Question: Creating A New Bioinformatics Unit
19
gravatar for Israel Barrantes
9.0 years ago by
Germany
Israel Barrantes790 wrote:

After all your experiences, how do you think is the best start for a novel, small bioinformatics unit?

Do you think that a person with strong programming background (e.g., with an IT engineering degree), plus another with a biology background (perhaps a junior bioinformatician), together with a senior scientist with a molecular biology degree, could make it, at least for a start?

Perhaps is it also needed at least one member with experience in data mining and/or statistics? And what about the software / hardware requirements?

job core career • 6.6k views
ADD COMMENTlink modified 4 weeks ago by Biostar ♦♦ 20 • written 9.0 years ago by Israel Barrantes790
5

Can you define what "making it" means in this scenario? Are you trying to start a business? Will you be the "bioinformatics core" for an institution? Are you just trying to have fun on the weekends?

ADD REPLYlink written 9.0 years ago by Steve Lianoglou5.0k
3

+1: What is the scope of your research.

ADD REPLYlink written 9.0 years ago by Pierre Lindenbaum129k
2

What kind of data are you going to analyse ? NGS, microarrays..? How many different projects are going on in your institution ? Are they based on the same kind of data ?

ADD REPLYlink written 9.0 years ago by toni2.2k

We are planning a new bioinformatics unit for the academic institute where I work, which it was decided to be better than having separate bioinformaticians on each department. The input from the BioStar community is always helpful!

ADD REPLYlink written 9.0 years ago by Israel Barrantes790

Is it so bad to have diffuse bioinformaticians? Or did you mean that the core would supplement/support the current people?

ADD REPLYlink written 9.0 years ago by Russh1.2k

The bioinformatics core will support mainly the systems biology oriented projects (syst.bio. of human diseases, systbio of microorganisms, cell fate, etc). Data comes mostly from proteomics, metabolomics and NGS experiments.

ADD REPLYlink written 9.0 years ago by Israel Barrantes790
18
gravatar for Casey Bergman
9.0 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

I would suggest starting with hiring two bioinformaticians at the senior scientist level (e.g. ~10 yrs research experience) - one with expertise in proteomics, one with expertise in genomics. Look for former biologists who are talented on the programming/unix side, who can run their own desktops, a BAS and a data storage unit, but avoid hiring computer scientists or hardware specialists initially. Instead, rely on central IT services or cloud services for advanced HPC, and gear your bioinformatics unit to provide data analysis and research programming support.

I would skip hiring a director/manager in the first instance, but instead leave management to the academic group leader with substantial bioinformatics experience who has an established group in your institute. You probably won't have unlimited funds, so unless you hire a manager who can do one of the essential roles as well, you are just squandering cash that could be spent on someone actually doing the work. A small team doesn't need a manager, if you hire the right people.

Once you establish good bioinformatics services in your institute, this proto-team will be stretched to the limit. The next step would be to grow the group to have more junior members doing "blue color bioinformatics" - mapping reads, doing Mascot searches, etc. Hire these people from a CS background, with strong coding and documentation skills, but without a requirement to undestand the biology. Let the senior people train them in the biology on the job, and let them take over the automation from the senior core members (and clean up their rapidly developed script archive.)

Lastly, hire a senior person to do systems biology and data integration, who can also take over management of the group and devolve responsibility from the academic lead. The manager should be at (almost) a PI level in your institute, and should be the one who coordinates with users and other non-core bioinformaticians embedded in wet-lab groups. They should also be involved in faculty meetings so they have access to scientific and infrastructure plans, and can evolve the group to meet the needs of your institute over time. If you don't have this high-level academic-core interface, you risk treating your core as a technical pool, rather than the engine that will make your 'omics data collection actually pay off.

EDIT 5 July 2011:

Just recalled that there are a couple interesting perspectives on this issue published in PLoS Com Biol in addition to the Bioinformatics editorial noted by Stefano:

You also might want to check out some of the discussions of the Bioinfo-core group or other resources on their wiki.

ADD COMMENTlink modified 9.0 years ago • written 9.0 years ago by Casey Bergman18k

Excellent. In addition to all responses below, these are the kind of experiences I wanted to hear about.

