Forum: Is Biostar Killing The Bioinformatics Core?
gravatar for Jeremy Leipzig
5.9 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

At many institutions there is a bioinformatics core that:

  • Does analysis
  • Advises those people doing the analysis

Biostar allows lone analysts embedded within labs to get support that was once only available from experts sitting behind a desk. I can't help but think that this supplants one of the historical roles of the bioinformatics core.

What are your thoughts?

forum biostar • 4.0k views
ADD COMMENTlink modified 5.9 years ago by Jorge Amigo11k • written 5.9 years ago by Jeremy Leipzig18k

I am sorry but that is really ridiculous. 1 Maybe many but for sure not most institutions, not to mention computational biologists that are isolated. Add to that that BioStar does not solve your pipeline problems, it is more directed at really dedicated questions which I believe will help the core units as well, BI has become very, very big and you would need a fairly large unit to cover all. 2 Bioinformatics and computational biology are at the front end of biology, combing with genomics, systems biology, reviving molecular evolution. There is so much new stuff going on. How about for instance multiple alignments? Surely one of the major things in BI. Every year up to ten new methods are being published. To ID the method you need requires more than the BI guys up down the hall, it requires a forum and I end with the same: I believe it will help the core units as well.......... We are just at the start of things.

ADD REPLYlink written 5.9 years ago by Arjen Ten Have340

I'm not sure we disagree entirely. Also I am inclined not to argue since you live in such an awesome city.

ADD REPLYlink written 5.9 years ago by Jeremy Leipzig18k

We could double our informatics staff tomorrow and within a month every one of them would be completely snowed under with analyses and a rapidly accelerating and untenable stream of incoming analysis/development/support requests related to data we already or soon will have. For reference we have 60-80 informatics staff (depending on how you count). About 50-60% of these might be considered 'core'. I don't see bioinformatics cores becoming less busy in the short to medium term. Especially since the academic funding system remains slow at increasing relative investment of resources in bioinformatics. This apparent inability to direct resources at a major research bottleneck is at times quite remarkable to behold. I have been working in the bioinformatics groups of genome centers for 10 years.

ADD REPLYlink written 5.9 years ago by Malachi Griffith17k

Intuitively the word "killing" makes me think that you think that it is a bad thing that biostar takes over some functionality of the current bioinformatic cores. But that is not the case right? Do you just want to bring up the discussion about Biostars role in the bioinformatics community?

ADD REPLYlink written 5.9 years ago by Irsan6.8k

i agree the headline is somewhat sensationalized. I wanted to see if people thought the advisory role of the core is diminishing when quick answers are so much easier to obtain. What I learned was that most responders never considered the core was really designed to dole out advice in the first place.

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Jeremy Leipzig18k

Are fledgling chess players killing world champion chess players? They are the reason why there will be champions in the future :)

ADD REPLYlink written 5.8 years ago by Eric Normandeau10k
gravatar for Sukhdeep Singh
5.9 years ago by
Sukhdeep Singh9.6k
Sukhdeep Singh9.6k wrote:

Only 2 points to this : Think of a lone guy, like me sitting alone in a office, doing work which few people understand in the lab. Biostar is fantastic platform, to give and take the thoughts/ideas/solutions and problems and helping you out when you really need someone around.

Regarding killing bioinformatics core, I have a feeling, Bioinformaticians now have a small pressure to do good research/analysis as at websites like Biostar, the papers can be exposed out for false/bad analysis. When we have journal clubs here in our lab, for some people, few graphs don't make sense, and some are not convinced with the analysis. People can now approach the forums, and ask for help, that is this really possible??

Biostars also provides a platform for discussing tools, methodologies and ideas, which a Bioinformatics core unit wont't discuss on a regular basis with other core facility. Here everything is global and people now have the power to discuss, analyse, asses the problems, provide solutions which can be readily cross-verified by the other experts in the field, else all work goes hidden, produced by few, supervised by some and analysed by others. If one is doing a good work, he/she really wants to be sure, if that's significant.

Asking experts globally is better than being in a state of state of confusion for long time or asking few people in a core facility. Also, with Biostars, I think most of the questions are asked by the people who are already doing computational studies or somehow are related to computers, having previous experience etc., there would quite a few posts, where pure wet lab experimentalists are asking core bioinformatics questions except how to install this software, path problems etc. implying the Bionformatics core units, are still in business!!

In lets say 10 years, most of work will go high-throughput, which will require the biologists to learn basic programming skills, running data analysis pipelines, generating statistical graphs by themselves, at that point Biostars will be super boon for them and the core teams would be involved either in sophisticated tool development, guiding people or managing projects.

