casey Bergman17k

I'm in the same space in Manchester, as part of the Bioinformatics Core Facility (which comprises 4 bioinformaticians and one software support person i.e. me). The whole group fits (just) into a single office, which is good for ad-hoc communication and knowledge exchange between group members, and overall I'd agree with your lists of pros and cons. I'd add:

  • The lack of a dedicated break-out space also impacts on bioinformaticians feeding back analysis results to researchers - everyone gets forced into a small space, which can be inconvenient and disruptive for all parties, and
  • New or "floating" members of the group have to be accommodated elsewhere in other offices, where they miss out on the benefits of being co-located with the rest of the group.
ADD REPLYlink written 3.4 years ago by Peter Briggs20
3
gravatar for mikhail.shugay
3.4 years ago by
mikhail.shugay3.3k
Czech Republic, Brno, CEITEC
mikhail.shugay3.3k wrote:

One important thing for me is to be able to discuss results with a biologist without needing to pass through the entire building, take my laptop with me and use my phone as a wifi spot. So the room needs to have additional monitors, chairs, whiteboard (ideally, a projector) in order to accommodate biologist parties. This also presumes there are at most 2 bioinformaticians per room and they are working on similar projects. I guess the optimal design of a bioinformatics facility is completely different, more closely resembling a software engineering office.

ADD COMMENTlink written 3.4 years ago by mikhail.shugay3.3k
2
gravatar for Istvan Albert
3.4 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

I think very close proximity to everyone on the team is very important. Our original setup required crossing a card activated door - very annoying to do so every time anyone wanted to check a piece of information.  Turns out there is always so much of ambiguity.

This is relevant for the case where offices may be available for bioinformaticians - it is also important to have these next to one another.

And I agree about open office environments - they are not really appropriate IMO.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Istvan Albert ♦♦ 77k
3

Also we have dedicated a piece of hardware to project tracking. Ten thousand years from now, once this dig this up, there will be a publication on the early man's bioinformatic related hieroglyphics.

whiteboard

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Istvan Albert ♦♦ 77k

Previously I was also in a building with lots of doors that required a card. Whenever I wanted to go to another wing to have a chat with someone it felt like I was intruding.

My best set-up is (and was) room with only another person; big desk for monitor(s), notes; big white board; shelf space for books and personal stuff; door always open. Cafeteria close by for meetings and informal chats.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by A. Domingues1.6k
1

so many people !!!

ADD REPLYlink written 3.4 years ago by Pierre Lindenbaum112k
1
gravatar for 5heikki
3.4 years ago by
5heikki7.6k
Finland
5heikki7.6k wrote:

For me optimal would be an adjustable table with two large screens at home..

ADD COMMENTlink written 3.4 years ago by 5heikki7.6k
1

Ugh, working from home is so hard for me. Maybe it's the small children running around trying to climb in my lap.

But on a serious note, I think so much of this job involves collaboration and interaction. If you work from home a lot, you better be good at skyping or something.

ADD REPLYlink written 3.4 years ago by Madelaine Gogol5.0k
2

For those of us with kids, s/working from home/working from quiet coffee shop/

Sadly, the latter requires pants. :)

ADD REPLYlink written 3.4 years ago by Chris Miller20k

LOL. I'm tempted to mark this as the answer.

ADD REPLYlink written 3.4 years ago by Casey Bergman17k
1
gravatar for CanyTon
3.4 years ago by
CanyTon10
United States
CanyTon10 wrote:

I like my workplace here. I won't ask for too much as long as people around are kind.

ADD COMMENTlink written 3.4 years ago by CanyTon10

subtle plug. Nice!

ADD REPLYlink written 3.4 years ago by RamRS17k
1
gravatar for zeeefa
3.4 years ago by
zeeefa80
Sverige
zeeefa80 wrote:

Good suggestions/comments! & Thanks to Casey for bringing up this topic! Here’s my input:

I should mention first that I’m an undergrad (currently on a placement year) working on a Bioinformatics-related project. My university doesn’t have a workspace for Bioinformatics students, so I just sit in a café or a library to do my work. I know that most people including my friends (mainly students working in a wet-lab) think that the good thing about computational projects is that “you can work whenever, and wherever you like!” Riiight, but it’s not that easy! because I can only sit in places where there are sockets, so I don’t have to waste time looking for a place to charge my laptop + you can’t really take a proper break, leave your stuff, and go out for a walk. Also, different rooms/areas have different temperatures and it’s annoying, tbh.

The thing is even postgrad students at my institution (who, by the way, get an office space) find it difficult to work, because: 1) small shared office space = not enough desk space 2) a student may be a Mac user, but most universities have Windows PCs so working on a different OS is always a bit of a pain, which brings me to my next point 3) most students prefer to work on their own laptops (and not just uni computers), but it’s not easy to use multiple devices when there’s not enough space.

I think Bioinformatics office space, whether it’s for researchers, postgrads, or even placement students like myself, should have:

  • a plenty of desk space for multi-monitor set-ups, and a printer
  • a space for a whiteboard, and a calendar.
  • enough space to accommodate 3-5 people for meetings
  • zero wet-lab scientists :P kidding! It’s just that I’d rather share an office with a person with similar research interests.

Also, Bioinformatics lab/workspace should be located near PI’s office (unless PI’s office is located inside a lab :S), so that students don’t have to struggle carrying their laptops all the way to a different floor or a building for a meeting with their advisors. Sorry for the lengthy comment, but thanks for reading my essay :D

ADD COMMENTlink written 3.4 years ago by zeeefa80
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