ADD REPLYlink written 9.0 years ago by Israel Barrantes790

could you post up a few more examples of what you'd consider " blue collar bioinformatics " I'm looking for more of this ... specifically what newbies would be doing in a bioinformatics lab...

ADD REPLYlink written 8.6 years ago by Delinquentme200
7
gravatar for Stefano Berri
9.0 years ago by
Stefano Berri4.1k
Cambridge, UK
Stefano Berri4.1k wrote:

I think you can't make a bioinformatics group capable of tacking every need in a department (unless the department does only a few things over and over). Every group tends to end up requiring a person (or more) 100% focused on the group needs. Keep the "embeded" bioinformaticians in the groups, maybe find an physical place where they can work, comunicate, and help each other.

I suggest this editorial http://bioinformatics.oxfordjournals.org/content/27/10/1345.full

You might want to set up a small cohordination unit that can take care of dealing with infrastructure, support and setting up shared tools (a local blast, galaxy, dedicated shared databases...) and maybe facilitate comunication and knowledge sharing across the "embedded" bioinformaticians. So, somebody that understand IT and somebody that understand how it is experimental work in the lab.

ADD COMMENTlink modified 9.0 years ago • written 9.0 years ago by Stefano Berri4.1k
5
gravatar for Madelaine Gogol
9.0 years ago by
Madelaine Gogol5.1k
Kansas City
Madelaine Gogol5.1k wrote:

It does depend somewhat on what you're going to be doing, but I think your basic setup sounds fairly reasonable.

It's actually good to have people originating from the three realms: programming, biology, and statistics. Ideally everyone has at least a little bit of all three. Programming and command line skills are pretty important, so I wouldn't bother with anyone who doesn't know some programming.

Communication with end users is really important when you're a core facility, make sure you get that part figured out.

ADD COMMENTlink written 9.0 years ago by Madelaine Gogol5.1k
4
gravatar for Jeremy Leipzig
9.0 years ago by
Philadelphia, PA
Jeremy Leipzig19k wrote:

I think the first step is to identify someone senior (a Core Director) who can lead the hiring effort. They would also be instrumental in choosing hardware or finding the right IT people to advise on this issue.

The wrong thing to do would be to have biologists select all these people and machines at once and expect them to work as a unit.

ADD COMMENTlink written 9.0 years ago by Jeremy Leipzig19k
3

I second the need to choose a good lead/director. Teams hardly function on their own and usually need someone to help the team members to focus and to collaborate.

ADD REPLYlink written 9.0 years ago by Joachim2.9k
4
gravatar for Simon Cockell
9.0 years ago by
Simon Cockell7.3k
Newcastle
Simon Cockell7.3k wrote:

We have run a bioinformatics core facility for the last 6 years or so, staffed by just the two of us. We are both former wet-lab biologists, turned bioinformaticians, and we focus on analysis of primary research data (mainly transcriptomics & proteomics, though these days the sequencing data is taking over), not algorithm or software development. In this context, having the skills and the knowledge to talk at a certain level with the lab-based scientists about their science has been absolutely vital, and I think someone without a strong biology background (ie doctoral level) would struggle at first to cope with this.

That said, if I had the opportunity to expand the unit, I think I'd want someone with a CS background to support bespoke software development, and probably a more junior bioinformatician (maybe fresh out of a Master's course) as a full-time data analyst, and less of a jack-of-all-trades than we currently have to be (in such a small unit, we have to be fluent in the biology, able to code, sysadmins, database admins &c &c. Not necessarily something I'd wish on anyone).

Hope this helps.

ADD COMMENTlink written 9.0 years ago by Simon Cockell7.3k

Serendipitous that you'd be answering this while I was writing, since the Newcastle core (http://bsu.ncl.ac.uk/support/) is the kind of nucleus I would suggest building in the first instance.

ADD REPLYlink written 9.0 years ago by Casey Bergman18k

@Casey :) your answer does sound rather reminiscent of our setup... it is expanding from the solid base that is the real challenge I think.

ADD REPLYlink written 9.0 years ago by Simon Cockell7.3k
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