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From the stats, just imagine if atleast 50% of the content created above enlightened few of us, derived to do better analysis and develop better tools, forced people to think hard and finally a discussion platform, where people can talk about science and using computation for solving some of the most challenging aspects, without paying any fees, I would say its awesome.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Sukhdeep Singh9.6k

Well said. BTW, I have a similar plight as you. I am the only guy in my lab who does bioinformatics and I have to depend on forums like Biostars in order to get help.

ADD REPLYlink written 5.9 years ago by Ashutosh Pandey11k
gravatar for KCC
5.9 years ago by
Cambridge, MA
KCC3.9k wrote:

Based on the cores I have to interact with, they are very busy people. They have very little available time to dispense advice and their time is always in high demand by many other labs. I am sure this varies from university to university. However, in my personal experience, this is what it's like. They often claim to be happy to help, but responses take a while and they are more terse than I would like.

I think Biostars lowers the bar for people who are interested in learning how to work in bioinformatics. It means that more labs can support motivated computer scientists and programmers as they learn with the help of Biostars. I am not saying Biostars offers a complete solution for learning bioinformatics, but it does help tremendously. So in the end, Biostars might be creating more jobs than it might be destroying. By lowering the bar, it means more people can do bioinformatics and it also means the cost to the lab, per bioinformatics specialist, doesn't have to be very high.

I don't think my local bioinformatics core has much to fear from me (an enthusiastic Biostars user). They seem to focus more on maintaining the computing cluster, running seminars, doing standard sequencing computations, advising the larger well-funded labs on big projects. Metaphorically speaking, they do wholesale bioinformatics and I do retail. So, I think generally the things I want to do and the things the core is interested in doing don't have a big overlap.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by KCC3.9k
gravatar for Casey Bergman
5.9 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

I don't think Biostars will kill off bioinformatics cores, but systems that lower the barrier to entry into bioinformatics (like Biostars or Galaxy) will change the role of researchers in bioinformatics cores. MacLean and Kamoun discuss this to some extent in their piece "Big data in small places", where they argue that the role of a Galaxy-enabled bioinformatics core shifts from service (which does not scale) to training and support of the Galaxy instance (which does scale). So maybe what we will see more of in the future (as we do already) is core bioinformaticians using Biostar as a scalable Q & A system to support not just their own institute, but others around the world.

ADD COMMENTlink written 5.9 years ago by Casey Bergman17k
gravatar for Ryan Thompson
5.9 years ago by
Ryan Thompson3.4k
TSRI, La Jolla, CA
Ryan Thompson3.4k wrote:

No. Making bioinformatics easier and more accessible will not make bioinformatics cores redundant. It will result in more people wanting to do bioinformatics, which will increase demand for the services of bioinformatics cores.

ADD COMMENTlink written 5.9 years ago by Ryan Thompson3.4k
gravatar for John
5.9 years ago by
John12k wrote:

The end user is like someone who drives a car.

The bioinformatic core team, are like the car salesman, car mechanics, and car manufactures - all under one roof.

I do not think that greater access to cars will reduce the need for salesmen, mechanics and manufacturers.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by John12k

odd you would choose that metaphor because I think the internet has drastically altered the public's relationship with salespeople, not to mention travel agents, stockbrokers and even doctors.

ADD REPLYlink modified 5.9 years ago • written 5.9 years ago by Jeremy Leipzig18k
gravatar for Jorge Amigo
5.9 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

I guess I read your entry too fast, because I was going to give a funny answer such as "biostar killed the bioinfo core". but then I kept on reading other people's answers and I realized that I definitely did not get your point. you were indeed talking seriously!

are you really doubting if access to knowledge should be restricted, or limited in any way? would you consider embedding a bioinformatics test on the registration page to distinguish who is and who isn't entitled not only to create, but even to access others' ideas? should the mighty powers of bioinformatics be only shared among a few illuminati? don't you think that the so called "bioinformatics cores" do also benefit from a resource like this one?

sure all formative fields have to adapt to this new information-sharing era, but is wikipedia interfering in a teacher's work? is google interfering in a librarian work? is amazon interfering in a salesman work? of course they all are, because the world changes, but we all must adapt. not only the one who learns, searches or buys, but also the one who provides the knowledge and the expertise. helping others to solve their problems in such a great collaborative platform can never be wrong.

ADD COMMENTlink written 5.9 years ago by Jorge Amigo11k
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