Question: Are Lots Of Bioinformaticians Embedded In Wet Labs? Any Ideas On Sources Of Demographic Data On Bioinformaticians?
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gravatar for aidan-budd
4.9 years ago by
aidan-budd1.9k
Germany
aidan-budd1.9k wrote:

several times recently, I wanted to write something like:

"over the last decade, increasing numbers of bioinformaticians work relatively isolated from each other, e.g. where small numbers of bioinformaticians are embedded in bench-biology labs/institutes/companies"

in the context of discussing the changing needs of support (careers services, professional networks, etc.) of the bioinformatics community.

But this is just my gut feeling, and isn't based on any concrete data; I could, of course, well be wrong!

I've spent some time, therefore, looking for publications/references/analyses of the demographics of bioinformaticians, the kinds of job they tend to have (postdocs, predocs, managers, tech support, core services), the kinds of contexts that they're working in (pharma, biotech, academic groups/departments; surrounded by many other bioinformaticans, or relatively isolated from others etc.), i.e. the demographics of the profession. But so far, I've not found anything that helps address these specific questions, back up these kinds of statements.

Maybe I'm not the only person who has wanted to write this kind of thing; in which case, it'd be great to hear how you went about referencing/assessing this kind of statement (or if you too were stuck, like me, and just went with your gut feelings! :) ).

Plenty of obvious problems with doing this kind of thing, not least defining what it is to be a bioinformatician, how to classify different kinds of jobs etc., so it may well be that there isn't anything like this out there.

I guess one possible source of information on this could be the ISCB membership data, maybe I should contact them and see if they have any comments/surveys/summaries of this...

career job • 3.6k views
ADD COMMENTlink modified 4.7 years ago by Obi Griffith16k • written 4.9 years ago by aidan-budd1.9k
7

I would take a look at Michael Barton et al's bioinformatics career survey https://github.com/michaelbarton/bioinformatics-career-survey/tree/master/2012

ADD REPLYlink written 4.9 years ago by Jeremy Leipzig17k
3

I'd add that being embedded in a wet lab is an appalling career choice for a bioinformatician :)

ADD REPLYlink written 4.9 years ago by Neilfws47k
1

Why is that? (I'm currently in a wet lab.)

ADD REPLYlink written 4.9 years ago by KCC3.8k
4

Because you run the risk of being forever seen as technical support and being unable to develop your own career. Go and work somewhere where bioinformaticians are recognised and valued in their own right.

ADD REPLYlink written 4.9 years ago by Neilfws47k
3

For sure this happens, and can be very frustrating for the bioininformatican in that position.

Having said that, I know of several people who have flourished, published a lot, and whose careers, as a result, benefited a lot from their time as (the only) bioinformatician in a wet lab. It, of course, depends on: - the attitude and set up of the wet-lab colleagues, in particular the lab head - your own level of experience as a bioinformatician (for sure, a set up like this is an awful place to learn bioinformatics i.e. without peers around to get easy help from, apart from BioStar, of course ;) ) - your own personal career goals - if you enjoy doing technical support, then of course this is fine

amongst other things. So I think it's not inherently a bad decision to work in such a context, but that it's something to do with caution, as it can easily go wrong

ADD REPLYlink written 4.9 years ago by aidan-budd1.9k
5

0

I echo aidan-budd's response. I have heard of cases where the bioinformatician basically becomes a button pusher for the lab, but I have also seen that you can get unique access to very good novel data, and as we all know- it's all about the data!

ADD REPLYlink written 4.9 years ago by md5sum50

Interesting points. My university provides free technical support. So everybody in the lab tends to use them, not me. Perhaps, that's the secret. I also think that sometimes the biologists can be the bioinformatician's 'button pushers' in the sense that one can ask for and sometimes get experimental verification of bioinformatics predictions.

ADD REPLYlink written 4.9 years ago by KCC3.8k
1

(currently doing bioinf PhD in wetlab)

Honest question: Without being associated with a wetlab, how do people get their data? Career wise, I'd like to be developing novel bioinf but also doing novel real world analysis. If one was to be in a pure bioinf lab, is it not all tool development or second hand data? is the career choice one or the other?

Currently I do my extractions and sample prep myself, send off for seq and then bioinformaticise whilst waiting for the data back to analyse.

However, as the only one with root I have spent the morning dodging skype requests to install every RNAseq aligner under the sun onto our server...

