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Stopping viruses by targeting human proteins
Tuesday, September 7, 2010
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Brian Krueger, PhD
Duke University
Durham NC USA

Brian Krueger is the owner, creator and coder of LabSpaces by night and Next Generation Sequencer by day. He currently runs Dr. David Goldstein's sequencing facility at the Center for Human Genome Variation (CHGV). In his blog you will find articles about technology, molecular biology, and editorial comments on the current state of science on the internet.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Recent Comments

Jaeson, that's not true at most places.  Top tier, sure, but 1100+ should get you past the first filter of most PhD programs in the sciences. . . .Read More
Jun 24, 2013, 8:39am

All I can say is that GRE's really do matter at the University of California....I had amazing grades, as well as a Master's degree with stellar grades, government scholarships, publication, confere. . .Read More
Jun 19, 2013, 11:00pm

Hi Brian, I am certainly interested in both continuity and accuracy of PacBio sequencing. However, I no longer fear the 15% error rate like I first did, because we have more-or-less worked . . .Read More
Feb 26, 2013, 12:13am

Great stuff Jeremy!  You bring up good points about gaps and bioinformatics.  Despite the advances in technology, there is a lot of extra work that goes into assembling a de novo genome on the ba. . .Read More
Feb 25, 2013, 10:20am

Brian,I don't know why shatz doesn't appear to be concerned about the accuracy of Pacbio for plant applications. You would have to ask him. We operate in different spaces- shatz is concerned a. . .Read More
Feb 25, 2013, 8:01am
Wednesday, January 19, 2011

I'm finally coming out of my Scio11 coma.  It was a super exciting weekend filled with talks about technology, blogging, and new media.  On Saturday, Kristy Meyer, Dr. Isis and I led a panel discussion on the use of new communication tools in academic and industry science.

The discussion covered a wide range of topics.  One of the first that was brought up was how new media tools might be used to increase collaboration between science and industry.  One participant stated that she was surprised by the lack of collaboration between academic and industry scientists in the Research Triangle Park area.  She said there really was no resource for expert discovery and thought that the creation of a local database would be helpful in finding connections.

Expanding on this researcher database idea, I asked the audience to talk about their use of currently available social networking tools like LabMeeting, MyNetResearch, BioKM, Mendeley, ResearchGate, etc.  One biotech researcher said that his company was open to using these tools privately, and that's really what I have seen and heard of over the years.  Companies and institutions want to find better ways to communicate as long as what they do or say on a network is kept private.  We all agreed that a researcher database would be a great idea, but that at least in industry, it can be hard to populate profiles with too much specific information due to the limitations imposed by legal departments trying to maintain intellectual property rights.

This idea of intellectual property rights is one of the barriers I mentioned in a previous blog post about why I think open social networking will take a very long time to be accepted in the sciences.  In short, companies and institutions make a lot of money on patents and scientists are all competing for spots in journals.  Employees or researchers talking about projects and ideas in an open and public forum can make getting patent rights for those ideas very difficult.  The same is also true regarding papers.  Discussion or pre-publication of results can limit your publication power, especially in "high impact" journals that have very strict publication guidelines.  I actually have two interesting examples which highlight both of these problems:

1) When I launched LabSpaces, the first person to contact me about the site was someone from the University of Iowa legal department who echoed the patent right concern.  He told me that I should put disclaimers all over the site warning researchers that discussing new ideas in the open will make their research ineligible for patent protection. I'm not sure how true this is, but I also told this story to the Scio11 panel and the biotech people in the discussion agreed that their legal departments have said similar things about divulging too much information in public forums (on the internet or in presentations).

2) A researcher recently had a press release posted to his university website containing a picture of unpublished data.  He submitted the manuscript to Science a few months ago and is in the final stages of publication.  The only problem is that his data is now posted across the internet and Science has told him that he must have every instance of the data removed from the internet before they would allow him to publish that piece of data with his paper.  I was happy to remove the data and replace it with another image he provided, but I'm not sure other outlets would be so willing.

The take home message here appears to be that researchers should be very careful about what they share on the internet.

However, closed social networking seems to be gaining traction.  A recent article over at Nature Jobs had a great interview with some of the other science social networking sites.  One of which was ResearchGate who said that their paid closed social networks for companies and universities are much more vibrant than their open one.  Other examples of closed networks include sites like LabMeeting and MyNetResearch.  These sites typically allow document sharing and provide user profiles along with messaging systems and group forums.  These closed social networks may be good for community building within silos, but they do not help to build an accessible global social network that benefit researchers outside of the walled garden.

