Forum: Is Biostar Killing The Bioinformatics Core?
11
gravatar for Jeremy Leipzig
6.6 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?

core forum biostar • 5.0k views
ADD COMMENTlink modified 6 months ago by JC8.8k • written 6.6 years ago by Jeremy Leipzig18k
13

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 6.6 years ago by Arjen Ten Have350
3

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 6.6 years ago by Jeremy Leipzig18k
5

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 6.6 years ago by Malachi Griffith17k

At least in terms of the bottleneck issue, I think one thing that probably should be made more clear is that the director of the core (probably) can't be involved with the specifics of every project. This may be a surprise to some people (if they are new starting a lab, for example).

From my experience, I believe this means the supporting staff kind of feel like they are bioinformaticians within labs (but are shared between multiple labs). In other words, I think this requires a fair amount of independence for the analyst assigned to a particular project / lab (and comfort in the PI suggesting biological ideas to critically assess results), but I don't really have a clear set of guidelines (agreed upon by other analysts/PIs/admins) that I can share as specific guidance.

ADD REPLYlink modified 6 months ago • written 6 months ago by Charles Warden7.3k
1

From my experience, I believe this means the supporting staff kind of feel like they are bioinformaticians within labs (but are shared between multiple labs). In other words, I think this requires a fair amount of independence for the analyst assigned to a particular project / lab (and comfort in the PI suggesting biological ideas to critically assess results),

Fully agree although it's usually the analyst that will step up and say: "This is what we can say based on the data and this is the part of your hypothesis that you need to further verify with additional experiments.

ADD REPLYlink modified 5 months ago • written 5 months ago by Friederike5.2k

I find discussions with the lab members important for thinking about what sort of hypothesis to test with the (and what is worth pursuing, among various candidates identified using different methods).

However, I think we are in agreement that setting appropriate expectations and confidence in results (and time required for analysis) are important.

ADD REPLYlink written 5 months ago by Charles Warden7.3k
1

Yes, I fully agree .

ADD REPLYlink written 4 months ago by Friederike5.2k
2

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 6.5 years ago by Irsan7.0k
1

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 6.5 years ago • written 6.5 years ago by Jeremy Leipzig18k
1

Well, this bioinformatics core employee is quite grateful that biostars exists. I have even found old answers that I made and forgot about. I also love teaching biologists to do their own analysis. If they ever don't need me anymore, I'll find something else interesting to do. : D

ADD REPLYlink written 6 months ago by Madelaine Gogol5.1k

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

ADD REPLYlink written 6.5 years ago by Eric Normandeau10k
20
gravatar for Sukhdeep Singh
6.6 years ago by
Sukhdeep Singh9.9k
Netherlands
Sukhdeep Singh9.9k 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.

Current stats We had 391 visitors in the past hour. 7,238 users have contributed 66,038 posts distributed as 9,296 questions, 20,052 answers and 34,197 comments

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 6.6 years ago • written 6.6 years ago by Sukhdeep Singh9.9k
6

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 6.6 years ago by Ashutosh Pandey11k
1

I think discussions on Biostars to help reduce errors in papers (and/or better prepare for more formal peer review) is a good idea. I also wish a lot more people would participate in discussions for preprints.

While I don't typically think of Biostars discussions being cited, I would be happy to see exceptions / examples.

ADD REPLYlink written 6 months ago by Charles Warden7.3k
1

I cited some in my thesis :)

ADD REPLYlink written 5 months ago by Sukhdeep Singh9.9k
10
gravatar for KCC
6.6 years ago by
KCC4.0k
Cambridge, MA
KCC4.0k 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 6.6 years ago • written 6.6 years ago by KCC4.0k

I think the project workload/management is important, but I am still working on putting my thoughts together.

I think the concern about "very busy people" relates to some of my thoughts in this answer: A: Bioinformatics cores pricing model

However, I don't yet have precise solutions to recommend (that I've seen work, for myself and/or other people). Nevertheless, this is definitely something that I am trying to work on!

At some point, I will hopefully have everything put together clearly enough to possibly ask for public feedback as well :)

ADD REPLYlink modified 6 months ago • written 6 months ago by Charles Warden7.3k
9
gravatar for Casey Bergman
6.6 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k 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 6.6 years ago by Casey Bergman18k
8
gravatar for Ryan Thompson
6.6 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 6.6 years ago by Ryan Thompson3.4k
5
gravatar for JC
6 months ago by
JC8.8k
Mexico
JC8.8k wrote:

Short answer: No

Long answer: Bioinformatics is too broad that even having BioStars and many other sources, you cannot solve all the problems, in particular, the problems that are stopping projects. Commonly, I see a lot of need in research groups to have either a Bioinformatician in their group or a Bioinformatics Core to help them in all project.

ADD COMMENTlink written 6 months ago by JC8.8k
1

Further, in the academic world, adding bioinformaticians as key personnel to grants is a big plus for grants that are NGS driven. In addition to a concise and well written methodology (which the bioinformatician can help), this will likely be seen as a well strategized research approach among reviewers. It amazes me how many people add a NGS project to their proposals, and have zero idea on how to analyze the data.

ADD REPLYlink written 5 months ago by lshepard370
4
gravatar for Jeremy Leipzig
6 months ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

Found this list tweeted from the EMBObioinfocore meeting. I was reminded of this question core discussion and my thesis that we no longer need a bioinformatics core when we have adequate support on the internet. Biostars killed the bioinformatics core, even if the core doesn't realize it.

enter image description here

ADD COMMENTlink written 6 months ago by Jeremy Leipzig18k
2

I think most of these quite general questions would also perfectly apply to any wet lab group, too

I honestly don't see how that allows to draw the conclusion that bioinformatic core facilities are less in demand than before. Our university clinic doesn't have a bioinformatic core, but would certainly need one. Currently, the labs rather rely on a few tech-savy, but overworked PhD students to google around and somehow get the data analyzed. Thus it takes ages, isn't standardized, sometimes plain wrong and the knowledge is being lost when people graduate.