ADD REPLYlink written 4.9 years ago by Daniel3.5k
2

Hm. I guess my situation is similar to quite a few others. The data I've worked with has been either: 1. publicly-available 2. obtained by close collaborators - in some cases in a cycle of data being collected, us analysing some if it, informing experiments with this, re-analysing new data - this depends on establishing good/effective collaborations with wet-lab people in a context where both sides see the motivation/benefit to the work

Based on the comments to this question, maybe it'd be interesting to ask directly some question(s) here on BioStars along the lines of: - what have been the features of the successful collaborations you've had with wet lab/bench scientists - what are the advantages and disadvantages, and things to be wary of, when working as the bioinformatician in a group of bench scientists

ADD REPLYlink written 4.9 years ago by aidan-budd1.9k

One can be associated with a wetlab (or many wetlabs) without being embedded. The key is to be recognised as more than technical support; embedding works against this in my experience.

ADD REPLYlink written 4.9 years ago by Neilfws47k

Of course, the joy of using "many" and "lots" is that you aren't giving any quantitative information. Also I'm not clear on what you mean by what kind of jobs people in the bioinformatics profession tend to have...

ADD REPLYlink written 4.9 years ago by Ben1.9k

re "many" and "lots": Aye, that's right. I should be more specific i.e. what I'd like to be able to do is use "more" and "less" etc., I'll edit my initial question to reflect this. In this case, I think some kinds of estimates of numbers (and how they change with time) is needed

ADD REPLYlink written 4.9 years ago by aidan-budd1.9k

re "what kinds of jobs people in the bioinformatics profession tend to have...", I was being deliberately vague, I could imagine various ways of classifying them, and that's presumably part of the reason why it's hard to find something on this. I'm particularly interested in ways of building and maintaining professional networks of bioinformaticians, so the kind of distinctions I'm interested in are ones that might make it more or less important/useful to develop such networks. For example, I'd be interested in e.g. the number of other professional bioinformaticans they tend to interact with in e.g. a day/week etc. I know it's asking a lot to expect to find this kind of thing out there, but there have been (I know as the result of answers to this and another question I've asked on BioStar Where/How To Assess Which Bioinformatics Tools/Databases Are Most Used/Accessed? some attempts to survey related issues amongst the bioinforamtics community, see cdsouthan's reply to the marked question.

ADD REPLYlink written 4.9 years ago by aidan-budd1.9k

I don't know if 'lots' are, but I know I am directly in the lab. :)

ADD REPLYlink written 4.9 years ago by Fwip480
3
gravatar for John
4.7 years ago by
John12k
Germany
John12k wrote:

I would say that you can not disagree that bioinformaticians are diffusing into wet labs, since bioinformaticians classically come from computer science/informatics and are working on biological problems and not the other way around - but to get data for the number of bioinformaticians working in wet labs over the years you would have to first define what makes a bioinformatician... and that would be a very difficult thing to do. Many wet-lab scientists in my group can use Tophat/Cufflinks/R from the command line, which is just about all the bioinformatics team at my institute do anyway. Are they bioinformaticists? I myself have qualifications in Genetics and Human Genetics, but I spend my evenings/weekends programming bioinformatic tools in Python and CUDA. I never did CS at school, so can I be a bioinformaticist?

So to get the graph you're looking for, you're going to have to define exactly what a bioinformaticist is. Picking a course or even surveying everyone on this site will lead to biases... so perhaps pick a few varied sources and hope they somewhat agree!

The other option is to focus on your problem (Is there a growing number of people who need high-level Bioinformatic support due to their isolation from other bioinformaticists) and see if you can get figures there.

ADD COMMENTlink written 4.7 years ago by John12k
2
gravatar for Obi Griffith
4.7 years ago by
Obi Griffith16k
Washington University, St Louis, USA
Obi Griffith16k wrote:

As others have pointed out above, the best source of demographic information for such questions might be Michael Barton et al's bioinformatics career survey. Although, I don't see any survey questions that address your specific question.

There is one question that addresses your demographic question in the annual bioinformatics survey from Eagle Genomics. From the blog discussing that survey:

The largest portion of the respondents were single-person teams (46/108), with almost all the remainder (45/108) having just 1-5 employees reporting to them. Only two respondents indicated that they managed teams of 15 or more. Compared to the total number of bioinformaticians in responding organisations (a pretty even spread in the 1-5, 5-15 and 15-50 categories) this suggests that the majority of respondents were in non-management roles as part of larger organisations, rather than working as lone-ranger bioinformaticians. About half the respondents had 5-15 years experience, whilst the bulk of the rest had less than 5. Around 10% had more than 15 years experience.

Its not much and the sample size is pretty small. But, you can compare to the previous year's survey as well.

ADD COMMENTlink written 4.7 years ago by Obi Griffith16k
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