The discussion changed gears a bit so we could talk about electronic tools currently being used by researchers.  Dr. Isis is a clinical researcher and she said that she has worked with both academic and clinical scientists.  On the clinical side, there are usually electronic tools used to keep track of data and participants while on the academic side it's usually "pen and paper."  She said that the two are so different because clinicians have been forced to use electronic systems to keep track of patient data so they are comfortable with doing their research the same way.  I asked her if she thought that her academic colleagues were missing out and she responded by saying that she didn't think so.  That's just the way that different groups of scientists do science and they both work.  She also said that for scientists to adopt a new system it has to greatly increase their efficiency or get them a ton of grant money.  I totally agree with her.

I was recently given a one year pass to an electronic notebook/information management system.  The tool is called BioKM and it allows you to add members to your group to keep track of lab chemicals, projects, papers, documents, etc. Since I just started running a core facility at the University of Florida, I decided that a system like this might be really helpful and populating it with information at the starting stages of a lab would make the whole process less daunting.  Of course, it was still a daunting process and I only got as far as inviting people to my "lab" and filling out my profile.  The unfortunate thing about these social tools for science is that they really take A LOT of work to get off of the ground.  It takes a time investment, and with a system like BioKM I can see and understand the benefits theoretically, but the lack of a concrete pay-off is holding me back.  That or I'm extremely lazy.  Though, I think I owe it to BioKM to man up and take advantage of the system since they did sponsor a contest we held a few months ago!  But I do think my own personal experience supports the idea that for social tools to really take off there needs to be a tangible incentive for adoption.

Another problem with creating a social network for scientists is choosing the correct social object.  A social object is really defined as anything a community can be built around.  For example, YouTube has videos, Flickr has pictures, and FaceBook dabbles in both.  In the sciences, the social objects in science really are ideas, data, and papers.  We could probably socialize things like questions or techniques too.  One of the people taking part in our discussion was everyone's favorite blog commentor, Becca, who had some interesting ideas for making science more social.  She said that she really liked the idea behind BenchFly because it includes a whole catalog of research techniques that help to show her how to properly perform experiments in lab.  She thought it also might be nice to have a Q&A website where she can crowd source answers to questions, kind of like a Craig's list for science.  I know that Academia.edu tried to launch a Q&A section with similar goals, but I'm not sure that it has taken off.  There's also that new site called Quora which is pretty much a twitter/friendfeed hybrid where users ask questions to be answered by the community.  Neither of these tools are science specific, but they could be used for such, or as a model for creating new tools for scientists.

At this point the discussion seemed to come full circle.  Becca said that she wished she had a better way of finding experts in her field and she thought that a researcher database could provide this.  Dr. Isis followed up by saying that she thought that social networks for the sciences are really unnescessary within the current system because we already have scientific meetings for discussion and you can find experts easily enough through papers on pubmed.  Although Becca agreed with Dr. Isis (crazy, right??) she wished that pubmed expanded the author list to include each author's contribution to the paper so she knew who to contact for information on repeating an experiment.  She said that too often she sees massive author lists and has no idea who to contact about the particular topic she's interested in.  I certainly agree with Becca, and I think that the NIH does too because they recently funded two research groups to implement the VIVO system to create and maintain a national researcher database.  Maybe we should suggest expansion of the network to include paper contributions.  VIVO is an interesting program that was pioneered at Cornell University and is now being implemented nationally.  The goal is to get every university in the country to run a VIVO server to keep track of their researchers.  These servers will then report back to a central hub to create the national network.  The beauty of VIVO is that it isn't curated by a human, it uses semantic technologies to autopopulate the database with information about researchers.  Of course there are limitations here, the database only keeps track of government funded academic scientists (Industry houses are left out), and I have seen no plans to make this database social.  There are no forums, blogs, newsfeeds, or places for scientists to actually interact and use this $50 million project to enhance science collaboration.  Personally, I don't understand why they got such a huge sum of money for this project, even after reading the RFA.