In our institute (that frequently generated NGS libraries) there are two out of 20 people, who have programmed before and are not scared to death by a command line. All others are on the IT level of "Whoa, you can CALCULATE in Excel? I thought its just for formatting tables". So I would love to see them solving their own data analysis problems with the help of Biostars at some point, but we are not there yet.

Lastly: Who is answering the questions on Biostars? I would suppose many of the experienced senior users are paid either by large labs or bioinformatic core facilities and thus can kindly devote some of their time to answering questions here.

ADD REPLYlink modified 6 months ago • written 6 months ago by zepper40
1

That might have happened at your institution but bioinformatics cores are alive and thriving at many other places (with even new ones starting up).

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax73k
1

I would like to know about the healthiest cores - I suspect the best ones are less like cores and more like in silico research groups that publish their own papers while collaborating with wet labs.

ADD REPLYlink modified 6 months ago • written 6 months ago by Jeremy Leipzig18k
2

define "healthy" -- does this refer to the ego of the core director? the mental health of the analysts? the reputation of the core within the institute in terms of helpfulness? the reputation of the core's members within the global scientific community? the financial stability?

These are all very different aspects, some if which are counteracting/cancelling each other. For example, I don't think that a group that does a lot of cutting-edge analyses of, say, the single-cell epigenomics world, is necessarily equipped to help out with bulk RNA-seq analyses for numerous groups within the same institute. Likewise, a core that's swamped with just churning out DEG lists will likely not get a lot of recognition in the broader scientific community.

ADD REPLYlink written 6 months ago by Friederike5.2k

The healthy cores 1) allow for the core members to grow professionally and be recognized and 2) show some functionality, productivity, or quality above what could be achieved by their members simply sitting in different labs and never talking to each other. My thesis is still that in the vast majority of cases the core is pointless, and made even more pointless by the internet.

ADD REPLYlink written 5 months ago by Jeremy Leipzig18k
1

Based on my own experience, I can say that one major advantage the members of a core have is the relatively large volume of very different data sets that they encounter. Thanks to that we're in a very good position to judge the quality of a given data set, whether it will suffice to address the question at hand and how to best handle complex experimental designs. In reality, very few experiments these days have only two conditions (which make up the bulk of the tutorial examples you can find on the web) and being able to point out flaws that will mandate a re-do or advice on work-arounds is a big selling point for us. I guess, it could all be summed up as "experience" -- since the cores tend to have more long-term personal that's not necessarily interested in specific research questions, but are (hopefully) geared towards gold standard analyses, a healthy core will be able to deliver custom-tailored analyses in a fairly time-efficient manner. More importantly, I can not only rely on my own expertise, but I can always ask my colleagues who all have slightly different pet analyses (e.g. we have different people typically handling the bulk of specific types of analyses, i.e. someone who's really into ATAC-seq or ChIP-seq and someone else who's mostly handling single-cell stuff etc. )

ADD REPLYlink modified 5 months ago • written 5 months ago by Friederike5.2k

I can tell that I need to work on fewer projects more in-depth, and I think having project support limits may be helpful (if those are not already implemented). So, I think I agree with parts of what each of you are saying, but I also think I need to take a little more time to have a few 1-on-1 discussions before having a more public discussion about my experiences.

I think training and indirect support may be important (beyond just doing analysis for someone, and having them continue to be dependent on you as you have an accumulation of other follow-up requests), but it looks that is already something taken into consideration in the Applied Bioinformatics Core where Friederike works?

ADD REPLYlink written 5 months ago by Charles Warden7.3k
1

I think training and indirect support may be important (beyond just doing analysis for someone, and having them continue to be dependent on you as you have an accumulation of other follow-up requests), but it looks that is already something taken into consideration in the Applied Bioinformatics Core where Friederike works?

Yes, although we also have customers who will use us for multiple projects (and we also have groups that approached us with requests for support after one of their members attended one of our training sessions realizing that they may have bitten off more than they could chew). It really depends on the specific group. Generally, scoping out a project before we start with the analysis is absolutely crucial to keeping everyone sane and on board.

ADD REPLYlink written 5 months ago by Friederike5.2k
1

My concern is that the projects often don't really end (although the amount of post-publication support will vary), but I think having similar projects can be very helpful for communication (at least for me).

In other words, I think working on 5 related projects (where new samples are an extension of topics from earlier studies) is easier than working on 5 unrelated projects.

I'm not sure if it helps (because I don't know exactly what is required for a sustainable workload for myself), but I can tell it is best if I can cap the total number of projects that I work on per-day at 3.

ADD REPLYlink written 5 months ago by Charles Warden7.3k

I agree that there are likely benefits to have a limited number of collaborators that can have frequent discussions for projects (and take responsibility for specific applications).

However, if you can understand both the wet and dry components, I think that is even better :)

ADD REPLYlink modified 6 months ago • written 6 months ago by Charles Warden7.3k
2
gravatar for Jorge Amigo
6.5 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 6.5 years ago by Jorge Amigo11k
1
gravatar for John
6.5 years ago by
John12k
Germany
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 6.5 years ago • written 6.5 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 6.5 years ago • written 6.5 years ago by Jeremy Leipzig18k
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