I think at this point it's important to draw attention to the fact that many of the tools that we talked about in this discussion were heavily focused on the life sciences.  It isn't clear if the VIVO network will include all academics, or just those funded by the NIH.  Also, how do researchers outside of the life sciences find research articles and experts?  I think sometimes we in the life sciences take databases and resources for granted and assume that other disciplines share similar systems.  I know Physics, Astronomy, and Math have an open community centered around arXive, but the other sciences have to rely on publisher curated databases that typically aren't open access.  Is there a way to put all of science under one house? Or do disparate fields necessitate this type of separation?

Finally, Kristy thinks that creating a workbook for researchers may help break some of the barriers to using web 2.0 tools in research.  She would like to create tutorials on topics such as using Skype, twitter, and facebook to enhance a researcher's productivity.  Dr. Isis made a great point that granting institutions now have RSS and Twitter feeds that update whenever new funds are available.  This can quickly clue researchers into new money pots that they may have missed previously.

There certainly are many things that we need to do in the scientific community to move away from using email, telephone, and FTP servers for science collaboration and data sharing; however, it may just be that the right tools are not available yet for scientists to make the jump from their current ways of doing business.  Can you, dear readers, think of any tools that you might find valuable in the sciences?  Please post any questions or commentary of this discussion summary below.

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Blog Comments

Thomas Joseph
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Two things:

1. Any mention of a particular line of research publically (via message board, manuscript, poster presentation) starts the clock on patent rights. It's consider the "public disclosure" event. In the US that means you have 1 year to file your patent, and in many foreign countries it PREVENTS you from filing a patent AT ALL (the public disclosure event needs to be the patent itself). So yes, legal teams have fits and a legit concerns over disclosure of ideas.

2. VIVO is spreading into non-medical research areas.


Brian Krueger, PhD
Duke University
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#1, open discussion of ideas and data before publication is always going to be dead. Unless some kind of massive cultural change occurs, closed networks will be king.

#2, Does it really cost $50 million dollars to give me this? https://vivo.ufl.edu/display/n1849065253 No publications, nothing about my background.  I'd think it'd be much better considering how much cash we're talking about.


Brian Krueger, PhD
Duke University
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Ohhh, follow up, I can totally edit my profile and add all of that stuff manually.  So again, why is this thing costing $50 million dollars?  Sounds like someone got a boatload of cash to fund a bunch of pet projects.


Thomas Joseph
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#1: I doubt it's going to occur. My work (outside of collaborations within my institution) is so tied up with agreements and legal forms, and it likely will only increase. If you want to shoot yourself in the foot and bury any chance of a patent on information ... by all means publically disclose (I've been tempted a couple of times), but expect a lot of backlash. Universities see this as a source of additional funds, so I think you'll see more of a crack down, not less.

#2: Probably not. My institution is part of this whole dealio, but I have no idea where to even begin because it's hidden somewhere deep within the bowels of the IT pages. Can't even search for "VIVO" unless I want to wade through hundreds of "in vivo" abstracts.

Tideliar

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Nice summation Brian


JaySeeDub
Dub C Med School
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Oh VIVO, and here I thought I'd never see it again after pointing out it was a waste at my current school (my opinion most likely didn't matter, but I played up to IS' inherent laziness). More aggregator than database, you annoy me with your lack of actual and obvious functionality. If I ever find your initial designers, we will have words. Whilst I dangle them from a ledge atop a tall building.


Brian Krueger, PhD
Duke University
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Jay, the PI on the grant is down here at Florida.  His name is Mike Conlon.  I contacted him when I heard about the grant to see if he was interested in some help in rolling it out or giving it features that researchers might be interested in using.  He totally blew me off.  I think that if the Republicans are looking to cut excess fat, they need to look at projects like this that have a ton of money and extremely poor implementation.  This project should have gone to a design company with backup from these computer scientists to figure out the intricacies of the backend.  Instead, half of this cash is probably paying for new Gator football helmets in the guise institutional overhead :P


JaySeeDub
Dub C Med School
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Man, you seriously want me to get arrested again? But, ok. I'm supposed to be out there for a tournament in March anyway...

There was an attempt at my previous school at making an aggregator that wasn't VIVO, but was pretty much the same and the department kept touting it as functional. I remember getting to look at what they were calling the "developmental backend" and...there was no backend. It was just a list of all the faculty, staff and what they were doing. In .rtf format. It was like we were being sold a Ferrari body and chasis, but the engine was a hamster in a wheel.


Brian Krueger, PhD
Duke University
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Oh, you mean like the cars used in Miami Vice?

http://en.wikipedia.org/wiki/Cars_in_Miami_Vice

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